Bioremediation

Adv Biochem Eng Biotechnol, 2003, 78, 51 - 74
Soil plant microbe interactions in phytoremediation; Karthikeyan R et al.; Use of vegetation in remediation of soil and groundwater contaminated with organic materials is a promising, cost-effective alternative to the more established treatment methods used at hazardous waste sites . Plants can transpire groundwater and lower the concentrations of organic contaminants in soils and groundwater . The evapotranspirational activity of vegetation acts as a natural pump-and-treatment system . Plants have shown the capacity to absorb, uptake, and convert organic contaminants to less toxic metabolites in laboratory and field studies . Vegetation also plays a significant role in bioremediation . This is because plants stimulate the degradation of organic compounds in the rhizosphere by the release of root exudates and enzymes . Success of any plant-based remediation system depends on the interaction of plants with the surrounding soil medium and the contaminant . Knowing the fate of an organic contaminant in the soil can help determine the persistence of the contaminant in the terrestrial environment and ultimately the success of any remediation method . Also, an understanding is needed of soil-plant-microbe interactions that determine the fate of organic contaminants in the soil-plant ecosystem . This paper presents an overview of the subsurface environment and fate and transport processes of organic contaminants as affected by soil-plant-microbe interactions.

Can J Microbiol, 2003 Jan, 49(1), 9 - 14
Reductive dechlorination of weathered Aroclor 1260 during anaerobic biotreatment of Arctic soils; Kuipers B et al.; We investigated the microbial reductive dechlorination of both weathered (aged) and nonweathered (freshly added) Aroclor 1260 in aerobic soil from Resolution Island, Nunavut, Canada . Initial polychlorinated biphenyl (PCB) concentrations were 106 and 100 ppm, respectively . The aerobic soil samples were inoculated with anaerobic sediment, incubated at 30 degrees C until methanogenic, inoculated with a dechlorinating enrichment culture, and incubated a further 8 weeks . The average number of chlorine substituents per biphenyl molecule was biologically reduced from 6.6 to 5.1 and from 6.2 to 4.5 for weathered and nonweathered Aroclor 1260, respectively . Removal of hexa- and heptachlorobiphenyls (CBs), the major homolog groups present, was significantly greater for nonweathered than for weathered Aroclor 1260 . Formation of dechlorination products, primarily 2,2',4,4'- and 2,2',4,6'-tetraCBs, was also significantly greater for nonweathered than for weathered Aroclor 1260 . We additionally compared the dechlorination at 21 degrees C of weathered Aroclor 1260 in soils from Resolution Island and Saglek, Labrador, Canada . The average number of chlorine substituents per biphenyl molecule was biologically reduced from 6.7 to 5.1 and from 6.5 to 4.6, respectively . This study demonstrated the potential for bioremediation of aerobic soil contaminated with Aroclor 1260 and showed that weathering may limit such treatment to an extent variable among different soils.

J Mol Evol, 2003 Apr, 56(4), 435 - 45
Evolution of bacterial and archaeal multicomponent monooxygenases; Notomista E et al.; We report the results of a comparative analysis of the sequences of multicomponent monooxygenases, a family of enzymes of great interest for bioremediation of contaminated soil . We show that their function, in terms of substrate specificity, can be deduced from their subunit organization and composition, that rearrangements of subunits as well as recruitments of new ones can be used to explain their different properties and functionalities, and that the observed pattern can be rationalized invoking a number of evolutionary events, including horizontal gene transfer . Our analysis highlights the plasticity and modularity of this family of enzymes, which might very well be the reason underlying the extremely rapid emergence of new bacterial strains able to grow on contaminated soils.

Appl Microbiol Biotechnol, 2003 Feb, 60(6), 624 - 32 Epub 2002 Dec 13.
Diatom cultivation and biotechnologically relevant products . Part II: current and putative products; Lebeau T et al.; While diatoms are widely present in terms of diversity and abundance in nature, few species are currently used for biotechnologically applications . Most studies have focussed on intracellularly synthesised eicosapentaenoic acid (EPA), a polyunsaturated fatty acid (PUFA) used for pharmaceutical applications . Applications for other intracellular molecules, such as total lipids for biodiesel, amino acids for cosmetic, antibiotics and antiproliferative agents, are at the early stage of development . In addition, the active principle component must be identified amongst the many compounds of biotechnological interest . Biomass from diatom culture may be applied to: (1) . aquaculture diets, due to the lipid- and amino-acid-rich cell contents of these microorganisms, and (2) . the treatment of water contaminated by phosphorus and nitrogen in aquaculture effluent, or heavy metal (bioremediation) . The most original application of microalgal biomass, and specifically diatoms, is the use of silicon derived from frustules in nanotechnology . The competitiveness of biotechnologically relevant products from diatoms will depend on their cost of production . Apart from EPA, which is less expensive when obtained from Phaeodactylum tricornutum than from cod liver, comparative economic studies of other diatom-derived products as well as optimisation of culture conditions are needed . Extraction of intracellular metabolites should be also optimised to reduce production costs, as has already been shown for EPA . Using cell immobilisation techniques, benthic diatoms can be cultivated more efficiently allowing new, biotechnologically relevant products to be investigated.

Environ Microbiol, 2003 Apr, 5(4), 287 - 95
Transformations of selenate and selenite by Stenotrophomonas maltophilia isolated from a seleniferous agricultural drainage pond sediment; Dungan RS et al.; A Gram-negative bacterium, identified as Stenotrophomonas maltophilia by fatty acid analysis and 16S rRNA sequencing, was isolated from a seleniferous agricultural evaporation pond sediment collected in the Tulare Lake Drainage District, California . In cultures exposed to the atmosphere, the organism reduces selenate (SeO4(2-)) and selenite (SeO3(2-)) to red amorphous elemental selenium (Se degrees ) only upon reaching stationary phase, when O2 levels are less than 0.1 mg l(-1) . In 48 h, S . maltophilia removed 81.2% and 99.8% of added SeO4(2-) and SeO3(2-) (initial concentration of 0.5 mM), respectively, from solution . Anaerobic growth experiments revealed that the organism was incapable of using SeO4(2-), SeO3(2-), SO4(2-) or NO3- as a terminal electron acceptor . Transmission electron microscopy of cultures spiked with either Se oxyanion were found to contain spherical extracellular deposits . Analysis of the deposits by energy-dispersive X-ray spectroscopy revealed that they consist of Se . Furthermore, S . maltophilia was active in producing volatile alkylselenides when in the presence of SeO4(2-) and SeO3(2-) . The volatile products were positively identified as dimethyl selenide (DMSe), dimethyl selenenyl sulphide (DMSeS) and dimethyl diselenide (DMDSe) by gas chromatography-mass spectrometry . Our findings suggest that this bacterium may contribute to the biogeochemical cycling of Se in seleniferous evaporation pond sediments and waters . This organism may also be potentially useful in a bioremediation scheme designed to treat seleniferous agricultural wastewater.

Appl Microbiol Biotechnol, 2003 Mar, 61(1), 32 - 9 Epub 2003 Jan 16.
Optimisation of cellobiose dehydrogenase production by the fungus Sclerotium (Athelia) rolfsii; Ludwig R et al.; The phytopathogenic fungus Sclerotium (Athelia) rolfsii CBS 191.62 is a very efficient producer of the hemoflavoprotein, cellobiose dehydrogenase (CDH), forming up to 225 mg l(-1) (15,000 units cytochrome c activity l(-1)) of this protein, which is of biotechnological interest for sensors, biocatalysis and bioremediation . Both cellulose as inducing substrate and the use of a rich medium containing increased concentrations of peptone from meat or suitable amino acids are important for attaining high CDH yields . CDH, containing a protease-sensitive linker region, can be cleaved by endogenous proteases into a catalytically active flavin fragment and an inactive heme domain . By using increased concentrations of peptone, or certain amino acids such as valine or leucine, or by adding exogenous protease inhibitors, this cleavage can be almost completely inhibited, so that more than 95% intact CDH is obtained under optimised culture conditions . When using non-inhibitory amino acids, e.g . glutamine or lysine, in the medium, more than 80% of the total cellobiose-oxidising activity can be attributed to the flavin fragment.

Chemosphere, 2003 Jan, 50(3), 415 - 27
Soil microbial parameters and luminescent bacteria assays as indicators for in situ bioremediation of TNT-contaminated soils; Frische T et al.; In situ bioremediation is increasingly being discussed as a useful strategy for cleaning up contaminated soils . Compared to established ex situ procedures, meaningful and reliable approaches for monitoring the remediation processes and their efficiency are of special importance . The subject of this study was the significance of two bioassays for monitoring purposes . The work was performed within the scope of a research project on the in situ bioremediation of topsoil contaminated with 2,4,6-trinitrotoluene (TNT) . To evaluate changes within different experimental fields during a 17-month remediation period, the results of soil microbial assays and luminescent bacteria assays were compared with chemical monitoring data . The luminescent bacteria assays showed a significant reduction of the water-soluble soil toxicants in the treated fields . This bioassay proved to be a sensitive screening indicator of toxicity and may effectively aid the ecotoxicological interpretation of chemical monitoring data . Microbial biomass (C(mic)), the metabolic quotient (qCO2), and the ratio of microbial to organic carbon (C(mic)/C(org)) showed a highly significant correlation with total concentrations of TNT in the soil . But, in contrast to luminescent bacteria assays, this approach did not reveal any recovery of the soil at the end of the remediation period . There is clear evidence for persistent adverse effects of chronic TNT contamination on the site-specific microbial community and the local carbon cycle in the soil . The study clearly exhibits the differences between, as well as the complementary value of both bioassay approaches for monitoring short-term and long-term effects of soil contamination and the efficiency of remediation.

J Proteome Res, 2002 May-Jun, 1(3), 239 - 52
Integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensis; VerBerkmoes NC et al.; Here we present a comprehensive method for proteome analysis that integrates both intact protein measurement ("top-down") and proteolytic fragment characterization ("bottom-up") mass spectrometric approaches, capitalizing on the unique capabilities of each method . This integrated approach was applied in a preliminary proteomic analysis of Shewanella oneidensis, a metal-reducing microbe of potential importance to the field of bioremediation . Cellular lysates were examined directly by the "bottom-up" approach as well as fractionated via anion-exchange liquid chromatography for integrated studies . A portion of each fraction was proteolytically digested, with the resulting peptides characterized by on-line liquid chromatography/tandem mass spectrometry . The remaining portion of each fraction containing the intact proteins was examined by high-resolution Fourier transform mass spectrometry . This "top-down" technique provided direct measurement of the molecular masses for the intact proteins and thereby enabled confirmation of post-translational modifications, signal peptides, and gene start sites of proteins detected in the "bottom-up" experiments . A total of 868 proteins from virtually every functional class, including hypotheticals, were identified from this organism.

J Protein Chem, 2002 Nov, 21(8), 529 - 36
Metallohistins: a new class of plant metal-binding proteins; Gupta RK et al.; Two small multimeric histidine-rich proteins, AgNt84 and Ag164, encoded by two nodule-specific cDNAs isolated from nodule cDNA libraries of the actinorhizal host plant Alnus glutinosa, represent a new class of plant metal binding proteins . This paper reports the characterization of the purified in vitro-expressed proteins by size exclusion chromatography, circular dichroism, equilibrium dialysis, metal affinity chromatography coupled with mass spectrometry, and nuclear magnetic resonance spectroscopy . These analyses reveal that each polypeptide is capable of binding multiple atoms of Zn2+, Ni2-, Co2+, Cu2+, Cd2+ and Hg2+ . A reversible shift in histidine Cepsilon1 and Cdelta2 protons in NMR analysis occurred during titration of this protein with ZnCl2 strongly suggesting that histidine residues are responsible for metal binding . AgNt84 and Ag164 are not related to metal binding metallothioneins and phytochelatins and represent a new class of plant metal binding proteins that we propose to call metallohistins . Possible biological roles in symbioses for AgNt84 and Ag164, and their potential for use in bioremediation are discussed.

J Appl Microbiol, 2003, 94(4), 608 - 17
Effects of carbon substrate enrichment and DOC concentration on biodegradation of PAHs in soil; Bengtsson G et al.; AIMS: Two common reasons to explain slow environmental biodegradation of polycyclic aromatic hydrocarbons (PAHs), namely lack of appropriate carbon sources for microbial growth and limited bioavailability of PAHs, were tested in a laboratory bioassay using a creosote-contaminated soil . METHODS AND RESULTS: The soil, containing a total of 8 mg g-1 of 16 PAHs, was sieved and incubated in bottles for 45 days . The first explanation was tested by enrichment with the analogue anthracene and the non-analogue myristic acid, and both failed to stimulate degradation of all PAHs except anthracene . The second explanation was tested by addition of different concentrations of dissolved organic carbon (DOC), with effects depending on the DOC concentration and the molecular size of the PAH . The degradation was enhanced from 10 to 35% for 12 PAHs when the soil was saturated . The degraded amounts of individual PAHs were proportional to their concentration in the soil . CONCLUSIONS: The slow in situ degradation of PAHs was enhanced by more than three times by adding water as a solvent . Addition of DOC facilitated the degradation of four- to six-ring PAHs . SIGNIFICANCE AND IMPACT OF STUDY: Bioremediation of PAH-contaminated sites may be facilitated by creating water-saturated conditions but retarded by addition of other carbon substrates, such as analogue compounds.

Trends Biotechnol, 2003 Mar, 21(3), 123 - 30
Secondary plant metabolites in phytoremediation and biotransformation; Singer AC et al.; For millennia, secondary plant metabolites have antagonized microorganisms, insects and humans alike, ultimately generating a complex and dynamic mixture of facultative and obligate interactions from symbioses to pathogenicity . Secondary plant metabolites have an important role in developing the myriad of organic pollutant-degrading enzymes found in nature . The link between secondary plant metabolites and enzymatic diversity has yet to be exploited, with potential applications in fields as varied as pest management, bioremediation and fine chemical production.

Environ Toxicol Chem, 2003 Mar, 22(3), 473 - 82
Studies on bioremediation of polycyclic aromatic hydrocarbon-contaminated sediments: bioavailability, biodegradability, and toxicity issues; Tabak HH et al.; The widespread contamination by polycyclic aromatic hydrocarbons (PAHs) has created a need for cost-effective bioremediation processes . This research studied a chronically PAH-contaminated estuarine sediment from the East River (ER; NY, USA) characterized by high concentrations of PAHs (approximately 4-190 ppm), sulfide, and metals and a marine sediment from New York/ New Jersey Harbor (NY/NJH; USA) with only trace quantities of PAHs (0.1-0.6 ppm) . The focus was to examine the relationship between bioavailability of PAHs and their biological removal in a slurry system . Freshwater and marine sediment toxicity tests were conducted to measure baseline toxicity of both sediments to amphipods, aquatic worms, fathead and sheepshead minnow larvae, and a vascular plant; to determine the cause of toxicity; and to evaluate the effectiveness of the biotreatment strategies in reducing toxicity . Results showed the ER sediment was acutely toxic to all freshwater and marine organisms tested and that the toxicity was mainly caused by sulfide, PAHs, and metals present in the sediment . In spite of the high toxicity, most of the PAH compounds showed significant degradation in the aerobic sediment/water slurry system if the initial high oxygen demand due to the high sulfide content of the sediment was overcome . The removal of PAHs by biodegradation was closely related to their desorbed amount in 90% isopropanol solution during 24 h of contact, while the desorption of model PAH compounds from freshly spiked NY/NJH sediment did not describe the bioavailability of PAHs in the East River sediment well . The research improves our understanding of bioavailability as a controlling factor in bioremediation of PAHs and the potential of aerobic biodegradation for PAH removal and ecotoxicity reduction.

OMICS, 2002, 6(4), 331 - 9
Analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter; Lovley DR; The proposed research will investigate two microbial communities that are of direct relevance to Department of Energy interests . One is the microbial community associated with the in situ bioremediation of uranium-contaminated groundwater . The second is a microbial community that harvests energy from waste organic matter in the form of electricity . These studies will address DOE needs for (1) remediation of metals and radionuclides at DOE sites and (2) the development of cleaner forms of energy and biomass conversion to energy . Our previous studies have demonstrated that the microbial communities involved in uranium bioremediation and energy harvesting are both dominated by microorganisms in the family Geobacteraceae and that the organisms in this family are responsible for uranium bioremediation and electron transfer to electrodes . The initial objectives of this study are to (1) describe the genetic potential of the Geobacteraceae that predominate in the environments of interest; (2) identify conserved patterns of gene expression within the Geobacteraceae family in response to a range of environmental conditions; (3) begin to identify mechanisms controlling the expression of key genes related to survival, growth, and activity in subsurface environments and on electrodes; and (4) use the results from subobjectives 1-3 to develop a conceptual model for predicting gene expression of Geobacteraceae in the environments of interest . This will serve as the basis for a subsequent simulation model of the growth and activity of Geobacteraceae in the subsurface and on electrodes.

Ying Yong Sheng Tai Xue Bao, 2002 Nov, 13(11), 1455 - 8
{Bio-remediation techniques of crude oil contaminated soils}; Li P et al.; The bioremediation of soils contaminated by different types of petroleum were carried out with composting process in a prepared bed . By the measures of nutrient- and microbiological agent addition, and moisture- and pH control, an ideal environment for microbes were obtained . When total petroleum hydrocarbons, which consist of thin oil, high condensation oil, special viscous oil, and viscous oil, were in the range of 25.8-77.2 g.kg-1 dry soil, the petroleum removal rate could reach 38.37-56.74% by 2 months operation . The contents of aromatic hydrocarbon, asphaltum and resin were important factors controlling the degradation of petroleum . 6 fungi, 6 bacteria and 1 actinomyces were found to be the dominant strains for petroleum degradation . The results could provide theoretical bases for remediation of soil contaminated by petroleum.

Rocz Panstw Zakl Hig, 2002, 53(3), 267 - 76
{Keratinolytic fungi in an acidic petroleum waste lagoon at a petroleum refinery.}; Ulfig K et al.; The incidence of keratinolytic fungi in an acidic petroleum waste lagoon (before bioremediation) at a petroleum refinery situated within a highly populated area was examined . High concentrations of petroleum hydrocarbons (aliphatics and PAHs) made the growth of keratinolytic fungi in clay and litter collected from the lagoon impossible . The natural self-purification process considerably decreased the hydrocarbon contamination, increased the pH and caused the abundant growth of Trichophyton ajelloi in organic soil that contained the root-adjacent material from the grass growing in green oases at the lagoon . Ecological and epidemiological aspects of the data were discussed.

J Ind Microbiol Biotechnol, 2003 Feb, 30(2), 107 - 13 Epub 2003 Jan 16.
Protocol for laboratory testing of crude-oil bioremediation products in freshwater conditions; Haines JR et al.; In 1993, the Environmental Protection Agency, National Risk Management Research Laboratory (EPA, NRMRL), with the National Environmental Technology Application Center (NETAC), developed a protocol for evaluation of bioremediation products in marine environments {18} . The marine protocol was adapted for application in freshwater environments by using a chemically defined medium and an oil-degrading consortium as a positive control . Four products were tested using the modified protocol: two with nutrients and an oleophilic component; one with nutrients, sorbent, and organisms; and one microbial stimulant . A separate experiment evaluated the use of HEPES and MOPSO buffers as replacements for phosphate buffer . The oleophilic nutrient products yielded oil degradation similar to the positive control, with an average alkane removal of 97.1+/-2.3% and an aromatic hydrocarbon removal of 64.8+/-1.2% . The positive control, which received inoculum plus nutrients, demonstrated alkane degradation of 98.9+/-0.1% and aromatic degradation of 52.9+/-0.1% . The sorbent-based product with inoculum failed to demonstrate oil degradation, while the microbial stimulant showed less oil degradation than the positive control . Replacement of phosphate buffer with other buffers had no significant effect on one product's performance . Differences in product performance were easily distinguishable using the protocol, and performance targets for alkane and aromatic hydrocarbon degradation are suggested.

Chem Biol Interact, 2003 Feb 1, 143-144, 411 - 23
Regulation of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase in Comamonas testosteroni: function and relationship of two operators; Xiong G et al.; Comamonas testosteroni 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-HSD/CR) is a key enzyme in the degradation of steroid compounds in soil, and may therefore play a significant role in the bioremediation of hormonally active substances in the environment . We previously reported the isolation of the 3alpha-HSD/CR gene (hsdA) from C . testosteroni and two repressor genes, repA and repB, for hsdA transcriptional and translational regulation, respectively . In this work, we found that the expression of 3alpha-HSD/CR is closely connected to the distance between two 10 bp operator elements (OP1 and OP2) to which the RepA protein binds and therefore blocks the transcription of hsdA . The two 10 bp palindromic operator sequences are located upstream of hsdA (at 0.935 kb and at 2.568 kb on an EcoRI fragment) and are separated by 1.644 kb . In order to elucidate how the distance between OP1 and OP2 influences the repression of hsdA expression, we used E . coli cells transformed with plasmids carrying a set of deletions between OP1 and OP2 . Our theory that a 'loop-structure' between the two operators is formed, which strongly influences hsdA transcriptional regulation, was proved by the increasing amounts of 3alpha-HSD/CR expression when the distance between the operators was too small to form the 'loop' structure . Moreover, additional -3, -5 and -7 nt deletions in each construct, known to result in DNA rotations and leading to altered orientations between the two operator sequences, reveal strong influences on hsdA expression the shorter the distance between the operators was . Our results demonstrate that a cis-regulating 'stem-loop' operator system is an important determinant in the regulation of the 3alpha-HSD/CR gene in Comamonas testosteroni.

Water Res, 2003 Mar, 37(6), 1378 - 84
Competition for oxygen by iron and 2,4,6-trichlorophenol oxidizing bacteria in boreal groundwater; Langwaldt JH et al.; Kinetics of simultaneous iron and 2,4,6-trichlorophenol (TCP) oxidation by groundwater enriched cultures were studied in order to reveal the competition for oxygen in aerobic in situ bioremediation of boreal groundwater . Chemical iron oxidation at near neutral pH in synthetic groundwater depended by the first order on the concentrations of ferrous iron and dissolved oxygen and by the second order on pH . The chemical iron oxidation rate constant was on average 2.2 x 10(13)mol(-2)L(2)atm(-1)min(-1) . Chemical iron oxidation was insignificantly affected by natural organic matter, 2,4,6-tri-, 2,3,4,6-tetra- or pentachlorophenol in groundwater . Biological oxidation of iron followed zero-order kinetics . At pH of 6.3 and dissolved oxygen (DO) concentration of 11.5 mgL(-1), the rate of biological iron oxidation was 3.8 x 10(-4)mmolL(-1)min(-1) and up to one order of magnitude higher than the chemical oxidation rate, 5.2 x 10(-6) mmolL(-1)min(-1) . Biological oxidation of iron was completely inhibited by pentachlorophenol at 23 micro mol-1 . With a groundwater enriched culture, oxygen was consumed at higher rates by 2,4,6-TCP oxidizers (2.5-7.6 x 10(-5)mmolDOL(-1)min(-1)) than the iron oxidizing bacteria (0.8-3.1 x 10(-5) mmolDOL(-1)min(-1)) at both low and saturated DO-concentrations . The results indicate that in situ iron oxidation is predominantly biogenic in the studied boreal aquifer . 2,4,6-TCP degrading bacteria consumed DO at higher rates than the iron oxidizing bacteria and thereby, favour bioremediation of the polychlorophenol contaminated groundwater.

Acc Chem Res, 2003 Feb, 36(2), 120 - 6
Chlorine kinetic isotope effects on enzymatic dehalogenations; Paneth P; Enzymatic dehalogenation reactions are important for the bioremediation of the environment because of the increasing anthropogenic pollution with halogen-containing organic compounds . Chlorine kinetic isotope effects have been measured for four hydrolytic dehalogenases . On the basis of these isotope effects, several details of the mechanisms of the enzymatic dehalogenation reactions have been revealed.

J Biol Inorg Chem, 2003 Feb, 8(3), 334 - 40 Epub 2002 Nov 20.
Engineering new metal specificity in EF-hand peptides; Le Clainche L et al.; Peptides (33-34 amino acids long) corresponding to the helix-turn-helix (EF-hand) motif of the calcium binding site I of Paramecium tetraurelia calmodulin have been synthesized . The linear sequence was unable to acquire a native-like conformation and calcium binding . However, incorporation of a well-positioned disulfide bond bridging the two putative helical regions greatly improved the ordered structure and binding properties . Analyzed by electrospray mass spectrometry, circular dichroism and time-resolved laser-induced fluorescence, such a disulfide-stabilized peptide is shown to acquire a calcium-dependent helical conformation and exhibits native-like affinity for calcium, terbium and europium ions with 30+/-1, 3.5+/-0.6 and 0.6+/-0.1 microM dissociation constants, respectively . Comparable affinities were calculated within the biological construct comprising the entire domain I of Arabidopsis taliana calmodulin . Single sequence mutation (Glu25Asp) in the binding loop of the peptide abolishes calcium affinity, but preserves lanthanide affinity, showing that metal selectivity can be modulated by specific mutations . Such disulfide-stabilized peptides represent useful models to engineer metal specificity in new calmodulin proteins, facilitating the development of new systems to monitor metal pollution in biosensors and to increase metal binding capability of bacterial and plant cells in bioremediation techniques.

Ying Yong Sheng Tai Xue Bao, 2002 Sep, 13(9), 1137 - 40
{Bioremediation for petroleum-contaminated soil by composting technology}; Ding K et al.; With composting technology of off-site bioremediation, the bioremediation of soil contaminated by crude oil from Liaohe Oil Field was studied . 4 treatments units were set, each units being 118.5 cm in length, 65.5 cm in width, and 12.5 cm in height . The results showed that when the soil was contaminated with 5.22 g.100 g-1 TPH, the degradation rate of TPH reached 54.2% after 55 days operation by Phanerochaete chrysosporium . The results also indicated that the major factors that effected the TPH bioremediation results were the content of O2 and CO2, the amounts of microorganism that degraded petroleum hydrocarbons, and the changes of pH in contaminated soil . These factors could directly reflect the effect of composting treatment technology, and be used to optimize the operation conditions of composting technology to reach the best result . The treatment engineering adopted periodical aired means, operated very simple, and costed very cheap, whtch provided a practical technology for the bioremediation of petroleum-contaminated soil.

J Environ Qual, 2003 Jan-Feb, 32(1), 47 - 54
Enrichment and isolation of endosulfan-degrading microorganisms; Siddique T et al.; Endosulfan (6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9-methano-2,3,4-benzo-dioxathiepin-3-oxide) is a cyclodiene organochlorine currently used as an insecticide all over the world and its residues are posing a serious environmental threat . This study reports the isolation and identification of enriched microorganisms, capable of degrading endosulfan . Enrichment was achieved by using the insecticide as either the sole source of carbon or sulfur in parallel studies . Two strains each of fungi (F1 and F4) and bacteria (BF2 and B4) were selected using endosulfan as a sole carbon source . A Pandoraea species (Lin-3) previously isolated in our laboratory using lindane (gamma-HCH) as a carbon source was also screened for endosulfan degradation . F1 and F4 (Fusarium ventricosum) degraded alpha-endosulfan by as much as 82.2 and 91.1% and beta-endosulfan by 78.5 and 89.9%, respectively, within 15 d of incubation . Bacterial strains B4 and Lin-3 degraded alpha-endosulfan up to 79.6 and 81.8% and beta-endosulfan up to 83.9 and 86.8%, respectively, in 15 d . Among the bacterial strains isolated by providing endosulfan as a sulfur source, B4s and F4t degraded alpha-endosulfan by as much as 70.4 and 68.5% and beta-endosulfan by 70.4 and 70.8%, respectively, after 15 d . Degradation of the insecticide occurred concomitant with bacterial growth reaching an optical density (OD600) of 0.366 and 0.322 for B4 and Lin-3, respectively . High OD600 was also noted with the other bacterial strains utilizing endosulfan as a sulfur source . Fungal and bacterial strains significantly decreased the pH of the nutrient culture media while growing on endosulfan . The results of this study suggest that these novel strains are a valuable source of potent endosulfan-degrading enzymes for use in enzymatic bioremediation.

J Environ Qual, 2003 Jan-Feb, 32(1), 8 - 22
Laboratory-scale measurement of trace gas fluxes from landfarm soils; Ausma S et al.; Trace gas emissions from refinery and bioremediation landfarms were investigated in a mesocosm-scale simulator facility . Five simulators were constructed and integrated with a data acquisition system and trace gas analyzers, allowing automated real-time sampling and calculation of total hydrocarbon (THC), CO2, and water vapor fluxes . Experiments evaluating the influence of simulated cultivation and rainfall on trace gas fluxes from the soil surfaces were conducted . Results were compared with published field results . Results showed that cultivating dry or moderately wet soil resulted in brief enhancements of THC fluxes, up to a factor of 10, followed by a sharp decline . Cultivating dry soil did not enhance respiration . Cultivating wet soil did result in sustained elevated levels of respiration . Total hydrocarbon emissions were also briefly enhanced in wet soils, but to a lesser magnitude than in dry soil . Hydrocarbon fluxes from refinery landfarm soil were very low for the duration of the experiments . This lead to the conclusion that elevated THC fluxes would only be expected during waste application . An evaluation of the influence of simultaneous water vapor fluxes on other trace gas fluxes highlighted the importance in lab-scale experiments of correcting trace gas fluxes from soils . The results from this research can be used to guide management practices at landfarms and to provide data to aid in assessing the effect of landfarms.

Toxicol Ind Health, 2001 Jun, 17(5-10), 236 - 46
Using landscape ecology to focus ecological risk assessment and guide risk management decision-making; Kapustka LA et al.; Ecological risk assessment (EcoRA) generally suffers from limited application of ecological knowledge in the definition and characterization of real-world sites . Not surprisingly, most remediation decisions, which follow, have little or no relationship to the valued ecological resources of the site or the broader region . The practice has evolved to favor engineering-based mitigation strategies, which eliminate excess chemical concentrations at sites, or otherwise break exposure pathways, but which may not be ecologically beneficial . The heavy emphasis of EcoRA on toxicity threshold levels tends to focus dollars on clean up of small areas or volumes with high concentrations . Moreover, intrusive remediation technologies often render an area uninhabitable to the very species that were to be protected . Infusion of ecological knowledge into EcoRA has been difficult . Most professional ecologists choose not to venture into the messy applied fields, leaving their impressive knowledge untapped . Moreover, narrowly defined responsibilities within government circles can limit cooperation and coordination . The realization that land use activities often have greater adverse consequences to wildlife than do chemicals provides an opportunity to change attitudes and practices . We are developing procedures that incorporate landscape features into the environmental management process . Specifically, we are using an iterative approach to: a) identify scenarios where habitat value is important in EcoRAs; b) guide selection of appropriate assessment species, i) keyed to wildlife distribution ranges; ii) keyed to a database of habitat suitability models; iii) cross-linked with the EPA exposure handbook species; iv) referenced to wildlife distributions (e.g., breeding bird survey); c) define data collection needs for reconnaissance-, screening-, and definitive-level characterization of habitat quality for potential assessment species; d) generate spatially explicit descriptions of habitat quality for various assessment species; and e) allocate exposure estimates using both habitat quality and spatial variations in chemical concentration . These refinements in theEcoRA process are expected to improve risk estimates and provide valuable information to be used instructuring risk management options . The approach can guide the planning process so that an assessment considers the most relevant species of the area and defines the relevant parameters to be measured . In risk characterization, these data are used to calculate more realistic exposure assessments . In guiding remediation, the approach logically considers a wider range of land management options than are considered at most sites today . For example, habitat enhancement can be used to draw animals away from contaminated zones . Contaminated localities that also have poor-quality habitat may be allowed to go through a slower, less costly bioremediation process until the risk level is lowered to acceptable levels . And direct comparisons of lost resources stemming from destructive remediation options can be assessed instead of merely focusing on the lowering of contaminant concentrations . This paper presents the conceptual foundation for incorporating landscape ecology into the risk assessment process.

J Appl Microbiol, 2003, 94(2), 248 - 57
Response of bacterial community during bioremediation of an oil-polluted soil; Zucchi M et al.; AIM: To study the response of the bacterial community to bioremediation of a soil with an aged contamination of crude oil . METHODS AND RESULTS: The bacterial community in laboratory soil columns during a 72-day biostimulation treatment was followed by analysing the number of total cultivable hydrocarbon-degrading bacteria, soil respiratory activity and the 16S-23S rDNA internal transcribed spacer homoduplex heteroduplex polymorphisms (ITS-HHP) of total soil bacterial DNA . ITS-HHP permits an estimate of both length and sequence polymorphism in a 16S-23S rDNA spacer population, using to advantage the homoduplex and heteroduplex fragments that are generated during PCR . The treatment, made by air sparging and biostimulation with a mineral nutrient and surfactant solution, resulted in a 39.5% decrease of the total hydrocarbon content . Within 4 days of treatment onset the bacterial community underwent a first phase of activation that led to a substantial increase in the observable diversity . Subsequently, after a 12-day period of stability, another activation phase was observed with further shifts of the community structure and an increase in the abundance and diversity of catechol-2,3-dioxygenase (C23O) genes . CONCLUSIONS: The overall data suggest an important contribution of uncultivable bacteria to the soil bioremediation, since, during the second activation phase, the increases of the respiratory activity, bacterial diversity and C23O gene abundance and diversity were not accompanied by a corresponding increase of the cultivable bacteria number . SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows that successive phases of activation of bacterial populations occur during a bioremediation treatment of oil-polluted soil.

J Appl Microbiol, 2003, 94(2), 230 - 9
Degradation of straight-chain aliphatic and high-molecular-weight polycyclic aromatic hydrocarbons by a strain of Mycobacterium austroafricanum; Bogan BW et al.; AIMS: Our goal was to characterize a newly isolated strain of Mycobacterium austroafricanum, obtained from manufactured gas plant (MGP) site soil and designated GTI-23, with respect to its ability to degrade polycyclic aromatic hydrocarbons (PAHs) . METHODS AND RESULTS: GTI-23 is capable of growth on phenanthrene, fluoranthene, or pyrene as a sole source of carbon and energy; it also extensively mineralizes the latter two in liquid culture and is capable of extensive degradation of fluorene and benzo{a}pyrene, although this does not lead in either of these cases to mineralization . Supplementation of benzo{a}pyrene-containing cultures with phenanthrene had no significant effect on benzo{a}pyrene degradation; however, this process was substantially inhibited by the addition of pyrene . Extensive and rapid mineralization of pyrene by GTI-23 was also observed in pyrene-amended soil . CONCLUSIONS: Strain GTI-23 shows considerable ability to mineralize a range of polycyclic aromatic hydrocarbons, both in liquid and soil environments . In this regard, GTI-23 differs markedly from the type strain of Myco . austroafricanum (ATCC 33464); the latter isolate displayed no (or very limited) mineralization of any tested PAH (phenanthrene, fluoranthene or pyrene) . When grown in liquid culture, GTI-23 was also found to be capable of growing on and mineralizing two aliphatic hydrocarbons (dodecane and hexadecane) . SIGNIFICANCE AND IMPACT OF THE STUDY: These findings indicate that this isolate of Myco . austroafricanum may be useful for bioremediation of soils contaminated with complex mixtures of aromatic and aliphatic hydrocarbons.

Water Res, 2003 Feb, 37(4), 891 - 901
Mechanisms for naphthalene removal during electrolytic aeration; Goel RK et al.; Batch tests were performed to investigate chemical and physical processes that may result during electrolytic aeration of a contaminated aquifer using naphthalene as a model contaminant . Naphthalene degradation of 58-66% took place electrolytically and occurred at the same rates at a pH of 4 and 7 . 1,4-naphthoquinone was identified as a product of the electrolysis . Stripping due to gases produced at the electrodes did not result in any naphthalene loss . Hydrogen peroxide (which may be produced at the cathode) did not have any effect on naphthalene, but the addition of ferrous iron (which may be present in aquifers) resulted in 67-99% disappearance of naphthalene . Chlorine (which may be produced from the anodic oxidation of chloride) can effectively degrade naphthalene at pH of 4, but not at a pH of 7 . Mono-, di- and poly chloronaphthalenes were identified as oxidation products . Ferric iron coagulation (due to the oxidation of ferrous iron) did not significantly contribute to naphthalene loss . Overall, electrolytic oxidation and chemical oxidation due to the electrolytic by-products formed are significant abiotic processes that could occur and should be accounted for if bioremediation of PAH-contaminated sites via electrolytic aeration is considered . Possible undesirable products such as chlorinated compounds may be formed when significant amounts of chlorides are present.

Nucleic Acids Res, 2003 Jan 1, 31(1), 152 - 5
BSD: the Biodegradative Strain Database; Urbance JW et al.; The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data . The BSD is being developed within the phylogenetic framework of the Ribosomal Database Project II (RDPII: to provide a biological complement to the chemical and degradative pathway data of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD: Data is accessible through a series of strain, chemical and reference lists or by keyword search . The web site also includes on-line data submission and user survey forms to solicit user contributions and suggestions . The current release contains information on over 250 degradative bacterial strains and 150 hazardous substances . The transformation of xenobiotics and other environmentally toxic compounds by microorganisms is central to strategies for biocatalysis and the bioremediation of contaminated environments . However, practical, comprehensive, strain-level information on biocatalytic/biodegradative microbes is not readily available and is often difficult to compile . Similarly, for any given environmental contaminant, there is no single resource that can provide comparative information on the array of identified microbes capable of degrading the chemical . A web site that consolidates and cross-references strain, chemical and reference data related to biocatalysis, biotransformation, biodegradation and bioremediation would be an invaluable tool for academic and industrial researchers and environmental engineers.

J Biol Chem, 2003 Apr 4, 278(14), 12214 - 21 Epub 2003 Jan 07.
The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1 . A new monooxygenase that functionalizes macrolide ring systems; Podust LM et al.; Evolutionary links between cytochrome P450 monooxygenases, a superfamily of extraordinarily divergent heme-thiolate proteins catalyzing a wide array of NADPH/NADH- and O(2)-dependent reactions, are becoming better understood because of availability of an increasing number of fully sequenced genomes . Among other reactions, P450s catalyze the site-specific oxidation of the precursors to macrolide antibiotics in the genus Streptomyces introducing regiochemical diversity into the macrolide ring system, thereby significantly increasing antibiotic activity . Developing effective uses for Streptomyces enzymes in biosynthetic processes and bioremediation requires identification and engineering of additional monooxygenases with activities toward a diverse array of small molecules . To elucidate the molecular basis for substrate specificity of oxidative enzymes toward macrolide antibiotics, the x-ray structure of CYP154C1 from Streptomyces coelicolor A3(2) was determined (Protein Data Bank code ) . Relocation of certain common P450 secondary structure elements, along with a novel structural feature involving an additional beta-strand transforming the five-stranded beta-sheet into a six-stranded variant, creates an open cleft-shaped substrate-binding site between the two P450 domains . High sequence similarity to macrolide monooxygenases from other microbial species translates into catalytic activity of CYP154C1 toward both 12- and 14-membered ring macrolactones in vitro.

Appl Environ Microbiol, 2003 Jan, 69(1), 490 - 4
Enhanced toxic metal accumulation in engineered bacterial cells expressing Arabidopsis thaliana phytochelatin synthase; Sauge-Merle S et al.; Phytochelatins (PCs) are metal-binding cysteine-rich peptides, enzymatically synthesized in plants and yeasts from glutathione in response to heavy metal stress by PC synthase (EC 2.3.2.15) . In an attempt to increase the ability of bacterial cells to accumulate heavy metals, the Arabidopsis thaliana gene encoding PC synthase (AtPCS) was expressed in Escherichia coli . A marked accumulation of PCs was observed in vivo together with a decrease in the glutathione cellular content . When bacterial cells expressing AtPCS were placed in the presence of heavy metals such as cadmium or the metalloid arsenic, cellular metal contents were increased 20- and 50-fold, respectively . We discuss the possibility of using genes of the PC biosynthetic pathway to design bacterial strains or higher plants with increased abilities to accumulate toxic metals, and also arsenic, for use in bioremediation and/or phytoremediation processes.

Environ Toxicol Chem, 2003 Jan, 22(1), 84 - 91
Toxicity evaluation of a commercial bioremediation agent mixed with crude oil; Bidwell JR et al.; The toxicity and efficacy of a bacteria-based commercial bioremediation agent (CBA) was assessed through bioassays with juvenile inland silverside minnows, Menidia beryllina, and flask studies of oil degradation . Addition of the CBA to weathered Alaska, USA North Slope crude oil (ANS-521) prior to testing increased toxicity of the water-soluble fraction (WSF) of the oil in both chronic (growth) and acute (mortality) toxicity tests . Time-course toxicity assessment of the water-soluble fraction of the CBA/oil combination indicated increases in effect after 7 to 14 d of mixing that coincided with elevated concentrations of both alkanes and aromatics in the WSF . Under controlled laboratory conditions, the CBA significantly enhanced degradation of the oil compared with a treatment with nutrients alone . The alkane fraction was degraded by nearly 100% over a 42-d period while the aromatic fraction was decreased by 70% . While toxicity testing is not currently required to list bioremediation agents on the product schedule of the National Oil and Hazardous Substances Pollution Contingency Plan, the potential interaction between bioremediation agents and oil should be further investigated and listing requirements reassessed as necessary . Recommendations for future investigations of this issue include characterization of temporal trends in toxicity of CBA and oil mixtures, use of multiple test methods (battery testing) when evaluating toxicity, comparative evaluations of indigenous versus product-derived microorganisms in efficacy studies, and the use of a comparable oil between studies to facilitate comparison of efficacy and toxicity data for different products.

J Contam Hydrol, 2002 Dec, 59(3-4), 231 - 45
Engineered and subsequent intrinsic in situ bioremediation of a diesel fuel contaminated aquifer; Hunkeler D et al.; A diesel fuel contaminated aquifer in Menziken, Switzerland was treated for 4.5 years by injecting aerated groundwater, supplemented with KNO3 and NH4H2PO4 to stimulate indigenous populations of petroleum hydrocarbon (PHC) degrading microorganisms . After dissolved PHC concentrations had stabilized at a low level, engineered in situ bioremediation was terminated . The main objective of this study was to evaluate the efficacy of intrinsic in situ bioremediation as a follow-up measure to remove PHC remaining in the aquifer after terminating engineered in situ bioremediation . In the first 7 months of intrinsic in situ bioremediation, redox conditions in the source area became more reducing as indicated by lower concentrations of SO4(2-) and higher concentrations of Fe(II) and CH4 . In the core of the source area, strongly reducing conditions prevailed during the remaining study period (3 years) and dissolved PHC concentrations were higher than during engineered in situ bioremediation . This suggests that biodegradation in the core zone was limited by the availability of oxidants . In lateral zones of the source area, however, gradually more oxidized conditions were reestablished again, suggesting that PHC availability increasingly limited biodegradation . The total DIC production rate in the aquifer decreased within 2 years to about 25% of that during engineered in situ bioremediation and remained at that level . Stable carbon isotope analysis confirmed that the produced DIC mainly originated from PHC mineralization . The total rate of DIC and CH4 production in the source area was more than 300 times larger than the rate of PHC elution . This indicates that biodegradation coupled to consumption of naturally occurring oxidants was an important process for removal of PHC which remained in the aquifer after terminating engineered measures.

Environ Pollut, 2003, 121(1), 103 - 13
Ecotoxicological evaluation of in situ bioremediation of soils contaminated by the explosive 2,4,6-trinitrotoluene (TNT); Frische T; To evaluate the environmental relevance of in situ bioremediation of contaminated soils, effective and reliable monitoring approaches are of special importance . The presented study was conducted as part of a research project investigating in situ bioremediation of topsoils contaminated by the explosive 2,4,6-trinitrotoluene (TNT) . Changes in soil toxicity within different experimental fields at a former ordnance factory were evaluated using a battery of five bioassays (plant growth, Collembola reproduction, soil respiration, luminescent bacteria acute toxicity and mutagenicity test) in combination to chemical contaminant analysis . Resulting data reveal clear differences in sensitivities between methods with the luminescent bacteria assay performed with soil leachates as most sensitive toxicity indicator . Complete test battery results are presented in so-called soil toxicity profiles to visualise and facilitate the interpretation of data . Both biological and chemical monitoring results indicate a reduction of soil toxicity within 17 months of remediation.

Water Res, 2003 Jan, 37(1), 238 - 44
Simulation of bioremediation of chlorophenols in a sandy aquifer; Antizar-Ladislao B et al.; Bioremediation of consecutive spills of phenol, 2-chlorophenol (2-MCP), 2,4,6-trichlorophenol (2,4,6-TCP) and pentachlororphenol as single pollutants was investigated in eight pilot plant scale sand columns system (100 cm l, 6 cm ID), simulating the conditions, which could be created in the saturated zone of a pristine aquifer following an accidental spill . Bioremediation in this study consisted of re-circulating local groundwater through the polluted site in a controlled manner following a closed-loop configuration . Intrinsic microbial development was enhanced by adding the necessary nutrients . Consecutive accidental spills of 480-mg phenol/kg soil; 140-mg 2-MCP/kg; 14-mg 2,4,6-TCP/kg soil and 17-mg pentachlorophenol (PCP)/kg soil under saturated conditions and a continuous specific discharge of 0.56 cm min(-1) were simulated . Degradation curves demonstrated first-order kinetics . Biodegradation rates (k1) were influenced by consecutive exposures . Calculated rate constants for biodegradation for sole substrate experiments were in the range of 0.06-0.15 day(-1), 0.21-1.20 day(-1), 0.04-2.28 day(-1) and 0.01-0.03 day(-1) for phenol, 2-MCP, 2,4,6-TCP and PCP, respectively . The acclimation of the aquifer to simulated consecutive accidental spills was found to be directly proportional to the cumulative load of each single chlorophenol . A relationship between the octanol water partitioning (Kow) values and the experimental degradation rates (k1) was found.

Water Res, 2003 Jan, 37(1), 27 - 38
Remediation of PCE-contaminated aquifer by an in situ two-layer biobarrier: laboratory batch and column studies; Kao CM et al.; The industrial solvent tetrachloroethylene (PCE) is among the most ubiquitous chlorinated compounds found in groundwater contamination . The objective of this study was to develop an in situ two-layer biobarrier system consisting of an organic-releasing material layer followed by an oxygen-releasing material layer . The organic-releasing material, which contained sludge cakes from a domestic wastewater treatment plant, is able to release biodegradable organics continuously . The oxygen-releasing material, which contained calcium peroxide, is able to release oxygen continuously upon contact with water . The first organic-releasing material layer was to supply organics (primary substrates) to reductively dechlorinate PCE in situ . The second oxygen-releasing material layer was to release oxygen to aerobic biodegrade or cometabolize PCE degradation byproducts from the first anaerobic layer . Batch experiments were conducted to design and identify the components of the organic and oxygen-releasing materials, and evaluate the organic substrate (presented as chemical oxygen demand (COD) equivalent) and oxygen release rates from the organic-releasing material and oxygen-releasing materials, respectively . The observed oxygen and COD release rates were approximately 0.0368 and 0.0416 mg/d/g of material, respectively . A laboratory-scale column experiment was then conducted to evaluate the feasibility of this proposed system for the bioremediation of PCE-contaminated groundwater . This system was performed using a series of continuous-flow glass columns including a soil column, an organic-releasing material column, two consecutive soil columns, and an oxygen-releasing material column, followed by two other consecutive soil columns . Anaerobic acclimated sludges were inoculated in the first four columns, and aerobic acclimated sludges were inoculated in the last three columns to provide microbial consortia for contaminant biodegradation . Simulated PCE-contaminated groundwater with a flow rate of 0.25 L/d was pumped into this system . Effluent samples from each column were analyzed for PCE and its degradation byproducts . Results show that up to 99% of PCE removal efficiency was obtained in this passive system . Thus, the biobarrier treatment scheme has the potential to be developed into an environmentally and economically acceptable remediation technology for the in situ treatment of PCE-contaminated aquifer.

Biosci Biotechnol Biochem, 2002 Oct, 66(10), 2001 - 16
Molecular bases of aerobic bacterial degradation of dioxins: involvement of angular dioxygenation; Nojiri H et al.; In the last decade, extensive investigation has been done on the bacterial degradation of dioxins and its related compounds, because this class of chemicals is highly toxic and has been widely distributed in the environment . These studies have revealed the primary importance of a novel dioxygenation reaction, called angular dioxygenation, in the aerobic bacterial degradation pathway of dioxin . Accompanied by the electron transport proteins, Rieske nonheme iron oxygenase catalyzes the incorporation of oxygen atoms to the ether bond-carrying carbon (the angular position) and an adjacent carbon, resulting in the irreversible cleavage of the recalcitrant aryl ether bond . The 2,2',3-trihydroxybiphenyl or 2,2',3-trihydroxydiphenyl ether derivatives formed are degraded through meta cleavage . In addition to the degradation system of dibenzofuran and dibenzo-p-dioxin (the nonchlorinated model compounds of dioxin), those of fluorene and carbazole were shown to function in dioxin degradation . Some dioxin degradation pathways have been studied biochemically and genetically . In addition, feasibility studies have shown that some dioxin-degrading strains can function in actual dioxin-contaminated soil . These studies provide useful information for the establishment of a bioremediation method for dioxin contamination . This review summarizes recent progress on molecular and biochemical bases of the bacterial aerobic degradation of dioxin and related compounds.

Biodegradation, 2002, 13(2), 79 - 90
Assessment of in-situ bioremediation at a refinery waste-contaminated site and an aviation gasoline contaminated site; Bhupathiraju VK et al.; A combination of geochemical, microbiological and isotopic methods were used to evaluate in-situ bioremediation of petroleum hydrocarbons at one site contaminated with refinery waste and a second site contaminated with aviation gasoline at Alameda Point, California . At each site, geochemical and microbiological characteristics from four locations in the contaminated zone were compared to those from two uncontaminated background locations . At both sites, the geochemical indicators of in-situ biodegradation included depleted soil gas and groundwater oxygen, elevated groundwater alkalinity, and elevated soil gas carbon dioxide and methane in the contaminated zone relative to the background . Radiocarbon content of methane and carbon dioxide measured in soil gas at both sites indicated that they were derived from hydrocarbon contaminant degradation . Direct microscopy of soil core samples using cell wall stains and activity stains, revealed elevated microbial numbers and enhanced microbial activities in contaminated areas relative to background areas, corroborating geochemical findings . While microbial plate counts and microcosm studies using soil core samples provided laboratory evidence for the presence of some microbial activity and contaminant degradation abilities, they did not correlate well with either contaminant location, geochemical, isotopic, or direct microscopy data.

Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 215 - 22
Breathing metals as a way of life: geobiology in action; Nealson KH et al.; Many microbes have the ability to reduce transition metals, coupling this reduction to the oxidation of energy sources in a dissimilatory fashion . Because of their abundance, iron and manganese have been extensively studied, and it is well established that reduction of Mn and Fe account for significant turnover of organic carbon in many environments . In addition, many of the dissimilatory metal reducing bacteria (DMRB) also reduce other metals, including toxic metals like Cr(VI), and radioactive contaminants like U(VI), raising the expectations that these processes can be used for bioremediation . The processes involved in metal reduction remain mysterious, and often progress is slow, as nearly all iron and manganese oxides are solids, which offer particular challenges with regard to imaging and chemical measurements . In particular, the interactions that occur at the bacteria-mineral interfaces are not yet clearly elucidated . One DMRB, Shewanella oneidensis MR-I offers the advantage that its genome has recently been sequenced, and with the availability of its genomic sequence, several aspects of its metal reducing abilities are now beginning to be seen . As these studies progress, it should be possible to separate several processes involved with metal reduction, including surface recognition, attachment, metal destabilization and reduction, and secondary mineral formation.

Appl Microbiol Biotechnol, 2002 Nov, 60(3), 352 - 60 Epub 2002 Sep 20.
Bioremediation of chromate: thermodynamic analysis of the effects of Cr(VI) on sulfate-reducing bacteria; Chardin B et al.; Developing new bioremediation processes for soils and effluents polluted by Cr(VI) requires the selection of the most efficient and the most heavy-metal-resistant bacteria . The effects of Cr(VI) on bioenergetic metabolism in two sulfate-reducing bacteria (SRB), Desulfovibrio vulgaris Hildenborough and Desulfomicrobium norvegicum, were monitored using isothermal microcalorimetry . The complete reduction of Cr(VI) to Cr(III) was studied by spectrophotometry and by speciation using a combination of high-performance liquid chromatography and inductively coupled plasma-mass spectrometry . Results revealed that Cr(VI) induces an inhibition of growth with concomitant production of energy, which can be compared to the reaction of the bacteria to a stress such as oxidative stress . Moreover, the sensitivity of bacteria towards this metal is as a characteristic of the strain, which leads to differences in the kinetics of Cr(VI) reduction . The study by microcalorimetry of heavy metal effects on SRB bioenergetic metabolism thus appears an appropriate tool to identify better strains to be used for industrial bioremediation process development.

Nat Struct Biol, 2002 Dec, 9(12), 934 - 9
Identification and analysis of a bottleneck in PCB biodegradation; Dai S et al.; The microbial degradation of polychlorinated biphenyls (PCBs) provides the potential to destroy these widespread, toxic and persistent environmental pollutants . For example, the four-step upper bph pathway transforms some of the more than 100 different PCBs found in commercial mixtures and is being engineered for more effective PCB degradation . In the critical third step of this pathway, 2,3-dihydroxybiphenyl (DHB) 1,2-dioxygenase (DHBD; EC 1.13.11.39) catalyzes aromatic ring cleavage . Here we demonstrate that ortho-chlorinated PCB metabolites strongly inhibit DHBD, promote its suicide inactivation and interfere with the degradation of other compounds . For example, k(cat)(app) for 2',6'-diCl DHB was reduced by a factor of approximately 7,000 relative to DHB, and it bound with sufficient affinity to competitively inhibit DHB cleavage at nanomolar concentrations . Crystal structures of two complexes of DHBD with ortho-chlorinated metabolites at 1.7 A resolution reveal an explanation for these phenomena, which have important implications for bioremediation strategies.

Trends Biotechnol, 2002 Nov, 20(11), 452 - 5
Bioremediation meets biomedicine: therapeutic translation of microbial catabolism to the lysosome; de Grey AD; Lysosomal degradation of damaged macromolecules is imperfect: many cell types accumulate lysosomal aggregates with age . Some such deposits are known, or are strongly suspected, to cause age-related disorders such as atherosclerosis and neurodegeration . It is possible that they also influence the rate of aging in general . Lysosomal degradation involves extensive cooperation between the participating enzymes: each generates a substrate for others until breakdown of the target material to recyclable units (such as amino acids) is complete . Hence, the age-related accumulation of lysosomal aggregates might be markedly retarded, or even reversed, by introducing just a few bacterial or fungal enzymes -'xenohydrolases' - that can degrade molecules that our natural machinery cannot . This article examines the feasibility and biomedical potential of such lysosomal enhancement as an approach to retarding or treating age-related physiological decline and disease.

FEMS Microbiol Rev, 2002 Nov, 26(4), 403 - 17
Biochemistry, genetics and physiology of microbial styrene degradation; O'Leary ND et al.; The last few decades have seen a steady increase in the global production and utilisation of the alkenylbenzene, styrene . The compound is of major importance in the petrochemical and polymer-processing industries, which can contribute to the pollution of natural resources via the release of styrene-contaminated effluents and off-gases . This is a cause for some concern as human over-exposure to styrene, and/or its early catabolic intermediates, can have a range of destructive health effects . These features have prompted researchers to investigate routes of styrene degradation in microorganisms, given the potential application of these organisms in bioremediation/biodegradation strategies . This review aims to examine the recent advances which have been made in elucidating the underlying biochemistry, genetics and physiology of microbial styrene catabolism, identifying areas of interest for the future and highlighting the potential industrial importance of individual catabolic pathway enzymes.

FEMS Microbiol Rev, 2002 Nov, 26(4), 327 - 38
Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution; Valls M et al.; The threat of heavy metal pollution to public health and wildlife has led to an increased interest in developing systems that can remove or neutralise its toxic effects in soil, sediments and wastewater . Unlike organic contaminants, which can be degraded to harmless chemical species, heavy metals cannot be destroyed . Remediating the pollution they cause can therefore only be envisioned as their immobilisation in a non-bioavailable form, or their re-speciation into less toxic forms . While these approaches do not solve the problem altogether, they do help to protect afflicted sites from noxious effects and isolate the contaminants as a contained and sometimes recyclable residue . This review outlines the most important bacterial phenotypes and properties that are (or could be) instrumental in heavy metal bioremediation, along with what is known of their genetic and biochemical background . A variety of instances are discussed in which valuable properties already present in certain strains can be combined or improved through state-of-the-art genetic engineering . In other cases, knowledge of metal-related reactions catalysed by some bacteria allows optimisation of the desired process by altering the physicochemical conditions of the contaminated area . The combination of genetic engineering of the bacterial catalysts with judicious eco-engineering of the polluted sites will be of paramount importance in future bioremediation strategies.

Appl Environ Microbiol, 2002 Nov, 68(11), 5537 - 48
Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation; Roling WF et al.; Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients . In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients . Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition . Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes . Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested . However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally . Very different microbial communities were selected in all of the microcosms . Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% +/- 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% +/- 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% +/- 7%) . Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms . Bioremediation treatments dramatically reduced the diversity of the bacterial community . The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group . On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred . However, although the overall diversity was similar, there were considerable qualitative differences in the community structure before and after the bioremediation treatments.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2002 Oct, 37(9), 1593 - 606
Biodegradation of diesel fuel by an Azolla-derived bacterial consortium; Cohen MF et al.; The widely distributed water fern Azolla was investigated for use as an amendment in the bioremediation of fuel-contaminated environments . In a field experiment Azolla pinnata as well as Pistia stratiotes and Salvinia molesta were applied to plots containing soil that had been surface-contaminated with diesel fuel (2.4 L m(-2)) and flooded with water . The plants quickly died and bacterial flocs developed around the dead A . pinnata fronds . After 16 weeks, diesel concentrations (as determined by levels of gas chromatography-detectable hydrocarbons) in the plant-added plots were less than half that of the control plot, and concentrations of xylenes and ethylbenzene were 50-100 times lower . In laboratory experiments, a consortium composed of A . pinnata-derived bacteria displayed dense growth in a 4% diesel-containing mineral salts medium and was found to lower the fluorescence from aromatic compounds by approximately 50% after 19d . It is concluded that the observed enhancement of diesel degradation in the plant-added plots was due to the release of bacteria (bioaugmentation) and physiochemical improvement of the plot conditions (biostimulation).

J Contam Hydrol, 2002 Oct, 58(3-4), 209 - 20
Numerical modeling of oxygen exclusion experiments of anaerobic bioventing; Mihopoulos PG et al.; A numerical and experimental study of transport phenomena underlying anaerobic bioventing (ABV) is presented . Understanding oxygen exclusion patterns in vadose zone environments is important in designing an ABV process for bioremediation of soil contaminated with chlorinated solvents . In particular, the establishment of an anaerobic zone of influence by nitrogen injection in the vadose zone is investigated . Oxygen exclusion experiments are performed in a pilot scale flow cell (2 x 1.1 x 0.1 m) using different venting flows and two different outflow boundary conditions (open and partially covered) . Injection gas velocities are varied from 0.25 x 10(-3) to 1.0 x 10(-3) cm/s and are correlated with the ABV radius of influence . Numerical simulations are used to predict the collected experimental data . In general, reasonable agreement is found between observed and predicted oxygen concentrations . Use of impervious covers can significantly reduce the volume of forcing gas used, where an increase in oxygen exclusion efficiency is consistent with a decrease in the outflow area above the injection well.

Appl Biochem Biotechnol, 2002 Jul-Dec, 102-103(1-6), 291 - 302
Engineering cytochrome P-450s: chimeric enzymes; Sukumaran S et al.; Cytochrome P-450 isozymes represent a critical component of nature's spectrum of detoxification catalysts that could be exploited for bioremediation . The ethanol-inducible human cytochrome P-450 2E1 serves as a model eukaryotic P-450 that complements the bacterial P-450 cam in dehalogenation and detoxification of environmental pollutants . We explored the construction of novel chimeric P-450s using cytochrome P-450 camC and 2E1 genes . For construction of chimera 1 (478 amino acids, 55.14 kDa), 145 amino acids from the N-terminus of P-450 2E1 protein (493 amino acids, 56.84 kDa) were replaced with 130 amino acids from the N-terminus of P-450 camC protein (415 amino acids, 46.66 kDa) . In chimera 2 (525 amino acids, 60.24 kDa) the strategy involves replacement of 28 amino acids in the C-terminus of chimera 1 with 75 amino acids from the C-terminus of P-450 camC gene . Homology models of both the chimeric proteins were developed using SWISS-MODEL based on the known crystal structure of cytochrome P-450 camC, BM-3, 1DT6A, and 2C17A . The models indicated that the proposed heme-binding site was intact, which is inevitable for catalytic activity of cytochrome P-450s . The expression of chimera 1 and 2 genes in Escherichia coli DH5alpha was evident from light-pink cell pellets, protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis, and diagnostic carbon monoxide-difference spectra . Our studies show that strategies can be developed to exploit the natural diversity of the P-450 superfamily to generate chimeric biocatalysts that would provide new templates amenable to directed evolution.

Appl Microbiol Biotechnol, 2002 Oct, 60(1-2), 45 - 59 Epub 2002 Jul 20.
Recent developments in molecular techniques for identification and monitoring of xenobiotic-degrading bacteria and their catabolic genes in bioremediation; Widada J et al.; The pollution of soil and water with xenobiotics is widespread in the environment and is creating major health problems . The utilization of microorganisms to clean up xenobiotics from a polluted environment represents a potential solution to such environmental problems . Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring, discovery and identification of novel bacteria and their catabolic genes involved in the degradation of xenobiotics . Application of these techniques to bioremediation has also improved our understanding of the composition, phylogeny, and physiology of metabolically active members of the microbial community in the environment . This review provides an overview of recent developments in molecular-biology-based techniques and their application in bioremediation of xenobiotics.

Appl Microbiol Biotechnol, 2002 Oct, 60(1-2), 33 - 44 Epub 2002 Sep 06.
The nitrile-degrading enzymes: current status and future prospects; Banerjee A et al.; Nitrile-converting enzymes are becoming commonplace in the synthesis of pharmaceuticals and commodity chemicals . These versatile biocatalysts have potential applications in different fields including synthetic biocatalysis and bioremediation . This review attempts to describe in detail the three major classes of nitrile-converting enzymes, namely nitrilases, nitrile hydratases and amidases . Various aspects of these enzymes including their occurrence, mechanism of action, characteristics and applicability in different sectors have been elaborately elucidated . Cloning of genes related to nitrile-converting enzymes is also discussed.

Environ Sci Technol, 2002 Oct 1, 36(19), 4127 - 34
In situ transformation of deuterated toluene and xylene to benzylsuccinic acid analogues in BTEX-contaminated aquifers; Reusser DE et al.; Techniques for detecting and quantifying anaerobic transformations of benzene, toluene, ethylbenzene, and xylene (BTEX) are needed to assess the feasibility of using in situ bioremediation to treat BTEX-contaminated groundwater aquifers . Deuterated surrogates of toluene (toluene-d8) and xylene (o-xylene-d10) were injected into BTEX-contaminated aquifers during single-well push-pull tests to monitor for the in situ formation of deuterated benzylsuccinic acid (BSA-d8) and o-methyl-BSA-d10 . Test solutions (250 L) containing toluene-d8 (9-22 microM) and o-xylene-d10 (4-9 microM) along with a conservative bromide tracer (1.3 mM) and nitrate (4 mM) as an electron acceptor were injected into four wells at two sites . Detection of BSA-d8 and o-methyl-BSA-d10 in groundwater samples collected from the same wells following injection unequivocally demonstrated anaerobic in situ toluene-d8 and o-xylene-d10 transformation with calculated zero-order formation rates ranging from 1.0 to 7.4 nM/day . Concurrent utilization of co-injected nitrate was rapid in all tests at both sites, with zero-order rates ranging from 13 to 39 microM/h . The field tests conducted in this study represent the first reported use of deuterated aromatic hydrocarbons to detect and quantify anaerobic BTEX transformation product formation in the subsurface.

Nat Biotechnol, 2002 Nov, 20(11), 1118 - 23 Epub 2002 Oct 07.
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis; Heidelberg JF et al.; Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems . Here we report the sequencing of the S . oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs . We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering . Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S . oneidensis, and a novel periplasmic {Fe} hydrogenase, which are integral members of the electron transport system . This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion-reducing capabilities.

Chemosphere, 2002 Nov, 49(5), 485 - 91
Enhanced degradation of carbazole and 2,3-dichlorodibenzo-p-dioxin in soils by Pseudomonas resinovorans strain CA10; Widada J et al.; We studied the degradation of carbazole (CAR) and 2,3-dichlorodibenzo-p-dioxin (2,3-DCDD) in soils inoculated with carbazole- and dioxin-degrader Pseudomonas resinovorans strain CA10 . By using Tn5-based transposon delivery systems, this bacterium was chromosomally marked with a tandem green fluorescent protein (gfp) gene . Real-time competitive PCR and direct counting using the (gfp) marker were employed to monitor the total number of carbazole 1,9a-dioxygenase gene (carAa) and survival of CA10 cells in the soil and soil slurry microcosms . Bioaugmentation studies indicated that the survival of the marked CA10 cells in soil microcosms was strongly influenced by pH and organic matter . While the number of the marked CA10 cells decreased rapidly in pH 6 with low organic matter, a high cell density was maintained in pH 7.3 with 2.5% organic matters up to 21 days after inoculation . In pH 7.3 soil, the period needed for complete degradation of CAR (100 microg kg(-1)) was markedly shortened from 21 to 7 days by the inoculation with the CA10 cells . Single inoculation of CA10 cells into the soil slurry system of 2,3-DCDD-contaminated soil enhanced the degradation of 2,3-DCDD from 25.0% to 37.0% . In this system, the population density of CA10 cells and the total number of carAa gene were maintained up to 14 days after inoculation . By repeated inoculation (every 2 days) with CA10 cells each at a density of 10(9) CFU g(-1) of soil, almost all of the 2,3-DCDD (1 microg kg(-1)) was degraded within 14 days . Results of these experiments suggest that P . resinovorans strain CA10 may be an important resource for bioremediation of CAR and chlorinated dibenzo-p-dioxin in contaminated soils.

Environ Sci Technol, 2002 Sep 1, 36(17), 3755 - 62
Detection of anaerobic metabolites of saturated and aromatic hydrocarbons in petroleum-contaminated aquifers; Gieg LM et al.; Recent investigations have demonstrated that several classes of petroleum hydrocarbons are susceptible to anaerobic decay, including alkanes and mono- and polycyclic aromatic compounds . In previous work, benzylsuccinates were shown to be useful indicators of in situ anaerobic alkylbenzene metabolism . In the present study, we sought to determine whether metabolites of alkanes and naphthalenes could similarly be used as indicators of the intrinsic decomposition of these compounds in petroleum-contaminated aquifers . Such metabolites include succinate derivatives of n-alkanes, cyclic alkanes, and alkylaromatic hydrocarbons as well as naphthoic acids . Using gas chromatography-mass spectrometry (GC-MS), we analyzed trimethylsilyl-derivatized organic extracts from six hydrocarbon-contaminated groundwaters for MS fragment ions indicative of such anaerobic metabolites . Geochemical indicators in these aquifers suggested the prevalence of anaerobic processes . In the groundwaters of the contaminated sites, we found compounds whose MS profiles suggested that they were indeed alkylsuccinic acids, ranging from C3 to C11 succinates . Propyl-, hexyl-, octyl-, and decylsuccinic acids were positively identified in the groundwaters by GC-MS matches with chemical or biologically produced standards . In two of the aquifers, we also detected components whose MS profiles matched with authentic standards of naphthoic acids and tetrahydronaphthoic acids . Metabolites were detected in nanomolar concentrations . The finding of these putative anaerobic metabolites of alkanes and naphthalenes signifies the in situ biodegradation of these hydrocarbons and attests to their value as indicators of intrinsic bioremediation.

J Theor Biol, 2002 Aug 21, 217(4), 459 - 77
Functional consequences of nutrient translocation in mycelial fungi; Boswell GP et al.; Fungi are of fundamental importance for plant and microbial nutrition with primary roles in decomposition and nutrient recycling . They also have great potential for use in areas of biotechnology such as bioremediation of organic and inorganic pollutants and biocontrol of plant pathogens . In all these contexts, environmental heterogeneity has a strong influence on growth and function . A large class of fungi overcome the difficulties encountered in such environments by the mechanism of translocation which results in the internal redistribution of nutrients within the fungal mycelium . In this paper, we use a combination of experimental techniques and mathematical modelling to examine fungal growth in general, and in particular, translocation in the common soil saprophytic fungus Rhizoctonia solani . A detailed mathematical model is presented where translocation is considered to have both diffusive and metabolically-driven components . A calibration experiment provided the necessary parameter values . Growth experiments were compared with model solutions and thus we provide strong evidence that diffusion is the dominant mechanism for translocation in homogeneous environments . In heterogeneous environments, we conclude that diffusion is still vital for exploration, i.e . the expansion of the fungal network into the surrounding area . However, we also conclude that localized resources may be utilized faster if energy is invested, i.e . when exploitation of the fungal microenvironment is enhanced by metabolically driven translocation.

Water Res, 2001 Nov, 35(16), 3941 - 9
Use of solvents to enhance PAH biodegradation of coal tar-contaminated soils; Lee PH et al.; Bioremediation of coal tar-contaminated soils containing polycyclic aromatic hydrocarbons (PAHs) is highly challenging because of the low solubility and strong sorption properties of PAHs . Five coal tar-contaminated soils from former manufactured gas plant (MGP) sites were pretreated with two solvents, acetone and ethanol to enhance the bioavailability of the PAH compounds . The biodegradation of various PAHs in the pretreated soils was assessed using soil slurry reactors . The total PAH degradation rates for soils pretreated with solvents were estimated to be about two times faster than soils that were not pretreated with solvents . For example, the total PAH first order degradation rate constants were 0.165+/-0.032, 0.147+/-0.020, and 0.076+/-0.009 day(-1) for Vandalia (EXC) soil that were pretreated with acetone, ethanol, and with no solvent, respectively . A distinctive advantage for soils pretreated with solvents was the enhanced removal of 5-ring PAH compounds such as benzo(a)pyrene and to a limited extent 4-ring compounds such as chrysene . Even for soils with 3.5% or more organic carbon content (two soils out of five), the degradation rate constants of chrysene were found to be two times faster than soils that were not pretreated . The degradation rate constants of benzo(a)pyrene were enhanced by 2-6 times for all five contaminated soils that were pretreated with solvents . To further elucidate trends that control the solvent treatment, the percent improvement in degradation rate constants (100 x rate constants for pretreated soils/rate constants for non-treated soils) for 16 PAHs were found to correlate well with the PAH partition coefficients (K(oc)) . Except for phenanthrene and the clay fraction of the soil, correlations between the percent improvement in degradation rates constants and several physical properties of the soils were poor and sporadic . This implies that the enhancement in PAH availability using solvent treatment was driven by the distribution of the PAHs between the solvent and the adsorbed PAHs.

Appl Microbiol Biotechnol, 2002 Sep, 59(6), 731 - 6 Epub 2002 Aug 10.
Quantitative and rapid detection of the trichloroethylene-degrading bacterium Methylocystis sp . M in groundwater by real-time PCR; Kikuchi T et al.; We developed a method based on real-time PCR for the specific and rapid enumeration of a trichloroethylene-degrading methanotroph, Methylocystis sp . M, with the aim of monitoring the strain in groundwater . A primer set designed from the nucleotide sequence of the mmoC gene of a soluble methane monooxygenase (sMMO) gene cluster from Methylocystis sp . M was specific to amplify the DNA region from the strain and no PCR products were amplified with the sMMO gene clusters from six other methanotroph strains . The real-time PCR reliably quantified Methylocystis sp . M over at least five orders of magnitude (5x10(6) to 5x10(2 )cells/PCR tube, or 2x10(8) to 2x10(4 )cells/ml) . Five cells of Methylocystis sp . M per PCR tube (2x10(2 )cells/ml) were detectable when the cells were suspended in distilled water . The concomitant presence of other methanotrophs in samples did not affect the reliability of enumeration; and recovery of the cells with a membrane filter enabled us to quantify cells of the strain in groundwater . This quantification procedure was completed within 3 h, including preparation time of environmental samples . We conclude that real-time PCR using the mmoC primer set can be used practically to analyze the behavior of Methylocystis sp . M at bioremediation sites.

Risk Anal, 2002 Aug, 22(4), 713 - 23
What number is "fifty-fifty"?: redistributing excessive 50% responses in elicited probabilities; Bruine de Bruin W et al.; Studies using open-ended response modes to elicit probabilistic beliefs have sometimes found an elevated frequency (or blip) at 50 in their response distributions . Our previous research suggests that this is caused by intrusion of the phrase "fifty-fifty," which represents epistemic uncertainty, rather than a true numeric probability of 50% . Such inappropriate responses pose a problem for decision analysts and others relying on probabilistic judgments . Using an explicit numeric probability scale (ranging from 0-100%) reduces thinking about uncertain events in verbal terms like "fifty-fifty," and, with it, exaggerated use of the 50 response . Here, we present two procedures for adjusting response distributions for data already collected with open-ended response modes and hence vulnerable to an exaggerated presence of 50% . Each procedure infers the prevalence of 50s had a numeric probability scale been used, then redistributes the excess . The two procedures are validated on some of our own existing data and then applied to judgments elicited from experts in groundwater pollution and bioremediation.

Biodegradation, 2002, 13(1), 53 - 64
Natural attenuation: what does the subsurface have in store?
Roling WF, van Verseveld HW.
Throughout the world, organic and inorganic substances leach into the subsurface as a result of human activities and accidents . There, the chemicals pose direct or indirect threats to the environment and to increasingly scarce drinking water resources . At many contaminated sites the subsurface is able to attenuate pollutants which, potentially, lowers the costs of remediation . Natural attenuation comprises a wide range of processes of which the microbiological component, which is responsible for intrinsic bioremediation, can decrease the mass and toxicity of the contaminants and is, therefore, the most important . Reliance on intrinsic bioremediation requires methods to monitor the process . The subject of this review is how knowledge of subsurface geology and hydrology, microbial ecology and degradation processes is used and can be used to monitor the potential and capacity for intrinsic bioremediation in the subsurface and to verify degradation in situ . As research on natural attenuation in the subsurface has been rather fragmented and limited and often allows only conclusions to be drawn of the site under investigation, we provide a concept based on Environmental Specimen Banking which will contribute to further understanding subsurface natural attenuation processes and will help to develop and implement new monitoring techniques.

Biodegradation, 2002, 13(1), 11 - 9
Microbial aspects of atrazine degradation in natural environments; Ralebits TK et al.; The potential toxicity of the s-triazine herbicide atrazine motivates continuous bioremediation-directed research . Several indigenous soil atrazine-catabolizing microbial associations and monocultures have been enriched/isolated from compromised sites . Of these, Pseudomonas sp . strain ADP has become a reference strain and has been used to elucidate sequences of the catabolic enzymes atzA, atzB, atzC and atzD involved in one aerobic degradation pathway and develop probes for the genes which encode these enzymes . Despite this, hitherto unknown or novel microorganisms, with unique sequences and different enzyme-mediated operative pathways, warrant continued investigations for effective site bioremediation . Also, the sustained effectiveness of natural attenuation must be demonstrated continually so regular site evaluations and results analyses, despite the limitations of chemical extraction methodologies, are crucial practices . For both directed and intrinsic bioremediation monitoring, traditional microbial association studies must be complemented by more advanced physiological and molecular approaches . The occurrence of catabolic plasmids, in particular, should be probed with DNA hybridization techniques . Also, PCR-DGGE and subsequent new sequence elucidation should be used prior to developing new primers for DNA sequences encoding novel catabolic enzymes, and for hybridization probe development, to establish the degradative potential of a compromised site, or adoption of FISH to, for example, monitor bioaugmented remediation.

Chemosphere, 2002 Sep, 48(9), 947 - 54
Burial, exportation and degradation of acyclic petroleum hydrocarbons following a simulated oil spill in bioturbated Mediterranean coastal sediments; Grossi V et al.; A field study was conducted in a French Mediterranean littoral (Gulf of Fos) in order to determine the role of bioturbation processes during the bioremediation of oil-contaminated sediments . Inert particulate tracers (luminophores) and Arabian light crude oil were deposited at the surface of sediment cores incubated in situ for 2, 6 and 12 months . After incubation, luminophores and hydrocarbons presented roughly similar depth distributions in the sediment, showing a continuous burial of material until 55 mm depth . Short-chain (< or = n-C25) n-alkanes were totally removed from the sedimentary column after 6 months, whereas approximately 20% of heavier n-alkanes (e.g . n-C30) and of isoprenoid hydrocarbons (pristane (Pr) and phytane (Ph)) remained at the end of the experiment . The determination of the degradation constant and the turn-over rate of individual hydrocarbon indicated that C17-25 n-alkanes were degraded two to three times faster than longer homologues and than pristane and phytane . Using the 17alpha,21beta-C30-hopane as an internal inert reference, we could demonstrate that, after 12 months of in situ incubation, 55% of the losses of the n-alkanes < or = C25 and 35% of the losses of the heavier n-alkanes and of Pr and Ph were due to biodegradation processes . These results demonstrate that the activity of benthic organisms can have a significant influence on the qualitative and quantitative fate of acyclic hydrocarbons following a petroleum contamination in marine coastal sediments.

Environ Microbiol, 2002 Sep, 4(9), 510 - 6
Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments; Finneran KT et al.; Microbiological reduction of soluble U(VI) to insoluble U(IV) has been proposed as a remediation strategy for uranium-contaminated groundwater . Nitrate is a common co-contaminant with uranium . Nitrate inhibited U(VI) reduction in acetate-amended aquifer sediments collected from a uranium-contaminated site in New Mexico . Once nitrate was depleted, both U(VI) and Fe(III) were reduced concurrently . When nitrate was added to sediments in which U(VI) had been reduced, U(VI) reappeared in solution . Parallel studies with the dissimilatory Fe(III)-, U(VI)- and nitrate-reducing microorganism, Geobacter metallireducens, demonstrated that nitrate inhibited reduction of Fe(III) and U(VI) in cell suspensions of cells that had been grown with nitrate as the electron acceptor, but not in Fe(III)-grown cells . Suspensions of nitrate-grown G . metallireducens oxidized Fe(II) and U(IV) with nitrate as the electron acceptor . U(IV) oxidation was accelerated when Fe(II) was also added, presumably due to the Fe(III) being formed abiotically oxidizing U(IV) . These studies demonstrate that although the presence of nitrate is not likely to be an impediment to the bioremediation of uranium contamination with microbial U(VI) reduction, it is necessary to reduce nitrate before U(VI) can be reduced . These results also suggest that anaerobic oxidation of U(IV) to U(VI) with nitrate serving as the electron acceptor may provide a novel strategy for solubilizing and extracting microbial U(IV) precipitates from the subsurface.

Biotechnol Bioeng, 2002 Sep 5, 79(5), 496 - 503
Cell-Surface display of heterologous proteins: From high-throughput screening to environmental applications; Chen W et al.; A variety of expression systems for the display of either short peptides or fully folded proteins on E.coli and, to a lesser extent, on Gram-positive bacteria have been developed . The expression of proteins on the surface of microbial cells has proved extremely important for numerous applications ranging from combinatorial library screening and protein engineering, to whole cell biocatalysts and adsorbants for bioremediation purposes .

Biotechnol Bioeng, 2002 Oct 20, 80(2), 175 - 84
Biodegradation of gasoline by gellan gum-encapsulated bacterial cells; Moslemy P et al.; Encapsulated cell bioaugmentation is a novel alternative solution to in situ bioremediation of contaminated aquifers . This study was conducted to evaluate the feasibility of such a remediation strategy based on the performance of encapsulated cells in the biodegradation of gasoline, a major groundwater contaminant . An enriched bacterial consortium, isolated from a gasoline-polluted site, was encapsulated in gellan gum microbeads (16-53 microm diameter) . The capacity of the encapsulated cells to degrade gasoline under aerobic conditions was evaluated in comparison with free (non-encapsulated) cells . Encapsulated cells (2.6 mg(cells) x g(-1) bead) degraded over 90% gasoline hydrocarbons (initial concentration 50-600 mg x L(-1)) within 5-10 days at 10 degrees C . Equivalent levels of free cells removed comparable amounts of gasoline (initial concentration 50-400 mg x L(-1)) within the same period but required up to 30 days to degrade the highest level of gasoline tested (600 mg x L(-1)) . Free cells exhibited a lag phase in biodegradation, which increased from 1 to 5 days with an increase in gasoline concentration (200-600 x mg L(-1)) . Encapsulation provided cells with a protective barrier against toxic hydrocarbons, eliminating the adaptation period required by free cells . The reduction of encapsulated cell mass loading from 2.6 to 1.0 mg(cells) x g(-1) bead caused a substantial decrease in the extent of biodegradation within a 30-day incubation period . Encapsulated cells dispersed within the porous soil matrix of saturated soil microcosms demonstrated a reduced performance in the removal of gasoline (initial concentrations of 400 and 600 mg x L(-1)), removing 30-50% gasoline hydrocarbons compared to 40-60% by free cells within 21 days of incubation . The results of this study suggest that gellan gum-encapsulated bacterial cells have the potential to be used for biodegradation of gasoline hydrocarbons in aqueous systems .

Biochem Soc Trans, 2002 Aug, 30(4), 658 - 62
The membrane-bound tetrahaem c-type cytochrome CymA interacts directly with the soluble fumarate reductase in Shewanella; Schwalb C et al.; Shewanella spp . demonstrate great variability in the use of terminal electron acceptors in anaerobic respiration; these include nitrate, fumarate, DMSO, trimethylamine oxide, sulphur compounds and metal oxides . These pathways open up possible applications in bioremediation . The wide variety of respiratory substrates for Shewanella is correlated with the evolution of several multi-haem membrane-bound, periplasmic and outer-membrane c-type cytochromes . The 21 kDa c-type cytochrome CymA of the freshwater strain Shewanella oneidensis MR-1 has an N-terminal membrane anchor and a globular tetrahaem periplasmic domain . According to sequence alignments, CymA is a member of the NapC/NirT family . This family of redox proteins is responsible for electron transfer from the quinone pool to periplasmic and outer-membrane-bound reductases . Prior investigations have shown that the absence of CymA results in loss of the ability to respire with Fe(III), fumarate and nitrate, indicating that CymA is involved in electron transfer to several terminal reductases . Here we describe the expression, purification and characterization of a soluble, truncated CymA ('CymA) . Potentiometric studies suggest that there are two pairs of haems with potentials of -175 and -261 mV and that 'CymA is an efficient electron donor for the soluble fumarate reductase, flavocytochrome c(3).

Curr Microbiol, 2002 Oct, 45(4), 287 - 92
Bioremediation of chlorate or perchlorate contaminated water using permeable barriers containing vegetable oil; Hunter WJ; A scale model of an in situ permeable barrier, formed by injecting vegetable oil onto laboratory soil columns, was used to remove chlorate and perchlorate from flowing groundwater . The hypothesis that trapped oil would serve as a substrate enabling native microorganisms to reduce chlorate or perchlorate to chloride as water flowed through the oil-rich zone had merit . Approximately 96% of the 0.2 mM chlorate and 99% of the 0.2 mM perchlorate present in the water was removed as water was pumped through columns containing vegetable oil barriers . The product formed was chloride . When nitrate at 1.4 mM was added to the water, both nitrate and chlorate were removed . High concentrations of chlorate or perchlorate can be treated; 24 m M chlorate and 6 mM perchlorate were completely reduced to chloride during microcosm incubations . Microorganisms capable of reducing perchlorate are plentiful in the environment.

Water Sci Technol, 2002, 45(10), 49 - 54
Influence of electron donors and acceptors on the bioremediation of soil contaminated with trichloroethene and nickel: laboratory- and pilot-scale study; El Mamouni R et al.; Laboratory- and pilot-scale studies were conducted in order to adjust and optimize the in-situ conditions for bioremediation of a soil contaminated with trichlororethene (TCE) and nickel . Results from laboratory studies showed that the indigenous microorganisms of the soil were limited by the type of electron donor . A better TCE dechlorination was obtained when the electron donor was composed of a mixture of methanol and lactate, as compared to that with methanol alone . Addition of up to 10 mM of sulphate as external electron acceptor (in combination with TCE) and with a mixture of methanol and lactate as electron donor had no significant effect on the TCE reducing activity of indigenous microorganisms of the soil, while higher concentrations (15 and 20 mM) yielded a lower dechlorination . Long term operation of a large pilot-scale soil reactor demonstrated the feasibility of a single-process in situ soil remediation . Results showed that, on one hand, TCE was progressively and stepwise reduced to cis-dichloroethene (DCE), vinyl chloride (VC) and finally to ethene, using only the indigenous microorganisms of the soil . On the other hand, stimulating the activity of sulphate-reducing bacteria of the soil with the addition of sulphate as electron acceptor was efficient in precipitating nickel as nickel sulphide.

Water Sci Technol, 2002, 45(10), 43 - 8
Reductive biodegradation of 1,2-dichloroethane by methanogenic granular sludge: perspectives for in situ remediation; De Wildeman S et al.; Granular methanogenic sludge was able to dechlorinate 1,2-dichloroethane (1,2-DCA) to ethene in UASB reactors . Ethanol served as the sole carbon and energy source . The average dechlorination rate measured on the basis of ethene production varied between 1.7 and 2.1 micromol 1,2-DCA/(h.gVSS) (46.7 and 57.4 mg/L.d) . In order to elucidate the microbial origin of this bioconversion, enrichment cultures of the methanogenic sludge were prepared with different carbon and electron sources: pyruvate, lactate, H2/CO2, ethanol and formate . Dithiothreitol (DTT) was the strong reductant in order to increase the negative redox potential in the media . A homo-acetogenic gram-positive strain could be isolated in the presence of formate . 16S rRNA of the isolated strain showed that the bacterium was closely related (99.7%) to Acetobacterium wieringae . The strain also grew on pyruvate, lactate, H2/CO2 and ethanol, although dechlorination rates of 1,2-DCA were at least 5 times higher when formate was the (only) electron source . Average conversion rates reached 3 micromol/(h.g(dry cells)) and appeared t relate to cometabolic biocatalysis on the corrinoid centers of the homo-acetogenic strain . Some perspectives of anaerobic in situ bioremediation of groundwater polluted with chloroethanes are presented.

Water Res, 2002 Jul, 36(13), 3398 - 403
Sulphadimethoxine and Azolla filiculoides Lam.: a model for drug remediation; Forni C et al.; Plants can be an interesting tool for in situ remediation of drug contaminated waters . In a laboratory model Azolla filiculoides Lam., an aquatic fern known to absorb pollutants, has been exposed to an environmental persistent antibiotic commonly used in intensive farming, sulphadimethoxine (S), to test its bioremediation capability . In a 5 week experiment, plants were cultivated outdoor at four drug concentrations (50, 150, 300 and 450 mg l(-1)) in N-free mineral medium . Drug affects growth rate (as biomass yield per week), N2-fixation, heterocyst frequency, but plants are able to survive . Notwithstanding, at all concentrations tested drug was actively removed from the medium and the accumulation in the biomass is in order of magnitude up to mg g(-1) plant dry weight (1000 ppm) . Drug uptake and degradation rates increase with S concentrations in the culture medium . The efficacy of the model was very high . These results demonstrated that Azolla can be taken into consideration as a tool for sulphonamides environmental monitoring and decontamination.

Ying Yong Sheng Tai Xue Bao, 2002 May, 13(5), 625 - 8
{Advances of studies on ecological risk of herbicide atrazine and its determination and remediation}; Li Q et al.; With wide application of chemical such as pesticide in farming, the coming problems of ecological risks and environmental pollution were increasingly serious . Residual material of atrazine was founded in the surface water, underground water, and atmospheric sedimentation, and it resulted in the global ecological influences . For atrazine could exit in soil for a long time and enrich in organism, it would bring about potential threaten on the safety of food . The results from experiments on animal indicated that atrazine had biological activity . So, there is an increasing demand for further studying on its ecological risks . In this paper, some viewpoints of the researches on atrazine were introduced . With the development of analytical techniques, the opportunities were created to study on the ecological risks of atrazine, and people should attach serious importance to the bioremediation techniques.

J Appl Microbiol, 2002, 93(3), 380 - 9
Isolation and characterization of a Mycobacterium strain that metabolizes the insecticide endosulfan; Sutherland TD et al.; AIM: The aim of this study was to isolate and characterize a bacterium capable of metabolizing endosulfan . METHODS AND RESULTS: A endosulfan-degrading bacterium (strain ESD) was isolated from soil inoculum after repeated culture with the insecticide as the sole source of sulfur . Analysis of its 16S rRNA gene sequence, and morphological and physiological characteristics revealed it to be a new fast-growing Mycobacterium, closely related to other Mycobacterium species with xenobiotic-degrading capabilities . Degradation of endosulfan by strain ESD involved both oxidative and sulfur-separation reactions . Strain ESD did not degrade endosulfan when sulfite, sulphate or methionine were present in the medium along with the insecticide . Partial degradation occurred when the culture was grown, with endosulfan, in the presence of MOPS (3-(N-morpholino)propane sulphonic acid), DMSO (dimethyl sulfoxide), cysteine or sulphonane and complete degradation occurred in the presence of gutathione . When both beta-endosulfan and low levels of sulphate were provided as the only sources of sulfur, biphasic exponential growth was observed with endosulfan metabolism being restricted to the latter phase of exponential growth . CONCLUSIONS: This study isolated a Mycobacterium strain (strain ESD) capable of metabolizing endosulfan by both oxidative and sulfur-separation reactions . The endosulfan-degrading reactions are a result of the sulfur-starvation response of this bacterium . SIGNIFICANCE AND IMPACT OF THE STUDY: This describes the isolation of a Mycobacterium strain capable of degrading the insecticide endosulfan . This bacterium is a valuable source of enzymes for use in enzymatic bioremediation of endosulfan residues.

Appl Microbiol Biotechnol, 2002 Aug, 59(4-5), 551 - 6 Epub 2002 Jun 29.
Biostimulation and bioaugmentation for on-site treatment of weathered diesel fuel in Arctic soil; Thomassin-Lacroix EJ et al.; Bioremediation of weathered diesel fuel in Arctic soil at low temperature was studied both on-site in small-scale biopiles and in laboratory microcosms . The field study site was on Ellesmere Island (82 degrees 30'N, 62 degrees 20'W) . Biostimulation was by fertilization with phosphorous and nitrogen . Bioaugmentation was with an enrichment culture originating from the field site . In biopiles, total petroleum hydrocarbons (TPH) were reduced from 2.9 to 0.5 mg/g of dry soil over a period of 65 days . In microcosms at 7 degrees C, TPH were reduced from 2.4 to 0.5 mg/g of dry soil over a period of 90 days . Inoculation had no effect on hydrocarbon removal in biopiles or in microcosms . Maximum TPH removal rates in the biopiles were approximately 90 micro g of TPH g(-1) of soil day(-1), occurring during the first 14 days when ambient temperature ranged from 0 to 10 degrees C . The fate of three phylotypes present in the inoculum was monitored using most-probable-number PCR, targeting 16S rRNA genes . Populations of all three phylotypes increased more than 100-fold during incubation of both uninoculated and inoculated biopiles . The inoculum increased the initial populations of the phylotypes but did not significantly affect their final populations . Thus, biostimulation on site enriched populations that were also selected in laboratory enrichment cultures.

Water Res, 2002 Jul, 36(12), 3130 - 40
Bioremediation of soil contaminated with alkyllead compounds; Gallert C et al.; Sandy soil, which was highly contaminated with alkyllead compounds, was taken from bore cores from a site of a former tetraalkyllead producing company . It was analyzed for its capacity to chemically and/or biologically degrade alkyllead contaminants . For this purpose, soil samples were supplied with oxygen or oxygen + minerals at different water saturation . For long-term elution, contaminated soil was packed into glass columns of 1.5m length and 10cm diameter . Oxygen-saturated water was recirculated in an upflow mode . Within a time span of 260 days tetraethyllead was completely eluted from the sandy soil and was apparently converted to triethyllead by chemical or microbiological reaction . The triethyllead concentration in the circulating water accounted for 60-80% of the maximal amount, that could be formed from tetraethyllead by a single dealkylation . This indicated that between 20-40% of the triethyllead were apparently further degraded . Only very little diethyllead accumulated in the water . The triethyllead concentration in the circulating water was highly toxic for non-adapted microorganisms . However, if a readily degradable carbon source was added, fast growth of indigenous soil bacteria was observed, but only little alkyllead degradation occurred.

Environ Toxicol Chem, 2002 Aug, 21(8), 1658 - 63
Effects of earthworm (Eisenia fetida) and wheat (Triticum aestivum) straw additions on selected properties of petroleum-contaminated soils; Callaham MA Jr et al.; Current bioremediation techniques for petroleum-contaminated soils are designed to remove contaminants as quickly and efficiently as possible, but not necessarily with postremediation soil biological quality as a primary objective . To test a simple postbioremediation technique, we added earthworms (Eisenia fetida) or wheat (Triticum aestivum) straw to petroleum land-farm soil and measured biological quality of the soil as responses in plant growth, soil respiration, and oil and grease (O&G) and total petroleum hydrocarbon (TPH) concentrations . Results indicated that plant growth was greater in earthworm-treated land-farm soil . Furthermore, addition of wheat straw resulted in greater total respiration in all soils tested (land-farm soil, noncontaminated reference soil, and a 1:1 mixture of land-farm and reference soils) . We observed a 30% increase in soil respiration in straw-amended oily soil, whereas respiration increased by 246% in straw-amended reference soil . Much of the difference between oily and reference soils was attributable to higher basal respiration rates of nonamended oily soil compared to nonamended reference soil . Addition of earthworms resulted in greater total respiration of all soil and straw treatments except two (the land-farm and the 1:1 mixture soil treatments without straw) . Straw and earthworm treatments did not affect O&G or TPH concentrations . Nevertheless, our findings that earthworm additions improved plant growth and that straw additions enhanced microbial activity in land-farm soil suggest that these treatments may be compatible with plant-based remediation techniques currently under evaluation in field trials, and could reduce the time required to restore soil ecosystem function.

J Contam Hydrol, 2002 Jul, 57(1-2), 99 - 127
Heat and mass transfer in the vadose zone with plant roots; Sung K et al.; The vadose zone is the intermediate medium between the atmosphere and groundwater . The modeling of the processes taking place in the vadose zone needs different approaches to those needed for groundwater transport problems because of the marked changes in environmental conditions affecting the vadose zone . A mathematical model to simulate the water flow, and the fate and transport of recalcitrant contaminants was developed, which could be applied to various bioremediation methods such as phytoremediation and natural attenuation in the vadose zone . Two-phase flow equations and heat flux models were used to develop the model . Surface energy, balance equations were used to estimate soil surface temperature, and root growth and root distribution models were incorporated to represent the special contribution of plant mots in the vegetated soils . Interactions between the roots and environmental conditions such as temperature and water content were treated by incorporating a feedback mechanism that made allowance for the effects of water and temperature stresses on root distribution and water uptake by roots . In conducting the modeling study, Johnson grass and unplanted soil were simulated to compare the effect of root water uptake on soil water content . After the numerical experiments were conducted to investigate model behavior, the proposed model was applied to estimate actual water flow and heat flow in field lysimeter experiments over a 1-year period . Root growth and distribution for Johnson grass and rye grass were simulated to compare the warm season grass to the cold season grass . A significant agreement was observed between the simulations and measured data.

J Air Waste Manag Assoc, 2002 Jul, 52(7), 769 - 80
Volatile hydrocarbon emissions from a diesel fuel-contaminated soil bioremediation facility; Ausma S et al.; Concerns have been expressed that emissions of volatile hydrocarbons (HCs) from bioremediation facilities containing soils contaminated with petroleum HCs may negatively impact regional air quality or human health . Little information is available regarding the emission of HCs from bioremediation sites, and few field studies have been performed during which the flux of HCs has been directly measured during bioremediation . To aid in answering questions about the impact of bioremediation facilities on the atmospheric environment, a two-part field study was conducted over summer 1996 at a remote landfarm in northern Ontario where diesel fuel-contaminated soil was undergoing bioremediation . Volatile total hydrocarbon (THC) atmospheric flux measurements were successfully taken over 18 days using a flux gradient micrometeorological technique incorporating a THC detector constructed in-house . Peak THC emissions reached 131 microg C/m2/sec shortly after implementation and tilling of the landfarm soil . The influence of soil temperature and tillage on THC emissions was examined . Off-site inhalation exposure was considered with the aid of an areal source model and results from speciated air samples collected on sorbent tubes and analyzed via gas chromatography/mass spectrometry (GCMS) techniques.

Ying Yong Sheng Tai Xue Bao, 2002 Mar, 13(3), 369 - 72
{Microbial reduction of iron, manganese as well as other metals and their individual significance in environmental bioremediation}; Zhu W et al.; In this paper, microbial reduction of iron, manganese and other metals in soils and waters were discussed . Microorganisms reducing to different metals such as iron, manganese and uranium as well as selenium and their enzymatic and non-enzymatic mechanisms for reducing to different metals were summarized . Moreover, the significance of reduction of different microorganisms of metals in the bioremediation of metals-contaminated environment was also evaluated.

Ying Yong Sheng Tai Xue Bao, 2002 Mar, 13(3), 327 - 30
{Bioremediation of PAHs contaminated soil using bio-slurry reactor process}; Li P et al.; Studies on bioremediation of PAHs contaminated soil were carried out using bio-slurry reactor process . Phenanthrene (PHE) and pyrene (PY) were chosen as the test pollutants . The results showed that the physical and chemical properties of the pollutants were key factor affecting the bio-remedying possibility of PAHs in soil . PAHs with less benzene rings and lower molecule weight were easier to be biodegraded . So, phenanthrene had higher bio-remedying possibility than pyrene . Temperature and airflow were important control factors in bio-slurry reactor process . In this research, the optimized parameters were operating temperature as 20-30 degrees C, ratio between water and soil as 2:1, airflow as 8 L.h-1.L-1, and the inoculating amount as 50 g.kg-1.

Phytochemistry, 2002 Jul, 60(6), 551 - 65
Laccase: new functions for an old enzyme; Mayer AM et al.; Laccases occur widely in fungi; they have been characterized less frequently in higher plants . Here we have focused on more recent reports on the occurrence of laccase and its functions in physiological development and industrial utility . The reports of molecular weights, pH optima, and substrate specificity are extremely diverse . Conclusive proof of the occurrence of laccase in a tissue must demonstrate that the enzyme be able to oxidize quinol with concomitant uptake of oxygen . Laccase is involved in the pigmentation process of fungal spores, the regeneration of tobacco protoplasts, as fungal virulence factors, and in lignification of cell walls and delignification during white rot of wood . Commercially, laccases have been used to delignify woody tissues, produce ethanol, and to distinguish between morphine and codeine . A very wide variety of bioremediation processes employ laccase in order to protect the environment from damage caused by industrial effluents . Research in recent years has been intense, much of it elicited by the wide diversity of laccases, their utility and their very interesting enzymology.

Environ Pollut, 2002, 119(1), 23 - 31
Bioremediation of diesel-contaminated soil with composting; Namkoong W et al.; The major objective of this research was to find the appropriate mix ratio of organic amendments for enhancing diesel oil degradation during contaminated soil composting . Sewage sludge or compost was added as an amendment for supplementing organic matter for composting of contaminated soil . The ratios of contaminated soil to organic amendments were 1:0.1, 1:0.3, 1:0.5, and 1:1 as wet weight basis . Target contaminant of this research was diesel oil, which was spiked at 10,000 mg/kg sample on a dry weight basis . The degradation of diesel oil was significantly enhanced by the addition of these organic amendments relative to straight soil . Degradation rates of total petroleum hydrocarbons (TPH) and n-alkanes were the greatest at the ratio of 1:0.5 of contaminated soil to organic amendments on wet weight basis . Preferential degradation of n-alkanes over TPH was observed regardless of the kind and the amount of organic amendments . The first order degradation constant of n-alkanes was about twice TPH degradation constant . Normal alkanes could be divided in two groups (C10-C15 versus C16-C20) based on the first order kinetic constant . Volatilization loss of TPH was only about 2% of initial TPH . Normal alkanes lost by volatilization were mainly by the compounds of C10 to C16 . High correlations (r=0.80-0.86) were found among TPH degradation rate, amount of CO2 evolved, and dehydrogenase activity.

Chemosphere, 2002 Jul, 48(2), 201 - 7
Degradation characteristics of a dibenzofuran-degrader Terrabacter sp . strain DBF63 toward chlorinated dioxins in soil; Habe H et al.; To obtain basic information towards applying a dibenzofuran (DF)-degrader Terrabacter sp . strain DBF63 to bioremediate dioxin-contaminated soil, we investigated the degradative potential of strain DBF63 for either chlorinated or polychlorinated dibenzo-p-dioxins and dibenzofurans (ClxDD/ClxDF) in soil . In the soil slurry system with a soil to water ratio of 1:5 (w/v), the DF-grown DBF63 cells degraded 90% of 1 ppm 2,8-Cl2DF, whereas only 40% of 1 ppm 2,3-Cl2DD during the 7-day incubation . The degradation rates of 2-CIDF, 2-ClDD, 2,8-Cl2DF and 2,3-Cl2DF by strain DBF63 in the soil slurry system (5-day incubation) were approximately 89%, 65%, 78% and 32%, respectively . These results suggest that strain DBF63 was able to degrade mono- to dichlorinated dibenzofurans more effectively than mono- to dichlorinated dibenzo-p-dioxins . Using the same soil slurry system, we performed a preliminary bioremediation experiment using the actual dioxin-contaminated soil at an incineration site . We found that approximately 10% of tetra- to hexa-chlorinated congeners was decreased by a single inoculation with DBF63 cells within a 7-day incubation.

Biotechnol Bioeng, 2002 Aug 20, 79(4), 389 - 97
Effect of complexing agents on reduction of Cr(VI) by Desulfovibrio vulgaris ATCC 29579; Mabbett AN et al.; The reduction of Cr(VI) at the expense of molecular hydrogen was studied using resting cells of Desulfovibrio vulgaris ATCC 29579 in anaerobic resting cell suspensions in MOPS buffer . Bioreduction occurred only in the presence of ligands or chelating agents (CO32-, citrate, NTA, EDTA, DTPA) . The stimulatory effect of these ligands on the rate of Cr(VI) reduction was correlated (r = 0.988) with the strength of the ligand/chelate complex of Cr(III) . The data are examined with respect to likely solution and redox equilibria in the ionic matrix of the carrier solution, and with respect to the potential for bioremediation of Cr(VI) .

Biotechnol Bioeng, 2002 Jun 5, 78(5), 556 - 66
Glass micromodel study of bacterial dispersion in spatially periodic porous networks; Lanning LM et al.; Successful implementation of bioremediation clean-up strategies depends on accurate predictions of the transport of bacteria within the subsurface . In this study, etched flat-plate glass micromodels were used to examine bacterial transport in a homogenous network . These networks were created by acid-etching interconnected channels into a glass plate and then fusing it to an unetched plate forming semi-cylindrical pores . The transparent nature of the micromodel allows for both qualitative observations of the bacteria within the pores and quantitative measurements of their concentration . The micromodels are designed to allow establishment of a well-characterized step change in bacterial concentration (Escherichia coli NR50) within the network . During the experiments, bacteria are dispersed through the network by flow . Light scattering is used to detect the change in turbidity within the pores as the bacteria travel through the network . The change in turbidity is used to construct breakthrough curves and spatial concentration profiles of bacteria within the network . The breakthrough curves are fit to the one-dimensional advection/dispersion equation to determine dispersion coefficients at different interstitial fluid velocities . From the breakthrough curves, dispersion coefficients were reproducible for replicate experiments over a range of velocities in the advection-dominated regime . The dispersivity values for two network designs resembling an interconnecting capillary network and a spatially periodic network of cylinders were 0.28 and 0.33 cm respectively, which are slightly greater than the literature values found for other pore networks . Experiments were also conducted within the diffusion-dominated regime to examine the effects of bacterial motility on dispersion . The accumulation of bacteria on the pore walls became significant at the low flow rates and extended experimental times thereby rendering the use of light scattering to determine concentrations ineffective . Bacterial chemotaxis, created by a self-imposed oxygen gradient, was also observed in the micromodel under stagnant fluid conditions .

Appl Microbiol Biotechnol, 2002 Jul, 59(2-3), 143 - 52 Epub 2002 Jun 01.
Biotechnology and bioremediation: successes and limitations; Dua M et al.; With advances in biotechnology, bioremediation has become one of the most rapidly developing fields of environmental restoration, utilizing microorganisms to reduce the concentration and toxicity of various chemical pollutants, such as petroleum hydrocarbons, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, phthalate esters, nitroaromatic compounds, industrial solvents, pesticides and metals . A number of bioremediation strategies have been developed to treat contaminated wastes and sites . Selecting the most appropriate strategy to treat a specific site can be guided by considering three basic principles: the amenability of the pollutant to biological transformation to less toxic products (biochemistry), the accessibility of the contaminant to microorganisms (bioavailability) and the opportunity for optimization of biological activity (bioactivity) . Recent advances in the molecular genetics of biodegradation and studies on enzyme-tailoring and DNA-shuffling are discussed in this paper.

Environ Sci Technol, 2002 Jun 15, 36(12), 2724 - 8
Analysis of benzylsuccinates in groundwater by liquid chromatography/tandem mass spectrometry and its use for monitoring in situ BTEX biodegradaton; Beller HR; Benzylsuccinic acid (BS) and methylbenzylsuccinic acid (MeBS) isomers have been proposed as distinctive indicators of anaerobic toluene and xylene metabolism in fuel-contaminated aquifers; however, labor-intensive analytical procedures have limited their analysis at field sites . In this article, a rapid electrospray LC/MS/MS (liquid chromatography/mass spectrometry/mass spectrometry) method for benzylsuccinates is described that involves selected reaction monitoring, internal standard quantification with {ring-2H5}BS, small sample size (<1 mL), and no extraction/concentration steps . The highly selective LC/MS/ MS method was shown to be sensitive (detection limits ca . 0.3 microg/L), accurate, and precise . The method was used to characterize geographic and temporal distributions of BS and MeBS isomers in an anaerobic, hydrocarbon-contaminated aquifer . BS was never detected, and MeBS isomers were detected in the three wells with the highest concentrations of BTEX (benzene, toluene, ethylbenzene, and xylenes); MeBS concentrations ranged from <0.3 to 205 microg/L . A strong linear correlation (r2 = 0.94; n = 12) was found between concentrations of total MeBS isomers and their parent compounds, xylenes, which suggests that anaerobic xylene metabolism at this site was probably first-order rather than zero-order . The novel LC/MS/MS method for BS and MeBS isomers is a promising technique for rapid and reliable monitoring of in situ bioremediation of gasoline-contaminated groundwater.

Environ Sci Technol, 2002 Jun 15, 36(12), 2630 - 5
Dehalogenation of chlorinated ethenes and immobilization of nickel in anaerobic sediment columns under sulfidogenic conditions; Drzyzga O et al.; A sediment column study was carried out to demonstrate the bioremediation of chloroethene- and nickel-contaminated sediment in a single anaerobic step under sulfate-reducing conditions . Four columns (one untreated control column and three experimental columns) with sediment from a chloroethene- and nickel-contaminated site were investigated for 1 year applying different treatments . By stimulating the activity of sulfate-reducing bacteria by the addition of sulfate as supplementary electron acceptor, complex anaerobic communities were maintained with lactate as electron donor (with or without methanol), which achieved complete dehalogenation of tetra- and trichloroethenes (PCE and TCE) to ethene and ethane . A few weeks after sulfate addition, production of sulfide increased, indicating an increasing activity of sulfate-reducing bacteria . The nickel concentration in the effluent of one nickel-spiked column was greatly reduced, likely due to the enhanced sulfide production, causing precipitation of nickel sulfide . At the end of the study, 94% of the initial amount of nickel added to that column was recovered in the sediment As compared to the untreated (nonspiked) control column, all chloroethene-spiked columns ladditions of PCE and TCE) showed a permanent release of small chloride ion quantities (approximately 0.5-0.7 mM chloride), which were detected in the effluents a few weeks after sulfide production was observed for the first time . The formation of ethene and ethane as final products after dechlorination of PCE and TCE was detected in some effluents and in some gas phases of the columns . Other metabolites or intermediates (such as DCE isomers) were only detected sporadically in negligible quantities . The results of this study demonstrated thatmicrobial activity stimulated under sulfate-reducing conditions can have a beneficial effect on both the precipitation of heavy metals and the complete dechlorination of organochlorines . The strongly negative redox potential created by the activity of sulfate-reducing bacteria may be one factor responsible for stimulating the activity of the dehalogenating bacteria in the test columns.

J Environ Sci Health B, 2002 Jul, 37(4), 297 - 305
Bioavailability and biodegradation of prosulfocarb in soil; Gennari M et al.; Active microbial degraders of the herbicide prosulfocarb (PSC) were isolated to evaluate their performance in soil with a view to their use for bioremediation . The isolated cultures (a microbial consortium and a Pseudomonas sp . strain) were active when tested in mineral medium with PSC as the only carbon source, but had an adverse effect on the soil indigenous microflora . Biodegradation in the inoculated soils was thus lower than in the uninoculated soil when only the indigenous microflora was present . Further tests showed that the strong affinity of PSC for soil organic matter affected its bioavailability and hence its biodegradation by the inocula . Bioremediation of PSC contaminated soils could thus be undertaken by biostimulation of indigenous microflora.

Microb Ecol, 2002 Aug, 44(2), 118 - 26 Epub 2002 Jun 13.
Effectiveness of bioremediation of crude oil contaminated subantarctic intertidal sediment: the microbial response; Delille D et al.; A field study was initiated in February 1996 in a remote sandy beach of The Grande Terre (Kerguelen Archipelago, 69 degrees 42 degrees E, 49 degrees 19 degrees S) with the objective of determining the long-term effects of some bioremediation agents on the biodegradation rate and the toxicity of oil residues under severe subantarctic conditions . A series of 10 experimental plots were settled firmly into sediment . Each plot received 2L of Arabian light crude oil and some of them were treated with bioremediation agents: slow release fertilizer Inipol EAP-22 (Elf Atochem) or fish composts . Plots were sampled on a regular basis over a 3-year period . A two-order of magnitude increase of saprophytic and hydrocarbon-utilizing microorganisms occurred during the first month of the experiment in all treated enclosures, but no clear differences appeared between the plots . Very high microbial populations were present during the experiment . Biodegradation within treated spots was faster than within the untreated ones and appeared almost complete after 6 months as indicated by the degradation index of aliphatic hydrocarbons within all plots . The analysis of interstitial water collected below the oily residues presented no toxicity . However, a high toxicity signal, using Microtox solid phase, appeared for all oiled sand samples with a noticeable reduction with time even if the toxicity signal remained present and strong after 311 days of oil exposition . As a conclusion, it is clear that the microbial response was rapid and efficient in spite of the severe weather conditions, and the rate of degradation was improved in presence of bioremediation agents . However, the remaining residues had a relatively high toxicity.

Curr Opin Microbiol, 2002 Jun, 5(3), 282 - 7
Bioelimination of trinitroaromatic compounds: immobilization versus mineralization; Heiss G et al.; Electron deficiency of trinitroaromatic compounds favors gratuitous reduction of nitro groups or unique ring hydrogenation . From nitro-group reduction of 2,4,6-trinitrotoluene (TNT), some highly reactive products are generated that are subject to further transformation or interaction with diverse electrophiles . Up to now, only initial ring hydrogenation of picric acid (2,4,6-trinitrophenol) opens perspectives of complete degradation . This review focuses on recent findings that may be relevant for bioremediation or complete degradation of TNT or picric acid.

Biochem Biophys Res Commun, 2002 May 31, 294(1), 76 - 81
A bacterial flavin reductase system reduces chromate to a soluble chromium(III)-NAD(+) complex; Puzon GJ et al.; Biological reduction of carcinogenic chromate has been extensively studied in eukaryotic cells partly because the reduction produces stable chromium(III)-DNA adducts, which are mutagenic . Microbial reduction of chromate has been studied for bioremediation purposes, but little is known about the reduction mechanism . In eukaryotic cells chromate is mainly reduced non-enzymatically by ascorbate, which is usually absent in bacterial cells . We have characterized the reduction of chromate by a flavin reductase (Fre) from Escherichia coli with flavins . The Fre-flavin system rapidly reduced chromate, whereas chemical reduction by NADH and glutathione was very slow . Thus, enzymatic chromate reduction is likely the dominant mechanism in bacterial cells . Furthermore, the end-product was a soluble and stable Cr(III)-NAD(+) complex, instead of Cr(III) precipitate . Since intracellularly generated Cr(III) forms adducts with DNA, protein, glutathione, and ascorbate in eukaryotic cells, we suggest that the produced Cr(III) is primarily complexed to NAD(+), DNA, and other cellular components inside bacteria.

Arch Biochem Biophys, 2002 May 1, 401(1), 91 - 8
Biodegradation of polychlorinated dibenzo-p-dioxins by recombinant yeast expressing rat CYP1A subfamily; Sakaki T et al.; Metabolism of polychlorinated dibenzo-p-dioxins (PCDDs) by recombinant yeast cells expressing either rat CYP1A1 or CYP1A2 was examined . When each of the dibenzo-p-dioxins (DDs), mono-, di-, and tri-chloroDDs, was added to the cell culture of the recombinant yeast, a remarkable metabolism was observed . The metabolism contained multiple reactions such as hydroxylation at an unsubstituted position, hydroxylation with migration of a chloride substituent, hydroxylation with elimination of a chloride substituent, and opening of dioxin ring . The distinct difference was observed in substrate specificity and reaction specificity between CYP1A1 and CYP1A2 . Kinetic analysis using microsomal fractions prepared from the recombinant yeast cells revealed that 2,7-dichloroDD and 2,3,7-trichloroDD were good substrates for both CYP1A1 and CYP1A2 . When 2,3,7-trichloroDD was added to the yeast cells expressing each of rat CYP1A1 and CYP1A2, most of 2,3,7-trichloroDD was first converted to 8-hydroxy-2,3,7-trichloroDD, and further metabolized to more hydrophilic compounds whose ethereal bridges were cleaved . These findings give essential information on the metabolism of PCDDs in mammalian liver . In addition, this study indicates the possibility of application of microorganisms expressing mammalian cytochrome P450 to bioremediation of contaminated soils with dioxins . (c) 2002 Elsevier Science (USA).

Environ Int, 2002 Apr, 28(1-2), 79 - 82
Determination of total petroleum hydrocarbons and heavy metals in soils within the vicinity of facilities handling refined petroleum products in Lagos metropolis; Adeniyi AA et al.; This article discusses the determination of total petroleum hydrocarbons (TPH) and heavy-metal contamination in soils within areas of refined petroleum products handling in Lagos metropolis . Soil samples were collected randomly from two petrol stations, two auto-mechanic workshops, and a National Electric Power Authority (NEPA) station . Control samples were taken from two low-density residential areas . TPH were estimated gravimetrically following standard methods of TPH analysis, while the heavy metals were determined by atomic absorption spectrophotometry . Sites studied had higher levels of TPH and heavy metals compared to the control samples . For TPH, the petrol stations have mean values of 399.83+/-106.19 and 450.83 +/- 90.58 microg/g, respectively; mechanic workshops, 362.60 +/- 185.84 and 428.55 +/- 119.00 microg/g, respectively; while the NEPA station has 356.20 +/- 210.30 microg/g compared to the control mean of 26.63 +/- 4.58 . It revealed that the improper handling of refined petroleum products are potential sources of soil contamination in the sampled sites . This is indicated by the statistically significant levels of TPH and heavy metals observed between the control samples and those collected from the petroleum products handling sites . Bioremediation using microorganisms and plants is recommended.

FEMS Microbiol Lett, 2002 May 7, 210(2), 227 - 32
Degradation of pyrene by indigenous fungi from a former gasworks site; Saraswathy A et al.; Indigenous fungi isolated from soil of a former gasworks site were investigated in submerged cultures with pyrene as the sole carbon source . Five fungal strains capable of degrading pyrene included one strain of Trichoderma harzianum and four strains with characteristics of the genus Penicillium . These are identified as Penicillium simplicissimum, Penicillium janthinellum, Penicillium funiculosum and Penicillium terrestre . A maximum of 75% of 50 mg l(-1) and 67% of 100 mg l(-1) of pyrene was removed by the fast degrading strain P . terrestre at 22 degrees C during 28 days of incubation . The slower degrader P . janthinellum was able to remove 57% of 50 mg l(-1) and about 31.5% of 100 mg l(-1) pyrene . Degradation of pyrene is directly correlated with biomass development . To the best of our knowledge, this is the first time that fungi have been reported to use pyrene as the sole carbon and energy source . They may be ideal candidates for effective bioremediation of polycyclic aromatic hydrocarbons.

Appl Environ Microbiol, 2002 Jun, 68(6), 2660 - 5
Substrate interactions during the biodegradation of benzene, toluene, ethylbenzene, and xylene (BTEX) hydrocarbons by the fungus Cladophialophora sp . strain T1; Prenafeta-Boldu FX et al.; The soil fungus Cladophialophora sp . strain T1 (= ATCC MYA-2335) was capable of growth on a model water-soluble fraction of gasoline that contained all six BTEX components (benzene, toluene, ethylbenzene, and the xylene isomers) . Benzene was not metabolized, but the alkylated benzenes (toluene, ethylbenzene, and xylenes) were degraded by a combination of assimilation and cometabolism . Toluene and ethylbenzene were used as sources of carbon and energy, whereas the xylenes were cometabolized to different extents . o-Xylene and m-xylene were converted to phthalates as end metabolites; p-xylene was not degraded in complex BTEX mixtures but, in combination with toluene, appeared to be mineralized . The metabolic profiles and the inhibitory nature of the substrate interactions indicated that toluene, ethylbenzene, and xylene were degraded at the side chain by the same monooxygenase enzyme . Our findings suggest that soil fungi could contribute significantly to bioremediation of BTEX pollution.

Curr Opin Chem Biol, 2002 Apr, 6(2), 130 - 5
Protein engineering of oxygenases for biocatalysis; Cirino PC et al.; Oxygenase enzymes have seen limited practical applications because of their complexity, poor stabilities, and often low catalytic rates . However, their ability to perform difficult chemistry with high selectivity and specificity has kept oxygenases at the forefront of engineering efforts . Growing understanding of structure-function relationships and improved protein engineering methods are paving the way for applications of oxygenases in chemical synthesis and bioremediation.

Environ Sci Technol, 2002 May 15, 36(10), 2262 - 8
Stable carbon isotope fractionation during enhanced in situ bioremediation of trichloroethene; Song DL et al.; Time-series stable carbon isotope monitoring of volatile organic compounds (VOCs) atthe Idaho National Engineering and Environmental Laboratory's (INEEL) field site Test Area North (TAN) was conducted during a pilot study to investigate the treatment potential of using lactate to stimulate in situ biologic reductive dechlorination of trichloroethene (TCE) . The isotope ratios of TCE and its biodegradation byproducts, cis-dichloroethene (c-DCE), trans-dichloroethene (t-DCE), vinyl chloride (VC), and ethene, in groundwater samples collected during the pilot studywere preconcentrated with a combination of purge-and-trap and cryogenic techniques in order to allow for reproducible isotopic measurements of the low concentrations of these compounds in the samples (down to 0.04 microM, or 5 ppb, of TCE) . Compound-specific stable isotope monitoring of chlorinated solvents clearly differentiated between the effects of groundwater transport, dissolution of DNAPL at the source, and enhanced bioremediation . Isotope data from all wells within the zone of lactate influence exhibited large kinetic isotope effects during the reduction of c-DCE to VC and VC to ethene . Despite these large effects, the carbon isotope ratio of ethene in all these wells reached the carbon isotope ratios of the initial dissolved TCE, confirming the complete conversion of dissolved TCEto ethene . Conversely, the carbon isotope ratios of t-DCE were only marginally affected during the study, indicating that minimal biologic degradation of t-DCE was occurring.

J Microbiol Methods, 2002 Aug, 50(3), 227 - 36
Effect of pollutants on the ergosterol content as indicator of fungal biomass; Barajas-Aceves M et al.; Ergosterol content was determined in 20 white-rot fungi isolates and the values ranged from 2380 to 13060 microg g(-1) fungal biomass . Significant changes of ergosterol content according the physiological stage for Bjerkandera adusta 4312 and Coriolopsis gallica 8260 were found, showing the highest values during the stationary phase . However, in the case of Phanerochaete chrysosporium 3642, no changes were detected during growth . The effect of pollutants, such as heavy metals and fungicides, on the ergosterol content of C . gallica was determined . Heavy metals (Cu 80 ppm, Zn 50 ppm or Cd 10 ppm) and fungicides (thiram 3 ppm or pentachlorophenol 1.5 ppm) at concentrations that reduce the metabolic activity between 18% and 53% (pollutant-stressed cultures) did not affect the ergosterol content . Only the fungicide zineb (25 ppm) reduced significantly the ergosterol content in biomass basis . In soil experiments with Cu (80 ppm) or thiram (10 ppm) after 15 and 30 days of incubation, the ergosterol content in soil was linearly correlated to the fungal biomass C in both polluted and control soil cultures . The ergosterol content was independent of the presence or the absence of pollutants . Thus, these results indicate that ergosterol can be a useful indicator for fungal biomass in polluted soils, and can be applied for monitoring bioremediation processes.

Microb Ecol, 2001 Oct, 42(3), 267 - 273
Monitoring the Size and Metabolic Activity of the Bacterial Community during Biostimulation of Fuel-Contaminated Soil using Competitive PCR and RT-PCR; Ka JO et al.; Efforts to understand and improve soil bioremediation are limited by our ability to determine how treatment variables affect microbial communities . A method was developed to monitor the density and metabolic activity of the total bacterial community in soil . This method was used to monitor the bacterial community in microcosms of Arctic soil after addition of N plus P to stimulate biodegradation of hydrocarbon contaminants . During 29 days of incubation, the total petroleum hydrocarbon level in the soil was reduced from 850 to 360 mg/g of soil . DNA and RNA were extracted from soil using a bead beating method, purified by ammonium acetate precipitation, and assayed by competitive PCR and RT-PCR assays with universal bacterial primers . The copy number of 16S rDNA in the soil microbial community was relatively stable and ranged from 1.7 x 109 to 4.5 x 109/g of soil throughout the incubation . The copy number of 16S rRNA changed substantially and ranged from 5.6 x 1010 to 1.0 x 1012/g of soil . The rRNA:rDNA ratio was highest during the phase of fastest hydrocarbon biodegradation . These results suggest that the treatment to stimulate hydrocarbon biodegradation did not substantially change the density of the bacterial community but did transiently increase its overall metabolic activity.

Microb Ecol, 2001 Dec, 42(4), 614 - 623
Survival of a GFP-Labeled Polychlorinated Biphenyl Degrading Psychrotolerant Pseudomonas spp . in 4 and 22 degrees C Soil Microcosms; Ahn YB et al.; The green fluorescent protein gene (gfp) was inserted into the chromosome of Pseudomonas spp . Cam-1 and Sag-50G, two psychrotolerant polychlorinated biphenyl (PCB)-degrading bacteria . The gfp-transformed microorganisms, designated Cam-1-gfp1, Cam-1-gfp2, Sag-50G-gfp1, and Sag-50G-gfp2, exhibited green fluorescence under an epifluorescent microscope . The gfp was inserted into the chromosome of each psychrotolerant strain and was stable with no apparent adverse affects on the metabolism and growth of each organism . Activity of gfp-transformed microorganisms against biphenyl and 2,3-dichlorobiphenyl was determined by assaying for BphC activity and by resting cell assays . The patterns of BphC activity at two different growth temperatures in batch cultures were similar for each of the gfp-transformed microorganisms . Resting cell assays of both the parent strains (Cam-1, Sag-50G) and the gfp-transformed strains (Cam-1-gfp1, Cam-1-gfp2, Sag-50G-gfp1, Sag-50G-gfp2), grown on glycerol or glucose, exhibited BphC activity to a lesser extent and at a slower rate than those observed for biphenyl grown cells . In addition, all gfp-transformed microorganisms degraded 2,3-dichlorobiphenyl (2,3-DCB) in broth to the same extent as the parent strains . When Cam-1-gfp1 and Sag-50G-gfp1 were used as a bioremediation amendment in soil microcosms spiked with 2,3-DCB, both strains survived in high numbers (5.6 to 7.9 log cfu g?1 and 5.6 to 8.0 log cfu g?1) when inoculated into nonsterilized soil over 16 weeks at 22 degrees C and 18 weeks at 4 degrees C, respectively . Biodegradation of 2,3-DCB was enhanced with the microbial amendment; however, the addition of sunflower oil did not help the PCB degrading bacteria and may have enhanced the growth of the indigenous population, thereby decreasing the amended PCB-degrading population.

J Environ Sci Health B, 2002 May, 37(3), 201 - 10
Assessment of the rhizosphere competency and pentachlorophenol-metabolizing activity of a pesticide-degrading strain of Trichoderma harzianum introduced into the root zone of corn seedlings; Rigot J et al.; To develop a dependable approach to introduce laboratory selected, pesticide-degrading microorganisms into soil environments for the purpose of in situ bioremediation, we tested the possibility of utilizing plant rhizospheres as the vehicle . We first established the rhizosphere competency of a strain of the soil fungus Trichoderma harzianum, a biocontrol species well studied by plant pathologists to colonize plant rhizosphere in many parts of the world . The strain we chose, T.h.2023 is resistant to many fungicides, and it has been shown to metabolize several pesticides . Second, we found that it readily metabolized pentachlorophenol (PCP), which is quickly and stochiometrically converted to pentachloroanisole (PCA) in liquid culture . Taking advantage of this specific feature, we have developed a sensitive metabolic marker approach that allowed us to monitor for the continuous presence and activity of this fungal strain in the corn rhizosphere soil in situ over time.

Trends Biotechnol, 2002 Jun, 20(6), 243 - 8
Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation; Samanta SK et al.; Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and relocated in the environment as a result of the incomplete combustion of organic matter . Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher systems including humans . Although various physicochemical methods have been used to remove these compounds from our environment, they have many limitations . Xenobiotic-degrading microorganisms have tremendous potential for bioremediation but new modifications are required to make such microorganisms effective and efficient in removing these compounds, which were once thought to be recalcitrant . Metabolic engineering might help to improve the efficiency of degradation of toxic compounds by microorganisms . However, efficiency of naturally occurring microorganisms for field bioremediation could be significantly improved by optimizing certain factors such as bioavailability, adsorption and mass transfer . Chemotaxis could also have an important role in enhancing biodegradation of pollutants . Here, we discuss the problems of PAH pollution and PAH degradation, and relevant bioremediation efforts.

Environ Microbiol, 2002 Mar, 4(3), 141 - 7
Predominant growth of Alcanivorax strains in oil-contaminated and nutrient-supplemented sea water; Kasai Y et al.; We found that bacteria closely related to Alcanivorax became a dominant bacterial population in petroleum-contaminated sea water when nitrogen and phosphorus nutrients were supplied in adequate quantity . The predominance of Alcanivorax bacteria was demonstrated under three experimental conditions: (i) in batch cultures of sea water containing heavy oil; (ii) in columns packed with oil-coated gravel undergoing a continuous sea water flow; and (iii) in a large-scale tidal flux reactor that mimics a beach undergoing tidal cycles with fresh sea water . These results suggest that bacteria related to Alcanivorax are major players in the bioremediation of oil-contaminated marine environments.

J Contam Hydrol, 2002 Mar, 55(1-2), 29 - 56
Nitrate-enhanced bioremediation of BTEX-contaminated groundwater: parameter estimation from natural-gradient tracer experiments; Schreiber ME et al.; Two natural-gradient pulse tracer tests were conducted in a petroleum-contaminated aquifer to evaluate the potential for benzene, toluene, ethylbenzene, and xylenes (BTEX) biodegradation under enhanced nitrate-reducing conditions . Addition of nitrate resulted in loss of toluene, ethylbenzene, and m,p-xylenes (TEX) after an initial lag period of approximately 9 days . Losses of benzene were not observed over the 60-day monitoring period . Tracer breakthrough curves (BTCs) were analyzed to derive transport and biodegradation parameters, including advective velocities, retardation factors, dispersion coefficients, biodegradation rate constants, and nitrate utilization ratios . Using the parameters derived from the BTC analysis, numerical simulations of one of the tracer experiments were conducted using BIONAPL/3D {Molson, J., BIONAPL/3D User Guide, A 3D Coupled Flow and Multi-Component Reactive transport model . University of Waterloo, Waterloo, Ontario, Canada} . Simulations using the BTC-derived transport and biodegradation parameters successfully reproduced benzene, TEX, and nitrate concentrations measured during the tracer experiment . Comparisons of observed and simulated nitrate concentrations indicate that the mass ratio of nitrate-N utilized to TEX degraded increased over time during the experiment, reaching values many times that expected based on stoichiometry of TEX oxidation coupled to nitrate reduction . Excess nitrate loss is likely due to oxidation of other organics in addition to TEX.

Water Res, 2002 Mar, 36(6), 1539 - 46
Degradation of trichloroethylene in wetland microcosms containing broad-leaved cattail and eastern cottonwood; Bankston JL et al.; Remediation of aquifers containing trichloroethylene (TCE) relies primarily on physical extraction of contaminated groundwater and soil . Unfortunately, this is typically expensive and does not always attain the desired treatment goals . In situ bioremediation via natural attenuation is an alternative treatment process in which TCE is transformed by indigenous microorganisms and plants . In this study, TCE was observed in a surficial aquifer that discharges into a wetland . Experiments were undertaken to determine whether natural attenuation of TCE in the wetland was possible . Microcosms were constructed using sandy soil+/-eastern cottonwoods (Populus deltoides) from the wetland's edge and organic soil+broad-leaved cattails (Typha latifolia) from the wetland's interior . {14C} TCE was added to each microcosm (1.27 microCi) . Overtime, 14C was recovered from four microcosm compartments: (1) as 14C bound to soil and water, (2) as volatilized {14C} TCE, (3) as {14C} CO2 produced by mineralization of {14C} TCE, and (4) as 14C incorporated into the plants . Total recoveries of the 14C-label ranged from 73.6% to 95.8% . Volatilized {14C} TCE accounted for the majority ( > 50%) of the recovered label . In microcosms without plants, {14C} CO2 represented 3.2% (organic soil) to 15.6% (sandy soil) of the recovered 14C, indicating that TCE was mineralized by indigenous microorganisms . The presence of the broad-leaved cattail resulted in increased production of {14C} CO2 to 5.3% in the organic soil . The data thus suggest that natural attenuation is a potential bioremediative strategy for TCE-contaminated wetlands.

J Biotechnol, 2002 Feb, 82(4), 393 - 409
Protein modified- and membrane electrodes: strategies for the development of biomolecular sensors; Bianco P; Different procedures used for constructing protein/enzyme-modified electrodes are examined, in particular adsorption, covalent attachment and film deposition . The performances of such modified electrodes with electroactive proteins or enzymes attached to their active surface are examined, especially in the case of c-type cytochromes, hydrogenases and glucose oxidase . Another strategy presented in this review consists of the use of membrane electrodes with an electroactive protein imprisoned between a dialysis membrane and the electrode surface . The versatility and other advantages of such a procedure are underlined . Applications of membrane electrodes to the bioremediation of soils and effluents and as models for investigating interactions between proteins and soils are described.

Biodegradation, 2001, 12(5), 311 - 6
Biostimulation-based bioremediation of diesel fuel: field demonstration; Seklemova E et al.; Ex-situ bioremediation of leached cynamonic forest soil at initial diesel oil contamination of 6,000 mg kg(-1), 4,000 mg kg(-1) and 2,000 mg kg(-1) was investigated after biostimulation with inorganic fertilizers . It was found that the added nutrients had no effect on the decontamination of polluted soils . A precise and reliable approach for evaluation of the biodegradation process is proposed . It comprises application of sensitive and easily accessible diagnostic parameters and relations, calculated on the basis of n-alkanes and isoprenoids--pristane (2.6.10.14-tetramethylpentadecane, i-C19H40) and phytane (2.6.10.14-tetramethylhexadecane, i-C20H42) distribution.

Biodegradation, 2001, 12(5), 303 - 9
Isolation and characterization of a pseudomonas strain that degrades 4-acetamidophenol and 4-aminophenol; Ahmed S et al.; Though many microorganisms that are capable of using phenol as sole source of carbon have been isolated and characterized, only a few organisms degrading substituted phenols have been described to date . In this study, one strain of microorganism that is capable of using phenol (3,000 ppm), 4-aminophenol (4,000 ppm) and 4-acetamidophenol (4,000 ppm) as sole source of carbon and energy was isolated and characterized . This strain was obtained by enrichment culture from a site contaminated with compounds like 4-acetamidophenol, 4-aminophenol and phenol in Pakistan at Bhai Pheru . The contaminated site is able to support large bacterial community as indicated by the viable cell counts (2 x 10(4) - 5 x 10(8)) per gram of soil . Detailed taxonomic studies identified the organisms as Pseudomonas species designated as strain STI . The isolate also showed growth on other organic compounds like aniline, benzene, benzyl alcohol, benzyl bromide, toluene, p-cresol, trichloroethylene and o-xylene . Optimum growth temperature and pH were found to be 30 degrees C and 7, respectively, while growth at 4, 25 and 35 degrees C and at pH 8 and 9 was also observed . Non growing suspended cells of strain ST1 degraded 68, 96 and 76.8% of 4-aminophenol (1,000 ppm), phenol (500 ppm) and 4-acetamidophenol (1,000 ppm), respectively, in 72 hrs . The isolation and characterization of Pseudomonas species strain STI, may contribute to efforts on phenolic bioremediation, particularly in an environment with very high levels of 4-acetamidophenol and 4-aminophenol.

Ying Yong Sheng Tai Xue Bao, 2002 Feb, 13(2), 247 - 51
{Molecular-ecological technology of microorganisms and its application to research on environmental pollution}; Zhong M et al.; Nucleicacid probe detection, PCR technique using primer, DNA sequential analysis, and electrophoresis separation and display were summarized and the application of these techniques to research on environmental pollution and future developing directions were discussed . It was pointed out that molecular-ecological technology of microorganisms are playing an important role in studying on relationships between microorganisms and contaminated environment . There are some important advances such as genetic adaptation and evolutionary mechanisms of microorganisms in contaminated environment, the positioning of pollutant-degrading genes of microorganisms and the construction of microbiological engineering bacteria, thus promoting the development of molecular ecology for bioremediation of contaminated environment.

Ying Yong Sheng Tai Xue Bao, 2002 Feb, 13(2), 243 - 6
{Bioremediation of low-level radionuclide contaminated soils and water}; Tang S; Different anthroponic factors have led up to increasing background concentrations of radionuclides in human ecosystems . As long as these radionuclides enter into soil-water substrates, they can pose hazards to human health through different pathways . Since most conventional chemical or physical procedures are not practical for dealing with low-level radionuclides in the water-soil substrates, new remediation technologies are being developed to tackle the problem . Bioremediation has attracted much attention because of its many advantages such as low cost and less environmental disturbance . The present paper summarizes the sources of radionuclides and introduces the concept of low-level radionuclide bioremediation . The state of the art in the field of bioremediation of low-level radionuclide contaminated water-soil substrates has also been reviewed and summarized in this paper . On the basis of above mentioned discussions the future developing trends were put forward.

J Ind Microbiol Biotechnol, 2002 May, 28(5), 252 - 60
Biodegradation of a crude oil by three microbial consortia of different origins and metabolic capabilities; Vinas M et al.; Microbial consortia were obtained three by sequential enrichment using different oil products . Consortium F1AA was obtained on a heavily saturated fraction of a degraded crude oil; consortium TD, by enrichment on diesel and consortium AM, on a mixture of five polycyclic aromatic hydrocarbons {PAHs} . The three consortia were incubated with a crude oil in order to elucidate their metabolic capabilities and to investigate possible differences in the biodegradation of these complex hydrocarbon mixtures in relation to their origin . The efficiency of the three consortia in removing the saturated fraction was 60% (F1AA), 48% (TD) and 34% (AM), depending on the carbon sources used in the enrichment procedures . Consortia F1AA and TD removed 100% of n-alkanes and branched alkanes, whereas with consortium AM, 91% of branched alkanes remained . Efficiency on the polyaromatic fraction was 19% (AM), 11% (TD) and 7% (F1AA) . The increase in aromaticity of the polyaromatic fraction during degradation of the crude oil by consortium F1AA suggested that this consortium metabolized the aromatic compounds primarily by oxidation of the alkylic chains . The 500-fold amplification of the inocula from the consortia by subculturing in rich media, necessary for use of the consortia in bioremediation experiments, showed no significant decrease in their degradation capability.

Microb Ecol, 2002 Jan, 43(1), 44 - 54 Epub 2002 Jan 23.
Characterization of Sphingomonas sp . Ant 17, an aromatic hydrocarbon-degrading bacterium isolated from Antarctic soil; Baraniecki CA et al.; Sphingomonas sp . strain Ant 17 was isolated from fuel-contaminated soil collected at Scott Base, Ross Island, Antarctica . We anticipated that Ant 17 would be a good model organism for studying cold climate bioremediation, and therefore determined its biodegradation capabilities and tolerance of potentially growth-limiting environmental conditions . Sphingomonas sp . Ant 17 degrades the aromatic fraction of several different crude oils, jet fuel, and diesel fuel at low temperatures and without nutrient amendment . It utilizes or transforms a broad range of pure aromatic substrates, including hydrocarbons, heterocycles, and aromatic acids and alcohols . Ant 17 grows at temperatures of 1 degree C to 35 degrees C and mineralizes radiolabeled phenanthrene over a range of more than 24 degrees C . This psychrotolerant isolate appears to utilize hydrocarbons more efficiently at low temperatures than would be predicted by mesophilic enzyme kinetics . The optimum pH for growth was 6.4 at 22 degrees C, with extended lag phases observed in more alkaline media . However, there was less effect of pH on lag phase at lower temperatures . Ant 17 displayed greater tolerance to UV irradiation and freeze-thaw cycles than the hydrocarbon-degrading isolate Sphingomonas sp . WPO-1, which may reflect adaptation to its Antarctic soil environment . However, it was more sensitive than expected to desiccation and to low concentrations of NaCl and CaCl(2) . Ant 17 was phenotypically stable and lacked detectable plasmids, suggesting a chromosomal location for genes encoding aromatic degradation enzymes . Its broad aromatic substrate range and tolerance of low and fluctuating temperature and low nutrients make Sphingomonas sp . Ant 17 a valuable microbe for examining fuel spill bioremediation in cold soils.

Appl Environ Microbiol, 2002 May, 68(5), 2300 - 6
Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments; Holmes DE et al.; Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments . In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex . In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms . At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca . 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated . Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species . Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites . No increase in Geobacteraceae sequences was observed in control sediments . In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments . These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process . The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.

J Hazard Mater, 2002 May 3, 92(1), 103 - 14
Effect of food-grade surfactant on bioremediation of explosives-contaminated soil; Boopathy R; The use of native soil bacteria to biodegrade explosives-contaminated soil under co-metabolic conditions has been demonstrated . The addition of food-grade surfactants could improve the process by enhancing the rates of explosives desorption from soil, thereby increasing the bioavailability of explosives for microbial degradation . The objective of this study was to decrease residence time in the slurry reactor, thereby increasing output and reducing clean-up costs . In this study, Tween 80 (monooleate), served not only as a surfactant but also as the carbon substrate for the soil microorganisms . Four 2l soil slurry reactors were operated in batch mode with soil containing 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) . The results indicated that TNT and RDX were removed in all reactors except the control (no added carbon source) . The reactor enriched with surfactant and molasses performed better than reactors with either molasses or surfactant alone . The TNT and its metabolite, 4-amino-2,6-dinitrotoluene were removed faster in the reactor with surfactant plus molasses (35 days) than in the reactor with molasses alone as carbon source (45 days) . A radiolabeling study of the mass balance of TNT in the slurry reactors showed substantial mineralization of TNT to CO2.

Nature, 2002 Apr 18, 416(6882), 767 - 9
Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis; Childers SE et al.; Microorganisms that use insoluble Fe(III) oxide as an electron acceptor can have an important function in the carbon and nutrient cycles of aquatic sediments and in the bioremediation of organic and metal contaminants in groundwater . Although Fe(III) oxides are often abundant, Fe(III)-reducing microbes are faced with the problem of how to access effectively an electron acceptor that can not diffuse to the cell . Fe(III)-reducing microorganisms in the genus Shewanella have resolved this problem by releasing soluble quinones that can carry electrons from the cell surface to Fe(III) oxide that is at a distance from the cell . Here we report that another Fe(III)-reducer, Geobacter metallireducens, has an alternative strategy for accessing Fe(III) oxides . Geobacter metallireducens specifically expresses flagella and pili only when grown on insoluble Fe(III) or Mn(IV) oxide, and is chemotactic towards Fe(II) and Mn(II) under these conditions . These results suggest that G . metallireducens senses when soluble electron acceptors are depleted and then synthesizes the appropriate appendages to permit it to search for, and establish contact with, insoluble Fe(III) or Mn(IV) oxide . This approach to the use of an insoluble electron acceptor may explain why Geobacter species predominate over other Fe(III) oxide-reducing microorganisms in a wide variety of sedimentary environments.

J Agric Food Chem, 2002 Apr 24, 50(9), 2548 - 55
Biodegradation of gamma-hexachlorocyclohexane (lindane) and alpha-hexachlorocyclohexane in water and a soil slurry by a Pandoraea species; Okeke BC et al.; Isomers of 1,2,3,4,5,6-hexachlorocyclohexane (HCH) were some of the most widely used pesticides . Despite reduction in their production and use, HCH isomers present a serious environmental hazard . In this study, two bacterial isolates (LIN-1 and LIN-3) that can grow on gamma-HCH as a sole source of carbon and energy were isolated from an enrichment culture . In liquid cultures of LIN-1 and LIN-3, 25.0 and 45.5% removal of gamma-HCH, respectively, were achieved in 2 weeks . LIN-3 was identified as Pandoraea sp . by 16S rRNA gene sequence analysis (99% identity) . Pandoraea sp . substantially degraded both gamma- and alpha-HCH isomers at concentrations of 10-200 mg L(-1) in liquid cultures . After 8 weeks of incubation in liquid culture, 89.9 and 93.3% of the gamma- and alpha-HCH isomers declined, respectively, at an initial concentration of 150 mg L(-1) . In soil slurry cultures of Pandoraea sp., simulating a soil slurry phase bioremediation treatment, substantial decreases in the levels of the HCH isomers were observed at concentrations of 50-200 mg L(-1) . After 9 weeks, 59.6 and 53.3% biodegradations of gamma- and alpha-HCH isomers, respectively, were achieved at 150 mg L(-1) . Using two 23-mer oligonucloetide primers targeting the 330 bp region of the 16S rRNA gene of Pandoraea sp., an approximately 330 bp PCR product was successfully amplified from DNA templates prepared from bacterial colonies and soil slurry culture . This system provides a direct and rapid PCR-based molecular tool for tracking Pandoraea sp . strain LIN-3 in water and soils . These results have implied implications for the treatment of soils and water contaminated with HCH isomers.

Appl Microbiol Biotechnol, 2002 Mar, 58(4), 428 - 34 Epub 2002 Jan 26.
An update on the use of unconventional substrates for biosurfactant production and their new applications; Makkar RS et al.; Biosurfactants are valuable microbial amphiphilic molecules with effective surface-active and biological properties applicable to several industries and processes . Microbes synthesize them, especially during growth on water-immiscible substrates, providing an alternative to chemically prepared conventional surfactants . Because of their structural diversity (i.e., glycolipids, lipopeptides, fatty acids, etc.), low toxicity, and biodegradability, these molecules could be widely used in cosmetic, pharmaceutical, and food processes as emulsifiers, humectants, preservatives, and detergents . Moreover, they are ecologically safe and can be applied in bioremediation and waste treatments . They can be produced from various substrates, mainly renewable resources such as vegetable oils, distillery and dairy wastes, which are economical but have not been reported in detail . In this review, we report advances made in using renewable substrates for biosurfactant production and their newer applications.

Environ Sci Technol, 2002 Mar 15, 36(6), 1276 - 80
Catalysis of PAH biodegradation by humic acid shown in synchrotron infrared studies; Holman HY et al.; The role of humic acid (HA) in the biodegradation of toxic polycyclic aromatic hydrocarbons (PAHs) has been the subject of controversy, particularly in unsaturated environments . By utilizing an infrared spectromicroscope and a very bright, nondestructive synchrotron photon source, we monitored in situ and, over time, the influence of HA on the progression of degradation of pyrene (a model PAH) by a bacterial colony on a magnetite surface . Our results indicate that HA dramatically shortens the onset time for PAH biodegradation from 168 to 2 h . In the absence of HA, it takes the bacteria about 168 h to produce sufficient glycolipids to solubilize pyrene and make it bioavailable for biodegradation . These results will have large implications for the bioremediation of contaminated soils.

J Biol Chem, 2002 Jul 5, 277(27), 24000 - 5 Epub 2002 Apr 09.
The cytochrome P450 complement (CYPome) of Streptomyces coelicolor A3(2); Lamb DC et al.; In the present study we describe the complete cytochrome P450 complement, the "CYPome," of Streptomyces coelicolor A3(2) . Eighteen cytochromes P450 (CYP) are described, in contrast to the absence of CYPs in Escherichia coli, and the twenty observed in Mycobacterium tuberculosis . Here we confirm protein identity as cytochromes P450 by heterologous expression in E . coli and measurement of reduced carbon monoxide difference spectra . We also report on their arrangement in the linear chromosome and relatedness to other CYPs in the superfamily . The future development of manipulation of antibiotic pathways and the use of streptomycetes in bioremediation and biotransformations will involve many of the new CYP forms identified here.

Biochemistry, 2002 Apr 16, 41(15), 4847 - 55
Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition; Oakley AJ et al.; The hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalyzed by alpha/beta-hydrolases called haloalkane dehalogenases . The study of haloalkane dehalogenases is vital for the development of these enzymes if they are to be utilized for bioremediation of organohalide-contaminated industrial waste . We report the kinetic and structural analysis of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) in complex with each of 1,2-dichloroethane and 1,2-dichloropropane and the reaction product of 1-chlorobutane turnover . Activity studies showed very weak but detectable activity of LinB with 1,2-dichloroethane {0.012 nmol s(-1) (mg of enzyme)(-1)} and 1,2-dichloropropane {0.027 nmol s(-1) (mg of enzyme)(-1)} . These activities are much weaker compared, for example, to the activity of LinB with 1-chlorobutane {68.2 nmol s(-1) (mg of enzyme)(-1)} . Inhibition analysis reveals that both 1,2-dichloroethane and 1,2-dichloropropane act as simple competitive inhibitors of the substrate 1-chlorobutane and that 1,2-dichloroethane binds to LinB with lower affinity than 1,2-dichloropropane . Docking calculations on the enzyme in the absence of active site water molecules and halide ions confirm that these compounds could bind productively . However, when these moieties were included in the calculations, they bound in a manner similar to that observed in the crystal structure . These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking.

Appl Microbiol Biotechnol, 2002 Mar, 58(3), 393 - 9 Epub 2001 Dec 04.
Effects of randomly methylated-beta-cyclodextrins (RAMEB) on the bioavailability and aerobic biodegradation of polychlorinated biphenyls in three pristine soils spiked with a transformer oil; Fava F et al.; The low bioavailability of polychlorinated biphenyls (PCBs) in soils often results in their slow and partial aerobic biodegradation . The process can be enhanced by supplementing soils with cyclodextrins . However, pure cyclodextrins are expensive and we have therefore explored the use of a less costly technical grade mixture of randomly methylated-beta-cyclodextrins (RAMEB) . RAMEB was tested at 0, 1, 3 and 5% (w/w) in the aerobic bioremediation and detoxification of a loamy-, a humic- and a sandy-soil, each artificially contaminated with a PCB-containing transformer oil (added PCBs: about 450 or 700 mg/kg), inoculated with an exogenous aerobic PCB-biodegrading bacterial co-culture and treated in slurry- and solid-phase laboratory conditions . Significant depletions of the spiked PCBs were observed in all microcosms of the three soils after 90 days of treatment; however, interesting yields of PCB dechlorination and detectable decreases of the original soil ecotoxicity were observed in the slurry-phase microcosms . RAMEB generally enhanced PCB-metabolism with effects which were dependent on the concentration at which it was applied, the physical-chemical nature of the amended soil, and the soil treatment conditions employed . RAMEB, which was slowly metabolized by soil microorganisms, enhanced the presence of PCBs and PCB-cometabolizing bacteria in the soil-water phase, suggesting that RAMEB enhances aerobic biodegradation of PCBs by increasing pollutant bioavailability in soil microcosms.

J Environ Qual, 2002 Mar-Apr, 31(2), 388 - 92
Improvements in the two-dimensional nuclear magnetic resonance spectroscopy of humic substances; Simpson AJ et al.; Understanding pollutant sorption, bioremediation of these pollutants, and their interactions with humic substances requires knowledge of molecular-level processes . New developments with nuclear magnetic resonance (NMR) experiments and labeled compounds have improved the overall understanding of these mechanisms . The advancements made with two-dimensional NMR show great promise, as structural information and hydrogen-carbon bond connectivity can be discerned . This communication presents the application of improved two-dimensional NMR methods, the double quantum filtered (DQF) correlation spectroscopy (COSY) and echo/anti-echo heteronuclear single quantum coherence (HSQC) experiments, for use in structural studies of humic substances . Both experiments were found to produce significant improvements over the conventional COSY and heteronuclear multiple quantum coherence (HMQC) experiments that have been previously employed in similar studies . The more sensitive echo/anti-echo HSQC experiment produced more cross-peaks with higher resolution when compared with the HMQC spectra . The DQF-COSY significantly suppressed the diagonal signals and allowed numerous signals previously hidden in the standard COSY experiment to be observed . These improvements will aid current characterization strategies of humic substances from soils, sediments, and water and their subsequent reactions with pollutants and microorganisms.

Acta Microbiol Pol, 2001, 50(3-4), 205 - 18
Use of molecular techniques in bioremediation; Plaza G et al.; In a practical sense, biotechnology is concerned with the production of commercial products generated by biological processes . More formally, biotechnology may be defined as "the application of scientific and engineering principles to the processing of material by biological agents to provide goods and services" (Cantor, 2000) . From a historical perspective, biotechnology dates back to the time when yeast was first used for beer or wine fermentation, and bacteria were used to make yogurt . In 1972, the birth of recombinant DNA technology moved biotechnology to new heights and led to the establishment of a new industry . Progress in biotechnology has been truly remarkable . Within four years of the discovery of recombinant DNA technology, genetically modified organisms (GMOs) were making human insulin, interferon, and human growth hormone . Now, recombinant DNA technology and its products--GMOs are widely used in environmental biotechnology (Glick and Pasternak, 1988; Cowan, 2000) . Bioremediation is one of the most rapidly growing areas of environmental biotechnology . Use of bioremediation for environmental clean up is popular due to low costs and its public acceptability . Indeed, bioremediation stands to benefit greatly and advance even more rapidly with the adoption of molecular techniques developed originally for other areas of biotechnology . The 1990s was the decade of molecular microbial ecology (time of using molecular techniques in environmental biotechnology) . Adoption of these molecular techniques made scientists realize that microbial populations in the natural environments are much more diverse than previously thought using traditional culture methods . Using molecular ecological methods, such as direct DNA isolation from environmental samples, denaturing gradient gel electrophoresis (DGGE), PCR methods, nucleic acid hybridization etc., we can now study microbial consortia relevant to pollutant degradation in the environment . These techniques promise to provide a better understanding and better control of environmental biotechnology processes, thus enabling more cost effective and efficient bioremediation of our toxic waste and contaminated environments.

Environ Sci Pollut Res Int, 2002, 9(1), 73 - 85
Phytoremediation to increase the degradation of PCBs and PCDD/Fs . Potential and limitations; Campanella BF et al.; Phytoremediation is already regarded as an efficient technique to remove or degrade various pollutants in soils, water and sediments . However, hydrophobic organic molecules such as PAHs, PCBs and PCDD/Fs are much less responsive to bioremediation strategies than, for example, BTEX or LAS . PCDD/Fs and PCBs represent 3 prominent groups of persistent organic pollutants that share common chemical, toxicological and environmental properties . Their widespread presence in the environment may be explained by their chemical and biological stability . This review considers their fate and dissipation mechanisms . It is then possible to identify major sinks and to understand biological activities useful for remediation . Public health and economic priorities lead to the conclusion that alternative techniques to physical treatments are required . This review focuses on particular problems encountered in biodegradation and bioavailability of PCDD/Fs and PCBs . It highlights the potential and limitations of plants and micro-organisms as bioremediation agents and summarises how plants can be used to augment bacterial activity . Phytoremediation is shown to provide some new possibilities in reducing risks associated with dioxins and PCBs.

Environ Sci Technol, 2002 Feb 15, 36(4), 724 - 8
Hydrogen isotopic composition of individual n-alkanes as an intrinsic tracer for bioremediation and source identification of petroleum contamination; Pond KL et al.; The isotopic signatures of crude oil hydrocarbons are potentially powerful intrinsic tracers to their origins and the processes by which the oils are modified in the environment . Stable carbon isotopic data are of limited use for studying petroleum contaminants because of the relatively small amount of isotopic fractionation that occurs during natural processes . Hydrogen isotopes, in contrast, are commonly fractionated to a much greater extent and as a result display larger variations in delta values . We studied the effect of in vitro aerobic biodegradation on the hydrogen isotopic composition of individual n-alkanes from crude oil . The isotopic analysis was conducted using gas chromatography-thermal conversion-isotope ratio mass spectrometry . In general, biodegradation rates decreased with increasing hydrocarbon chain length, consistent with previous studies . More importantly the n-alkanes that were degraded at the fastest rates (n-C15 to n-C18) also showed the largest overall isotopic fractionation (approximately 12-25 per thousand deuterium enrichment), suggesting that the lower molecular weight n-alkanes can be used to monitor in-situ bioremediation of crude oil contamination . The hydrogen isotopic compositions of the longer chain alkanes (n-C19 to n-C27) were relatively stable during biodegradation (<5%o overall deuterium enrichment), indicating that these compounds are effective tracers for oil-source identification studies.

J Appl Microbiol, 2002, 92(3), 541 - 8
Enrichment of a microbial culture capable of degrading endosulphate, the toxic metabolite of endosulfan; Sutherland TD et al.; AIMS: The aim of this study was to isolate a source of enzymes capable of degrading endosulphate (endosulfan sulphate), the toxic metabolite of the pesticide endosulfan . METHODS AND RESULTS: A microbial broth culture capable of degrading endosulphate was enriched from endosulfan-contaminated soil by providing the metabolite as the sole source of sulphur in broth culture . No microbial growth was observed in the absence of endosulphate . In the presence of endosulphate, growth of the culture occurred with the concomitant formation of three chlorine-containing compounds . Thin layer chromatography and gas chromatography--mass spectral analysis identified these metabolites as endosulfan monoaldehyde, 1,2,3,4,7,7-hexachloro-5,6-bis(methylene)bicyclo{2.2.1}-2-heptene and 1,2,3,4,7,7-hexachloro-5-hydroxymethylene-6-methylenebicyclo{2.2.1}-2-heptene . The second and third compounds have not been reported in previous metabolic studies . The enriched culture was also able to utilize alpha- and beta-endosulfan as sulphur sources, each producing the hydrolysis product endosulfan monoaldehyde as the sole chlorine-containing metabolite . Alpha-endosulfan was more readily hydrolysed than the beta-isomer . CONCLUSIONS: This study isolated a mixed microbial culture capable of degrading endosulphate . The products of degradation were characterized as novel endosulfan metabolites . SIGNIFICANCE AND IMPACT OF THE STUDY: This study describes the isolation of a mixed microbial culture that is potentially a valuable source of hydrolysing enzymes for use in enzymatic bioremediation, particularly of endosulphate and alpha-endosulfan residues.

J Appl Microbiol, 2002, 92(2), 276 - 88
Microbial communities in different soil types do not converge after diesel contamination; Bundy JG et al.; AIMS: To study the comparative effect of diesel addition and simulated bioremediation on the microbial community in three different soil types.METHODS AND RESULTS: Three different soils were amended with diesel and bioremediation treatment simulated by addition of nutrients . The progress of bioremediation, and the effect on the indigenous microbial communities, was monitored using microbiological techniques . These included basal respiration, sole carbon source utilization patterns using both a commercially-available substrate set and a set designed to highlight changes in hydrocarbon-utilizing bacteria, and phospholipid fatty acid (PLFA) profiling . The development of active hydrocarbon-degrading communities was indicated by the disappearance of diesel, increases in soil respiration and biomass, and large changes in the sole carbon source utilization patterns and PLFA profiles compared with control soils . However, comparison of the relative community structure of the three soils using PLFA profiling showed that there was no tendency for the community structure of the three different soil types to converge as a result of contamination . In fact, they became more dissimilar as a result . Changes in the sole carbon source utilization patterns using the commercially-available set of carbon sources indicated the same result as shown by PLFA profiling . The specially selected set of carbon sources yielded no additional information compared with the commercially-available set.CONCLUSIONS: Diesel contamination does not result in the development of similar community profiles in different soil types.SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that different soils have different inherent microbial potential to degrade hydrocarbons, a finding that should be taken into account in impact and risk assessments . Following the development of the microbial community and its recovery is a useful and sensitive way of monitoring the impact and recovery of oil-contaminated soils.

Biosci Biotechnol Biochem, 2001 Dec, 65(12), 2673 - 81
Quantitative and specific detection of a trichloroethylene-degrading methanotroph, Methylocystis sp . strain M, by a most probable number-polymerase chain reaction method; Kikuchi T et al.; We developed a rapid and specific enumeration method for a trichloroethylene-degrading methanotroph, Methylocystis sp . strain M, based on a most probable number-polymerase chain reaction method for monitoring the bacterium at bioremediation sites . The primers designed for the mmoC gene of the soluble methane monooxygenase gene cluster were specific to strain M . Recovery of the cells with a membrane filter enabled us to detect strain M in trichloroethylene-contaminated groundwater . We used the enumeration method to monitor the number of strain M cells in effluent from soil columns supplied with trichloroethylene-contaminated groundwater . The number of strain M cells in the effluent depended on the amount of the strain M inoculated and the number of cells measured by the most probable number-polymerase chain reaction method was correlated with that measured by a culture method . The detection limit for strain M in effluent detected by MPN-PCR method was 4 to 8 x 10(2) cells/ml.

Biodegradation, 2001, 12(4), 235 - 45
Bioremediation of DDT in soil by genetically improved strains of soil fungus Fusarium solani; Mitra J et al.; Bioremediation of DDT in soil by genetically improved recombinants of the soil fungus Fusarium solani was studied . The parent strains were isolated from soil enriched with DDD or DDE (immediate anaerobic and aerobic degradation products of DDT), as further degradation of these products are slow processes compared to the parent compound . These naturally occurring strains isolated from soil, however, are poor degraders of DDT and differed in their capability to degrade its metabolites such as DDD, DDE, DDOH and DBP and other organochlorine pesticides viz . kelthane and lindane . Synergistic effect was shown by some of these strains, when grown together in the medium containing DDD and kelthane under mixed culture condition . No synergism in DDE degradation was observed with the strains isolated from enriched soil . DDD-induced proteins extracted from individual culture filtrate (exo-enzyme) when subjected to SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) showed complementary polypeptide bands in these strains i.e., each strain produced distinct DDD degrading polypeptide bands and the recombinant or hybrid strains produced all of the bands of the two parents and degraded DDD better than the parental strains . Recombinant hybrid strains with improved dehalogenase activity were raised by parasexual hybridisation of two such complementary isolates viz . isolate 1(P-1) and 4(P-2) showing highest complementation and are compatible for hyphal fusion inducing heterokaryosis . These strains are genetically characterised as Kel+Ben(R)DBP-Lin- and Kel-Ben(r)DBP+Lin+ respectively . Recombinants with mixed genotype, i.e., Kel+Ben(R)DBP+Lin+ showing superior degradation quality for DDT were selected for bioremediation study . Recombination was confirmed by polypeptide band analysis of DDD induced exo-proteins from culture filtrate using SDS-Polyacrylamide Gel Electrophoresis (PAGE) and RAPD (Random Amplified Polymorphic DNA) of genomic DNA using PCR (Polymerase Chain Reaction) technique . SDS-PAGE showed combination of DDD induced polypeptide bands characteristic of both the parents in the recombinants or the hybrids . PCR study showed the parent specific bands in the recombinant strains confirming gene transformation.

Appl Environ Microbiol, 2002 Feb, 68(2), 485 - 95
Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe; Hendrickson ER et al.; The environmental distribution of Dehalococcoides group organisms and their association with chloroethene-contaminated sites were examined . Samples from 24 chloroethene-dechlorinating sites scattered throughout North America and Europe were tested for the presence of members of the Dehalococcoides group by using a PCR assay developed to detect Dehalococcoides 16S rRNA gene (rDNA) sequences . Sequences identified by sequence analysis as sequences of members of the Dehalococcoides group were detected at 21 sites . Full dechlorination of chloroethenes to ethene occurred at these sites . Dehalococcoides sequences were not detected in samples from three sites at which partial dechlorination of chloroethenes occurred, where dechlorination appeared to stop at 1,2-cis-dichloroethene . Phylogenetic analysis of the 16S rDNA amplicons confirmed that Dehalococcoides sequences formed a unique 16S rDNA group . These 16S rDNA sequences were divided into three subgroups based on specific base substitution patterns in variable regions 2 and 6 of the Dehalococcoides 16S rDNA sequence . Analyses also demonstrated that specific base substitution patterns were signature patterns . The specific base substitutions distinguished the three sequence subgroups phylogenetically . These results demonstrated that members of the Dehalococcoides group are widely distributed in nature and can be found in a variety of geological formations and in different climatic zones . Furthermore, the association of these organisms with full dechlorination of chloroethenes suggests that they are promising candidates for engineered bioremediation and may be important contributors to natural attenuation of chloroethenes.

Antonie Van Leeuwenhoek, 2001 Sep, 79(3-4), 269 - 76
N-Alkane uptake and utilisation by Streptomyces strains; Barabas G et al.; Streptomyces strains isolated from the Kuwait Burgan oil field were defined as S . griseoflavus, S . parvus, and S . plicatus utilised n-hexadecane, n-octadecane (purified fractions of mineral oil), kerosene, and crude oil as sole carbon and energy sources . The strains were incubated with n-alkanes and increase of the fatty acid content with chain length equivalent to the employed n-alkanes was observed . Signal transducing GTP-binding proteins (GBPs) play an important role in n-alkane uptake in streptomycetes . Specific activators of GBPs increased the uptake of hydrocarbons . Using the hydrophobic fluorescent dye diphenylhexatrien (DPH) as a probe, it was found that the microviscosity of the hydrophobic inner region of the cellular membrane is significantly lower in hydrocarbon utilisers than in non-utilisers . This difference probably reflects differences in the fatty acid composition of the strains . When cultures were grown in n-alkane containing media, electron microscopy revealed that the hydrocarbon utilisers showed less-electron dense areas as inclusions in the cytoplasm . Soil samples inoculated with Streptomyces strains eliminated hydrocarbons much faster than those not containing these strains, serving as control . When inorganic medium was supplied with n-hexadecane-1-14C as sole carbon and energy source, radioactive CO2 was detected . Since streptomycetes have not been used until now for oil elimination, though they are known as abundant soil bacteria tolerating extreme conditions, their possible use for bioremediation of hydrocarbon contaminated soils is discussed.

Ying Yong Sheng Tai Xue Bao, 2001 Feb, 12(1), 108 - 12
{Bioremediation of mineral oil and polycyclic aromatic hydrocarbons (PAHs) in soils with two plant species}; Song Y et al.; With alfalfa (Medicago sativa) and paddy rice as test plants, and with pollutant level, specific bacteria, fungi and organic fertilizer as control factors, the bioremediation of mineral oil and polycyclic aromatic hydrocarbons (PAHs) in soils with two plant species was conducted . The results showed that the degradation rate of mineral oil was promoted by fertilization in alfalfa soil, but not in paddy rice soil . The degradation rate of total PAHs (11 PAH listed in USEPA) was increased by fertilization both in alfalfa and in paddy rice soil, and the promotion effect of fertilizer was better in paddy rice soil than in alfalfa soil . The fertilization rate was positively related to the rhizospheric indigenous fungi and bacteria's CFU in alfalfa soil, but only to the indigenous bacteria's CFU in paddy rice soil . The fungi and bacteria's CFU in both test soils had no positive relation with the amount of specific bacteria and fungi spiked . The degradation rate of 3-ring PAHs was enhanced in both alfalfa and paddy rice soil by fertilization, and the effect was stronger in paddy rice soil than in alfalfa soil . However, fertilization had no positive effect on the degradation of 4-ring PAHs.

Science, 2002 Jan 18, 295(5554), 483 - 5
Electrode-reducing microorganisms that harvest energy from marine sediments; Bond DR et al.; Energy in the form of electricity can be harvested from marine sediments by placing a graphite electrode (the anode) in the anoxic zone and connecting it to a graphite cathode in the overlying aerobic water . We report a specific enrichment of microorganisms of the family Geobacteraceae on energy-harvesting anodes, and we show that these microorganisms can conserve energy to support their growth by oxidizing organic compounds with an electrode serving as the sole electron acceptor . This finding not only provides a method for extracting energy from organic matter, but also suggests a strategy for promoting the bioremediation of organic contaminants in subsurface environments.

Risk Anal, 2001 Oct, 21(5), 967 - 77
Risk perception of heavy metal soil contamination and attitudes toward decontamination strategies; Weber O et al.; Contaminated soils are a common environmental risk all over the world . One major source of risk is heavy metal soil contamination caused by industrial emissions . This quasiexperimental study investigated the perception of these risks by exposed and nonexposed people, their attitudes toward bioremediation methods using hyperaccumulating plants, and the influence of long-term aspects of sustainability on the acceptance of bioremediation methods . Major findings were that people living in a contaminated area perceived the risk of the heavy metal soil contamination as higher than the general risk of contamination . Second, a factor analysis showed that the factors dread, control, and catastrophic potential were relevant for the perception and valuation of low-dose environmental risks such as the contamination of the investigated area . In addition, a cluster analysis showed that the risk of heavy metal soil contamination was perceived as similar to that of oil contamination, ozone layer, preservatives and genetic technology . It was perceived indifferently with regard to dread . The uncontrollability of heavy metal soil contamination was estimated as medium, and its catastrophic potential as low . Third, exposed and nonexposed participants preferred bioremediation methods to classical methods (e.g., excavation and chemical treatment of the soil), because they perceived the environmental and esthetical performance of the bioremediation as important criteria . Sustainability or precautionary issues, such as the prevention of harm for future generations, were highly correlated with the acceptance of the use of bioremediation methods in people's residential areas.

Appl Environ Microbiol, 2002 Jan, 68(1), 326 - 34
Spatial and resource factors influencing high microbial diversity in soil; Zhou J et al.; To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach . While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant . Two diversity indices, the reciprocal of Simpson's index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns . For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities . In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth . The uniform distribution implies that competition does not shape the structure of these microbial communities . Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure . Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone . Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity . Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.

Ying Yong Sheng Tai Xue Bao, 2001 Jun, 12(3), 439 - 42
{Preliminary study on anaerobic bioremediation process for pentachlorophenol (PCP)-contaminated soil}; Xu X et al.; The performances of soil-slurry process with supplement of anaerobic granular sludge for remediating PCP-contaminated soil was investigated . The results showed that inherent anaerobic microbes in soil exhibited a little dechlorinating activity for simulative contaminated soil with 30 mg.kg-1 of PCP, the average PCP degradation rates within 28 d was 0.258 mg.kg-1.d-1 . In soil slurry processes with 5 g.kg-1 granular sludge at aerobic, aerobic/anaerobic and anaerobic operation, the average PCP degradation rates within 28 d were 0.269, 0.291/0.842 and 0.892 mg.kg-1.d-1, respectively . PCP degradation rates were increased with increasing the amounts of anaerobic granular sludge, 0.834, 0.843, 0.928 mg.kg-1.d-1 of the average PCP degradation rates within 35 d were achieved in soil slurry processes supplemented with 5, 10, 25 g.kg-1 of granular sludge, respectively . This bioremediation process also presented higher initial PCP degradation rate for higher concentration(60 mg.kg-1) of PCP in soil.

Environ Sci Technol, 2001 Nov 15, 35(22), 4577 - 83
PAH release during water desorption, supercritical carbon dioxide extraction, and field bioremediation; Hawthorne SB et al.; Removal rates of polycyclic aromatic hydrocarbons (PAHs) from manufactured gas plant (MGP) soils were determined using water desorption for 120 days and mild supercritical carbon dioxide extraction (SFE) for 200 min . Both techniques were used to compare the changes in desorption rates for individual PAHs from untreated and treated soils that were obtained from a field biotreatment unit after 58, 147, and 343 days . Water desorption profiles (plotted in days) and SFE profiles (plotted in minutes) were very similar regardless of whether a PAH was rapidly or slowly removed . Water and SFE profiles were fit with a simple two-site (fast and slow) model to obtain the fraction of each PAH that was rapidly released (F) . There was agreement between the F values obtained from water desorption and SFE for PAHs ranging from naphthalene to benzo{a}pyrene from all soils, with an overall correlation coefficient (r2) of 0.81 . F values from water desorption and SFE also agreed with the actual removal of PAHs obtained after 147 and 343 days of field remediation (r2 ca . 0.80) . The use of shorter desorption times (2-4 days for water and 20-40 min for SFE) allowed F values to be estimated for all PAHs and showed excellent agreement with the removal of individual PAHs obtained with 147-343 days of field remediation (r2 > 0.9) . The comparisons indicate that short-term SFE can provide a reasonable estimate of the fraction of a PAH that is readily released and available for microbial treatment.

Ying Yong Sheng Tai Xue Bao, 2001 Apr, 12(2), 279 - 82
{An off site petroleum-contaminated soil bioremediation technology: soil compositing in windrow}; Jiang C et al.; With off-site bioremediation technology, a soil contaminated by crude oil from Liaohe Oil Field was treated on a 20 x 10 m prepared bed . 8 composting windrow units were set, each measured 8 m in length, 2 m in width, and 0.35 m in height . The results showed that when the pollutant petroleum hydrocarbon(TPH) was within the range of 4.16-7.72 g.100 g-1 soil, the total degradation rate of TPH reached 45.19%-56.74% after 53 days operation, which indicated that a technological basis would be provided for the bioremediation of oil-contaminated soil.

Biotechnol Bioeng, 2002 Jan 20, 77(2), 204 - 11
Effects of humic substances on the bioavailability and aerobic biodegradation of polychlorinated biphenyls in a model soil; Fava F et al.; The very high hydrophobicity of polychlorinated biphenyls (PCBs) strongly reduces their bioavailability in aged contaminated soils, thus limiting their bioremediation . The biodegradability of PCBs in heavily contaminated soils can be significantly enhanced by soil treatment with surface-active agents . In this work, the effects of naturally occurring surfactants such as humic substances (HS) on the aerobic biodegradation of PCBs in a model soil were studied . The soil was amended with biphenyl (4 g/kg), Fenclor 42 (1,000 mg/kg), the aerobic PCB-biodegrading bacterial co-culture ECO3 (inoculum: 10(8)CFU/mL), and treated in aerobic batch slurry-phase conditions (17.5% w/v) with and without the addition of HS at the rates of 1.5 and 3.0% (w/w) . Low PCBs biodegradation and dechlorination yields were observed in the HS-free microcosms, probably as a result of the rapid disappearance of inoculated bacteria . The presence of HS influenced significantly the activity of the specialized biomass and the biodegradation of PCBs in the microcosms . The microcosms that received HS at the 1.5% rate showed a higher persistence of the specialized bacteria and yields of PCB biodegradation and dechlorination about 150 and 100%, respectively, larger than those found for the HS-free microcosms . Lower stimulating effects were observed in the microcosms added with the HS at 3.0% rate . These effects were attributed to an increased solubilization of PCBs in the hydrophobic domains of the humic supramolecular associations and to a different accessibility of PCBs by the specialized bacteria at the different rates of HS addition . Although the slurry-phase treatment generally showed a decrease of the original soil ecotoxicity, the addition of the originally non-toxic HS decreased soil ecotoxicity for the Collembola animal biomarker and increased that towards the Lepidium sativum vegetal biomarker .

Appl Environ Microbiol, 2001 Dec, 67(12), 5467 - 73
Novel Zn(2+)-chelating peptides selected from a fimbria-displayed random peptide library; Kjaergaard K et al.; The display of peptide sequences on the surface of bacteria is a technology that offers exciting applications in biotechnology and medical research . Type 1 fimbriae are surface organelles of Escherichia coli which mediate D-mannose-sensitive binding to different host surfaces by virtue of the FimH adhesin . FimH is a component of the fimbrial organelle that can accommodate and display a diverse range of peptide sequences on the E . coli cell surface . In this study we have constructed a random peptide library in FimH . The library, consisting of approximately 40 million individual clones, was screened for peptide sequences that conferred on recombinant cells the ability to bind Zn(2+) . By serial selection, sequences that exhibited various degrees of binding affinity and specificity toward Zn(2+) were enriched . None of the isolated sequences showed similarity to known Zn(2+)-binding proteins, indicating that completely novel Zn(2+)-binding peptide sequences had been isolated . By changing the protein scaffold system, we demonstrated that the Zn(2+)-binding seems to be uniquely mediated by the peptide insert and to be independent of the sequence of the carrier protein . These findings might be applied in the design of biomatrices for bioremediation purposes or in the development of sensors for detection of heavy metals.

Biodegradation, 2001, 12(2), 127 - 40
Transport issues and bioremediation modeling for the in situ aerobic co-metabolism of chlorinated solvents; Goltz MN et al.; For aerobic co-metabolism of chlorinated solvents to occur, it is necessary that oxygen, a primary substrate, and the chlorinated compound all be available to an appropriate microorganism--that is, a microorganism capable of producing the nonspecific enzyme that will promote degradation of the contaminant while the primary substrate is aerobically metabolized . Thus, the transport processes that serve to mix the reactants are crucial in determining the rate and extent of biodegradation, particularly when considering in situ biodegradation . These transport processes intersect, at a range of scales, with the biochemical reactions . This paper reviews how the important processes contributing to aerobic co-metabolism of chlorinated solvents at different scales can be integrated into mathematical models . The application of these models to field-scale bioremediation is critically examined . It is demonstrated that modeling can be a useful tool in gaining insight into the physical, chemical, and biological processes relevant to aerobic co-metabolism, designing aerobic co-metabolic bioremediation systems, and predicting system performance . Research needs are identified that primarily relate to gaps in our current knowledge of inter-scale interactions.

Biodegradation, 2001, 12(2), 105 - 26
Kinetics of aerobic cometabolism of chlorinated solvents; Alvarez-Cohen L et al.; The objectives of this paper are to review the wide range of kinetic models that have been introduced to describe the cometabolic oxidation of chlorinated solvents, to compare modeling approaches and associated experimental data, and to discuss knowledge gaps in the general topic of cometabolism kinetics . To begin, a brief description of the mechanism of oxygenase enzyme metabolism and its qualitative effects on cometabolic degradation kinetics is given . Next, a variety of kinetic expressions that have been used to describe cometabolism, ranging from adaptations of simple metabolic relationships to the development of complex equations that account for intracellular concentrations of key reaction species, are presented . A large number of kinetic coefficients published for a variety of oxygenase populations degrading a broad range of chlorinated solvents are categorized and compared . The discussion section of the paper contains an exploration of knowledge gaps that exist in our understanding of the kinetics of aerobic chlorinated solvent cometabolism . Specific topics covered include: the use of half saturation constants (Ksc and Ksg) as estimates for inhibition constants (Kisc and Kisg) in saturation modeling expressions, the specific nature of chlorinated solvent induced product toxicity and the capability for cells to recover from toxic effects, and methods for incorporating reducing energy limitations into cometabolism models . Finally, the applicability of the broad range of kinetic modeling approaches to scale-up and field applications for in situ bioremediation of chlorinated solvents is discussed.

Bioresour Technol, 2002 Jan, 81(1), 25 - 32
Bioremediation of gasoline contaminated soil by a bacterial consortium amended with poultry litter, coir pith and rhamnolipid biosurfactant; Rahman KS et al.; The aim of the present study was to find methods for enhancing rates of hydrocarbon biodegradation in gasoline contaminated soil by ex situ bioremediation . Red soil (RS) was treated with gasoline-spilled soil (GS) from a gasoline station and different combinations of amendments were prepared using (i) mixed bacterial consortium (MC), (ii) poultry litter (PL), (iii) coir pith (CP) and (iv) rhamnolipid biosurfactant (BS) produced by Pseudomonas sp . DS10-129 . The study was conducted for a period of 90 days during which bacterial growth, hydrocarbon degradation and growth parameters of Phaseolus aureus RoxB including seed germination, chlorophyll content, shoot and root length were measured . Approximately 67% and 78% of the hydrocarbons were effectively degraded within 60 days in soil samples amended with RS + GS + MC + PL + CP + BS at 0.1% and 1% . Maximum percentage of seed germination, shoot length, root length and chlorophyll content in P . aureus were recorded after 60 days in the above amendments . Further incubation to 90 days did not exhibit significant improvements . Statistical analysis using analysis of variance (ANOVA) and Duncan's multiple range test (DMRT) revealed that the level of amendments, incubation time and combination of amendments significantly influenced bacterial growth, hydrocarbon degradation, seed germination and chlorophyll content at a 1% probability level . All tested additives MC, PL, CP and rhamnolipid BS had significant positive effects on the bioremediation of GS.

Environ Pollut, 2001, 115(2), 209 - 18
Kinetics of chromium (VI) reduction by a type strain Shewanella alga under different growth conditions; Guha H et al.; We conducted kinetic batch experiments to determine the reduction of Chromium(VI) by a type strain of Shewanella alga (BrY-MT) ATCC 55627 . Chromium(VI) was reduced to Chromium(III) by BrY-MT grown in three different substrates: BHIB (brain heart infusion broth), TSB (tryptic soy broth), and M9 (minimum broth) . Four different Cr(VI) concentrations 4.836, 10.00, 37.125, and 260.00 mg l-1 were reduced at different rates by BrY-MT in both aerobic and anaerobic conditions . BrY-MT grown in BHIB reduced the maximum amount of Cr(VI) followed by TSB and M9 . Carbondioxide produced from bacterial respiration varied with and without Cr(VI) under both aerobic and anaerobic conditions . The Cr(VI) reduction data under anaerobic condition was fitted by a monod model to determine the bacterial kinetic parameters . The kinetic parameters determined by fitting the anaerobic experimental data were used to run a forward simulation for experiments conducted under aerobic conditions . The monod model was modified to account for an inhibition parameter for the Cr(VI) experiment at 260 mg l-1 . All the parameters varied within a narrow range, and were distinct for different substrates . Our studies show that, successful in situ bioremediation of Cr(VI) is depended on the type of substrates (electron donors) and the concentration of Cr(VI) in geologic medium.

Adv Space Res, 2001, 27(9), 1497 - 504
Closed Artificial ecosystems as a means of ecosystem studies for Earth and space needs; Pechurkin NS et al.; Closed Artificial ecosystems (CAES) have good prospects for wide use as new means for quantitative studies of different types of both natural ecosystems and man-made ones . The paper deals with the discussion of three points of CAES applications . The first one is of importance for theoretical ecology development and is connected with bringing together "holistic" and "merological" approaches in ecosystems studies . Using CAES, we can combine both approaches, taking into account the biotic turnover of limiting substrates which few in number even for complicated natural ecosystems . The second CAES use concerns the development of "ecosystems health" concept and application of a key-factor-approach for the indication and measurement of healthy unhealthy state and functioning of ecosystems or their links . The third use is more of an applied nature, oriented to the intensification of bioremediation or biodepollution processes in different types of ecosystems, including the global biosphere . Grant numbers: N 99-04-96017, N25 . c 2001 . COSPAR . Published by Elsevier Science Ltd . All rights reserved.

Appl Microbiol Biotechnol, 2001 Oct, 57(1-2), 248 - 56
Toward the bioremediation of dioxin-polluted soil: structural and functional analyses of in situ microbial populations by quinone profiling and culture-dependent methods; Hiraishi A et al.; In order to obtain basic information toward the bioremediation of dioxin-polluted soil, microbial communities in farmland soils polluted with high concentrations of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) were studied by quinone profiling as well as conventional microbiological methods . The concentration of PCDD/Fs in the polluted soils ranged from 36 to 4,980 pg toxicity equivalent quality (TEQ) g(-1) dry weight of soil . There was an inverse relationship between the levels of PCDD/Fs and microbial biomass as measured by direct cell counting and quinone profiling . The most abundant quinone type detected was either MK-6 or Q-10 . In addition, MK-8, MK-8(H2), and MK-9(H8) were detected in significant amounts . Numerical analysis of quinone profiles showed that the heavily polluted soils (> or = 1,430 pg TEQ g(-1)) contained different community structures from lightly polluted soils (< or = 56 pg TEQ g(-1)) . Cultivation of the microbial populations in the heavily polluted soils with dibenzofuran or 2-chlorodibenzofuran resulted in enrichment of Q-10-containing bacteria . When the heavily polluted soil was incubated in static bottles with autoclaved compost as an organic nutrient additive, the concentrations of PCDD/Fs in the soil were decreased by 22% after 3 months of incubation . These results indicate that dioxin pollution exerted a significant effect on microbial populations in soil in terms of quantity, quality, and activity . The in situ microbial populations in the dioxin-polluted soil were suggested to have a potential for the transformation of PCDD/Fs and oxidative degradation of the lower chlorinated ones thus produced.

Appl Microbiol Biotechnol, 2001 Oct, 57(1-2), 242 - 7
On site bioremediation of hydrocarbon-contaminated Arctic tundra soils in inoculated biopiles; Mohn WW et al.; There is a need to develop technology to allow the remediation of soil in polar regions that have been contaminated by hydrocarbon fuel spills . Bioremediation is potentially useful for this purpose, but has not been well demonstrated in polar regions . We investigated biopiles for on-site bioremediation of soil contaminated with Arctic diesel fuel in two independent small-scale field experiments at different sites on the Arctic tundra . The results were highly consistent with one another . In biopiles at both sites, extensive hydrocarbon removal occurred after one summer . After 1 year in treatments with optimal conditions, total petroleum hydrocarbons were reduced from 196 to below 10 mg per kg of soil at one site, and from 2,109 to 195 mg per kg of soil at the other site . Addition of ammonium chloride and sodium phosphate greatly stimulated hydrocarbon removal and indicates that biodegradation was the primary mechanism by which this was achieved . Inoculation with cold-adapted, mixed microbial cultures further stimulated hydrocarbon removal during the summer immediately following inoculation . At one site, soil temperature was monitored during the summer season, and a clear plastic cover increased biopile soil temperature, measured as degree-day accumulation, by 30-49% . Our results show that on-site bioremediation of fuel-contaminated soil at Arctic tundra sites is feasible.

Appl Microbiol Biotechnol, 2001 Oct, 57(1-2), 20 - 33
Feasibility of bioremediation by white-rot fungi; Pointing SB; The ligninolytic enzymes of white-rot fungi have a broad substrate specificity and have been implicated in the transformation and mineralization of organopollutants with structural similarities to lignin . This review presents evidence for the involvement of these enzymes in white-rot fungal degradation of munitions waste, pesticides, polychlorinated biphenyls, polycyclic aromatic hydrocarbons, bleach plant effluent, synthetic dyes, synthetic polymers, and wood preservatives . Factors relating to the feasibility of using white-rot fungi in bioremediation treatments for organopollutants are discussed.

Ecotoxicol Environ Saf, 2001 Oct, 50(2), 107 - 13
Freshwater ecosystems--structure and response; Jones JG; Before it is possible to predict the impact of human activities on the natural environment it is necessary to understand the forces that drive and, therefore, control that environment . This paper is concerned with the freshwater component of the aquatic environment . The driving forces involved (some of which are under man's control) can be divided into the physical and the chemical, but the response is, almost entirely, biological . Although most impacts of the food processing industry might be perceived to be on running waters, this is not always the case, but we can apply the same basic rules to both static and running waters . The physical forces that determine how a lake functions are as follows . In early spring, in the temperate zone, the temperature of the surface water in lakes rises and the sunlight input increases . This results in stratification of the water body . The cooler, deeper water is separated, physically, by gravity . This isolated water plays a very different role in the function of the lake and is analogous to how a river works . Man's activities drive these systems by our input of inorganic and organic substances . The inorganic inputs, particularly of phosphorous, stimulate undesirable algal growths, some of which may produce particularly dangerous toxins . We must now accept that climate change, driven by man, will exacerbate these problems . Organic inputs from the food industry, i.e., carbohydrates, lipids, and proteins, will all impact lakes and rivers by increasing the biological oxygen demand . The worst case scenario is total loss of oxygen from the water as a result of microbial activity . Lipids create the greatest oxygen demand but carbohydrates (more easily biodegradable) also result in unsightly "sewage fungus." Protein waste can be degraded to produce ammonia and sulfide, both of which produce toxicity problems . Bioremediation processes, particularly phytoremediation, can alleviate these problems in a cost-effective manner and this paper will address these options .

Curr Microbiol, 2001 Nov, 43(5), 328 - 35
In situ bioremediation potential of an oily sludge-degrading bacterial consortium; Mishra S et al.; A field-scale study was conducted in a 4000 m2 plot of land contaminated with an oily sludge by use of a carrier-based hydrocarbon-degrading bacterial consortium for bioremediation . The land belonged to an oil refinery . Prior to this study, a feasibility study was conducted to assess the capacity of the bacterial consortium to degrade oily sludge . The site selected for bioremediation contained approximately 300 tons of oily sludge . The plot was divided into four blocks, based on the extent of contamination . Blocks A, B, and C were treated with the bacterial consortium, whereas Block D was maintained as an untreated control . In Block A, at time zero, i.e., at the beginning of the experiment, the soil contained as much as 99.2 g/kg of total petroleum hydrocarbon (TPH) . The application of a bacterial consortium (1 kg carrier-based bacterial consortium/10 m2 area) and nutrients degraded 90.2% of the TPH in 120 days, whereas in block D only 16.8% of the TPH was degraded . This study validates the large-scale use of a carrier-based bacterial consortium and nutrients for the treatment of land contaminated with oily sludge, a hazardous hydrocarbon waste generated by petroleum industry.

Environ Sci Technol, 2001 Oct 15, 35(20), 4054 - 9
Hydrogen peroxide effects on chromium oxidation state and solubility in four diverse, chromium-enriched soils; Rock ML et al.; High concentrations of H2O2 are being tested for in situ oxidation and remediation of buried organic contaminants in soils and groundwater . Peroxide is being considered as a direct chemical oxidant in Fenton-type reactions or as a source of oxidizing equivalents in bioremediation schemes . How H2O2 affects the oxidation state and solubility of Cr(III) and Cr(VI), common co-contaminants with organic chemicals, is explored here in four chemically diverse soils containing elevated levels of Cr . Soil contaminated with soluble Cr(VI) from chromite ore processing residue and soil containing high levels of recently reduced Cr (III) from electroplating waste both released dissolved Cr(VI) after single applications of up to 24 mM H2O2 . In no case was there evidence that H202 reduced preexisting Cr(VI) to Cr(III), even though this would be allowed thermodynamically . Chromate in the leachates exceeded the U.S . EPA drinking water standard for total dissolved Cr (2 microM) by a factor of 10-1000 . Anaerobic conditions in an organic-rich, tannery waste-contaminated soil protected Cr(III) from oxidation and mobilization . Mineral forms of Cr in serpentinitic soil near a former chromite mine also resisted oxidation on the time scale of days . Mobilization of Cr(VI) could be a hazardous consequence of using H2O2 for in situ remediation of chemically complex wastes, but H2O2 could prove attractive for ex situ treatment (i.e., soil washing) . This paper demonstrates marked differences among Cr-contaminated soils in their capacity to release Cr(VI) upon chemical treatment with H2O2.

Environ Sci Technol, 2001 Oct 15, 35(20), 4038 - 45
Assessment of natural attenuation of chlorinated aliphatics and BTEX in subarctic groundwater; Richmond SA et al.; We examined biogeochemistry and microbiology associated with natural attenuation of trichloroethene (TCE), trichloroethane (TCA), and benzene in a subarctic aquifer . Identification of a predominant terminal electron-accepting process (TEAP) and characterization of typical natural attenuation footprints was difficult . Hydrogen and ferrous iron concentrations suggested that iron reduction was the predominant TEAP; calculated in situ Gibbs free energies for iron reduction were energetically feasible at all wells although a source of ferric iron has not been conclusively determined . The presence of dissolved sulfide and favorable free energies for sulfate reduction provided support of concurrent iron and sulfate reduction . Methanogenesis from H2/CO2 was generally not energetically favorable . The presence of TCE and TCA degradation intermediates suggested that biological reductive dechlorination occurred, although proportions of intermediates relative to parent compounds remained stable . By September 2000, contaminant concentrations were within regulatory standards at most sampling points . However, low rates of microbial activity and incomplete degradation imply that intrinsic bioremediation did not likely represent an important contribution to contaminant removal atthis site, where dilution appeared to be the primary attenuation mechanism.

Appl Environ Microbiol, 2001 Nov, 67(11), 5154 - 60
Detection and quantification of methyl tert-butyl ether-degrading strain PM1 by real-time TaqMan PCR; Hristova KR et al.; The fuel oxygenate methyl tert-butyl ether (MTBE), a widely distributed groundwater contaminant, shows potential for treatment by in situ bioremediation . The bacterial strain PM1 rapidly mineralizes and grows on MTBE in laboratory cultures and can degrade the contaminant when inoculated into groundwater or soil microcosms . We applied the TaqMan quantitative PCR method to detect and quantify strain PM1 in laboratory and field samples . Specific primers and probes were designed for the 16S ribosomal DNA region, and specificity of the primers was confirmed with DNA from 15 related bacterial strains . A linear relationship was measured between the threshold fluorescence (C(T)) value and the quantity of PM1 DNA or PM1 cell density . The detection limit for PM1 TaqMan assay was 2 PM1 cells/ml in pure culture or 180 PM1 cells/ml in a mixture of PM1 with Escherichia coli cells . We could measure PM1 densities in solution culture, groundwater, and sediment samples spiked with PM1 as well as in groundwater collected from an MTBE bioaugmentation field study . In a microcosm biodegradation study, increases in the population density of PM1 corresponded to the rate of removal of MTBE.

Environ Sci Technol, 2001 Oct 1, 35(19), 3924 - 30
Monte Carlo analysis of uncertainty attached to microbial pollutant degradation rates; Goovaerts P et al.; Prediction of bioremediation performance relies on models of microbial activity that are typically fitted to few data, which can lead to large errors in parameter estimates and uncertain prediction of reaction rates and degradation times . This paper presents a Monte Carlo approach to propagate the uncertainty about model parameters and error component through the Michaelis-Menten equation, yielding a probability distribution for both pollutant degradation rate and time for cleanup to some prescribed level . The procedure is illustrated using data related to the degradation kinetics of halogenated hydrocarbons by Methylomicrobium album BG8 . It is shown that the assumption of homoscedasticity of the error variance in the Michaelis-Menten model is usually inappropriate, and analytical expressions are derived to account for the dependence of the error variance on the concentration of substrate . Depending on the substrate, the addition of formate might have a significant impact on the expected degradation rates and times, and the proposed approach allows one to test statistically such an impact for various substrate concentrations.

J Ind Microbiol Biotechnol, 2001 Aug, 27(2), 72 - 9
Microbial community dynamics and evaluation of bioremediation strategies in oil-impacted salt marsh sediment microcosms; Bachoon DS et al.; Microbial community dynamics in wetlands microcosms emended with commercial products (surfactant, a biological agent, and nutrients) designed to enhance bioremediation was followed for 3 months . The effectiveness of enhanced degradation was assessed by determining residual concentrations of individual petroleum hydrocarbons by GC/MS . The size and composition of the sediment microbial community was assessed using a variety of indices, including bacterial plate counts, MPNs, and DNA hybridizations with domain- and group-specific oligonucleotide probes . The addition of inorganic nutrients was the most effective treatment for the enhancement of oil degradation, resulting in marked degradation of petroleum alkanes and a lesser extent of degradation of aromatic oil constituents . The enhanced degradation was associated with increases in the amount of extractable microbial DNA and Streptomyces in the sediment, although not with increased viable counts (plate counts, MPN) . Bacteria introduced with one of the proprietary products were still detected in the microcosms after 3 months, but were not a major quantitative constituent of the community . The biological product enhanced oil degradation relative to the control, but to a lesser extent than the nutrient additions alone . In contrast, application of the surfactant to the oil-impacted sediment decreased oil degradation.

Appl Microbiol Biotechnol, 2001 Sep, 56(5-6), 803 - 8
Pyrene degradation by two fungi in a freshwater sediment and evaluation of fungal biomass by ergosterol content; Ravelet C et al.; Mucor racemosus var . sphaerosporus and Phialophora alba were investigated for their abilities to degrade pyrene in a freshwater sediment, with or without glucose supply as nutrient or carbon source, during 90 days . The ergosterol contents in sediment were quantified to estimate fungal biomass and to assess the correlation between fungal activity and biodegradation of pyrene . Results showed that, in an heterogeneous environment, these fungi presented different abilities to degrade pyrene . P . alba increased the degree of pyrene degradation by 9%, compared to the native micro-organisms, but a supply of glucose acted as an inhibitor to pyrene disappearance . M . racemosus var . sphaerosporus was not efficient at sediment bioremediation (with or without glucose added), because it reduced the rate of pyrene degradation by the native microflora . In any case, there was no increase of ergosterol in boxes during bioremediation experiments . In our experimental conditions, ergosterol content could not be correlated to pyrene degradation.

Appl Microbiol Biotechnol, 2001 Sep, 56(5-6), 788 - 95
Preliminary examinations for applying a carbazole-degrader, Pseudomonas sp . strain CA10, to dioxin-contaminated soil remediation; Habe H et al.; A method for bioremediation of chlorinated dibenzo-p-dioxins (CDDs) and dibenzofurans (CDFs) by a carbazole-utilizing bacterium, Pseudomonas sp . strain CA10, was developed . CA10 cells transferred to carbon- and nitrogen-free mineral medium supplemented with 1 mg carbazole (CAR)/ml grew rapidly during the first 2 days; and the cells at the end of this rapid growth period showed the highest 2,3-dichlorodibenzo-p-dioxin (2,3-Cl2DD)-degrading activity . The CA10 cells pregrown for 2 days efficiently degraded 2,3-Cl2DD in aqueous solution at either 1 ppm or 10 ppm . The effect of inoculum density on the efficiency of 2,3-Cl2DD degradation was investigated in a soil slurry microcosm {ratio of soil:water = 1:5 (w/v)} . The results showed that a single inoculation with CA10 cells at densities of 10(7) CFU/g soil and 10(9) CFU/g soil degraded 46% and 80% of 2,3-Cl2DD, respectively, during the 7-day incubation . The rate of degradation of each CDD congener, 2-ClDD, 2,3-Cl2DD, and 1,2,3-Cl3DD (1 ppm each) by strain CA10 in the soil slurry system was not significantly influenced by the coexistence of the other congeners . Using this soil slurry system, we tried an experimental bioremediation of the actual dioxin-contaminated soil, which contained mainly tetra- to octochlorinated dioxins . Although the degradation rate of total CDD and CDF congeners by a single inoculation with CA10 cells was 8.3% after a 7-day incubation, it was shown that strain CA10 had a potential to degrade tetra- to hepta-chlorinated congeners including the most toxic compound, 2,3,7,8-tetrachlorinated dibenzo-p-dioxin.

Appl Microbiol Biotechnol, 2001 Sep, 56(5-6), 757 - 61
Bioconversion of nitriles by Candida guilliermondii CCT 7207 cells immobilized in barium alginate; Dias JC et al.; Nitrile degradation by Candida guilliermondii CCT 7207 using free and immobilized cell systems was compared . Different specific growth rates were observed for immobilized (mumax=0.021 h(-1)) and the free cells (mumax=0.029 h(-1)) . The maximum specific rate of acetic acid formation was 0.387 h(-1) and 0.266 h(-1) for free and immobilized cells, respectively . Cell adhesion to the support materials was confirmed by scanning electron microscopy . When immobilized, the yeast was able to use high nitrile and amide concentrations (aliphatic and aromatic) as nitrogen sources . The results suggest that C . guilliermondii CCT 7207 presents a physiological pattern potentially useful for the bioremediation of polluted environments or for the bioproduction of amides and organic acid of high commercial value.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2001 Sep, 36(8), 1491 - 503
Comparison of ex situ and in situ bioremediation of unsaturated soils contaminated by petroleum; Carberry JB et al.; The most feasible bioremediation technologies of unsaturated soils contaminated by Petroleum are (1) the on-site controlled remediation of the excavated contaminated plume in the contained system; and (2) the in situ sub-surface, highly controlled process in which nutrients and microbes or air are injected into the plume volume via a grid of wells and reversing the direction of the pumping . The detailed results of ex situ (controlled aerobic bioremediation) of ten sites with differing petroleum contamination and four in situ cases are reported and compared . It is concluded, that bioremediation of petroleum contaminated soil is an effective, safe and economically feasible remediation technique for the remediation of such contaminated sites, contingent on the providing of the site-specific appropriate conditions . However, the biodegradation rate of the NAPL is more variable in the in situ than in the ex situ aerobic process, correlating best in the latter with the molecular weight of the petroleum contaminants.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2001 Sep, 36(8), 1451 - 71
Feasibility of in situ NAPL-contaminated aquifer bioremediation by biodegradable nutrient-surfactant mix; Zoller U et al.; Entrapped non-aqueous liquid phase (NAPL) pollutants (e.g., fuels) constitute one of the biggest current problems in the bioremediation efforts of contaminated soil and aquifers worldwide . On site, in situ surfactant-enhanced bioremediation, in the presence of sufficient nutrients and dissolved oxygen, has the potential of becoming the remediation method of choice in terms of both technological and economical feasibility . This approach was applied in our lab-scale column-based flow system with the aid of which an optimized, below CMC, of biodegradable surfactant-nutrient surfactant mix has been established for the best solubilization/ mobilization of NAPL (hexane, toluene, kerosene and their mixtures as "representatives") in sandy matrix . For kerosene, the highest f values (the enhancement factors) were obtained for the systems containing either the amphoteric cocoamphodiacetate or the anionic linear dodecylbenzene sulfonate (0.1-0.3 g/L) with one or both the nutrient-surfactants L and B (0.05 g/L).

Environ Toxicol Chem, 2001 Oct, 20(10), 2179 - 83
Effect of petrochemical sludge concentrations of changes in mutagenic activity during soil bioremediation process; Morelli IS et al.; The present study was performed to assess the effect of the petrochemical sludge application rate on the mutagenic activity (Ames test) of soil and the persistence of mutagenic activity during laboratory soil bioremediation process . Sludge-soil systems were prepared at four different sludge application rates (1.25, 2.5, 5, and 10% w/w) . Unamended soil was used as a control . Immediately following sludge application, in the absence or presence of S9, a linear correlation between sludge application rates and mutagenicity was found but differed significantly (p < 0.05) from the control system only at higher application rates (5 and 10% w/w) . The direct mutagenicity of all systems decreases during the bioremediation process, and after a year of treatment only the 10% system induced a mutagenic response that was significantly different from the control system . On the other hand, an initial increase of the indirect mutagenicity was observed at all application rates . The time required for observing this increase was inversely proportional to the initial sludge concentration . After a year of treatment, the indirect mutagenicity of all sludge-amended soils was not significantly different but was significantly different from the unamended soils . The persistence of the direct mutagenic activity of the sludge-amended soils was related to the sludge concentration, whereas the indirect mutagenic persistence was related to the relationship between easily degradable hydrocarbons and polynuclear aromatic hydrocarbons concentration and independent from the initial application rate.

Rev Argent Microbiol, 2001 Jul-Sep, 33(3), 141 - 8
{Typing and evaluation of hydrocarbon-degrading activity of a bacterial strain isolated from the Bahía Blanca estuary, Argentina}; Cubitto MA et al.; During screening for oil-degrading bacteria in sediments of Bahia Blanca estuary, a bacterial strain was isolated which uses a limited number of organic compounds, especially lineal hydrocarbons . The goals of this study were to characterize the strain and to evaluate its activity on crude oil . Based on phenotypic characteristics and the analysis of 16S rDNA sequences, it was determined that the strain is strongly related to Alcanivorax borkumensis . The strain was cultured, under quasicontinuous conditions, with crude oil as sole source of carbon and energy . After 30 days of incubation, n-alkane decrease reached 86% . The isoalkanes pristane and phitane were degraded more slowly, but a decrease of about 63% was obtained . The strain studied would be useful for the bioremediation of the local coasts, so that this study will be continued in order to obtain its successful application in the environment.

Biodegradation, 2000, 11(6), 391 - 9
Nutrient-limited biodegradation of PAH in various soil strata at a creosote contaminated site; Breedveld GD et al.; The effects of nutrient addition on the in situ biodegradation of polycyclic aromatic hydrocarbons in creosote contaminated soil were studied in soil columns taken from various soil strata at a wood preserving plant in Norway . Three samples were used: one from the topsoil (0-0.5 m), one from an organic rich layer (2-2.5 m) and one from the sandy aquifer (4.5-5 m) . The addition of inorganic nitrogen and phosphorous stimulated the degradation of polycyclic aromatic hydrocarbons (PAHs) in the top soil and the aquifer sand . These two soils, which differed strongly in contamination levels, responded similarly to nutrient addition with the corresponding degradation of 4-ring PAHs . The ratio between available nitrogen (N) and phosphorous (P) might explain the degree of degradation observed for the 4-ring PAHs . However, the degree of degradation of 3-ring PAHs did not significantly increase after nutrient addition . An increase in the respiration rate, after nutrient addition, could only be observed in the topsoil . In the aquifer sand, 4-ring PAH degradation was not accompanied by an increase in the respiration rate or the number of heterotrophic micro-organisms . PAH degradation in the organic layer did not respond to nutrient addition . This was probably due to the low availability of the contaminants for micro-organisms, as a result of sorption to the soil organic matter . Our data illustrate the need for a better understanding of the role of nutrients in the degradation of high molecular weight hydrocarbons for the successful application of bioremediation at PAH contaminated sites.

Biodegradation, 2000, 11(6), 385 - 9
Bioremediation of oil polluted aquatic systems and soils with novel preparation 'Rhoder'; Murygina V et al.; This paper summarises the experience accumulated during the field application of biopreparation 'Rhoder' (solely or in a combination with preliminary mechanical collection of free oil) for remediation of oil polluted aquatic systems and soils in the Moscow region and Western Siberia during 1994-1999 . It was demonstrated that 'Rhoder' had a very high efficiency (>99%) for bioremediation of the open aquatic surfaces (100 m2 bay of the River Chernaya, two 5,000 m2 lakes in Vyngayakha) at initial level of oil pollution of 0.4-19.1 g/l . During remediation of the wetland (2,000 m2) in Urai (initial level of oil pollution of 10.5 g/l), a preliminary mechanical collection of oil was applied (75% removal) followed by a triple treatment with 'Rhoder' . It resulted in an overall treatment efficiency of 94% . Relatively inferior results of bioremediation of the 10,000 m2 wetland in Vyngayakha (65% removal) and the 1,000 m2 marshy peat soil in Nizhnevartovsk (19% removal) can be attributed to the very high initial level of oil pollution (24.3 g/l and >750 g/g dry matter, respectively) aggravated by the fact that it was impossible to apply a preliminary mechanical collection of oil on these sites . A possible strategy for remediation of such heavily polluted sites is discussed.

Mar Pollut Bull, 2001 Sep, 42(9), 773 - 9
Effects of chitin on microbial emulsification, mineralization potential, and toxicity of bunker C fuel oil; Richmond SA et al.; Bunker C, one of the most frequently spilled petroleum products in the US, is difficult to remove from oiled surfaces and is relatively recalcitrant to biodegradation; therefore, emulsification and biodegradability must be optimized before bioremediation can be considered a viable treatment option . Sand from a freshly oiled beach near Dutch Harbor, Alaska, was incubated at 10 degrees C with nutrients (Bushnell-Haas (BH)) or nutrients with crab shell chitin (BH-C) . BH-C amendment resulted in greater numbers of bunker C emulsifiers and greater mineralization potentials for hexadecane, phenanthrene, and fluorene than with BH only . Compared to BH alone, mineralization potentials for bunker C also were higher in BH-C, with an estimated 8% of fuel oil mineralized after 6 weeks . Microbially emulsified oil was more toxic than in uninoculated controls (p < 0.05) as measured by Microtox assays . However, toxicity was significantly lower in BH-C than BH after 4 and 6 weeks incubation (p < 0.05).

Appl Environ Microbiol, 2001 Oct, 67(10), 4671 - 7
Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation; Futamata H et al.; The sequences of the largest subunit of bacterial multicomponent phenol hydroxylases (LmPHs) were compared . It was found that LmPHs formed three phylogenetic groups, I, II, and III, corresponding to three previously reported kinetic groups, low-K(s) (the half-saturation constant in Haldane's equation for trichloroethylene {TCE}), moderate-K(s), and high-K(s) groups . Consensus sequences and specific amino acid residues for each group of LmPH were found, which facilitated the design of universal and group-specific PCR primers . PCR-mediated approaches using these primers were applied to analyze phenol/TCE-degrading populations in TCE-contaminated aquifer soil . It was found that the aquifer soil harbored diverse genotypes of LmPH, and the group-specific primers successfully amplified LmPH fragments affiliated with each of the three groups . Analyses of phenol-degrading bacteria isolated from the aquifer soil confirmed the correlation between genotype and phenotype . Competitive PCR assays were used to quantify LmPHs belonging to each group during the enrichment of phenol/TCE-degrading bacteria from the aquifer soil . We found that an enrichment culture established by batch phenol feeding expressed low TCE-degrading activity at a TCE concentration relevant to the contaminated aquifer (e.g., 0.5 mg liter(-1)); group II and III LmPHs were predominant in this batch enrichment . In contrast, group I LmPHs overgrew an enrichment culture when phenol was fed continuously . This enrichment expressed unexpectedly high TCE-degrading activity that was comparable to the activity expressed by a pure culture of Methylosinus trichosporium OB3b . These results demonstrate the utility of the group-specific monitoring of LmPH genes in phenol-stimulated TCE bioremediation . It is also suggested that phenol biostimulation could become a powerful TCE bioremediation strategy when bacteria possessing group I LmPHs are selectively stimulated.

Appl Environ Microbiol, 2001 Oct, 67(10), 4471 - 8
Anaerobic mineralization of toluene by enriched sediments with quinones and humus as terminal electron acceptors; Cervantes FJ et al.; The anaerobic microbial oxidation of toluene to CO(2) coupled to humus respiration was demonstrated by use of enriched anaerobic sediments from the Amsterdam petroleum harbor (APH) and the Rhine River . Both highly purified soil humic acids (HPSHA) and the humic quinone moiety model compound anthraquinone-2,6-disulfonate (AQDS) were utilized as terminal electron acceptors . After 2 weeks of incubation, 50 and 85% of added uniformly labeled {(13)C}toluene were recovered as (13)CO(2) in HPSHA- and AQDS-supplemented APH sediment enrichment cultures, respectively; negligible recovery occurred in unsupplemented cultures . The conversion of {(13)C}toluene agreed with the high level of recovery of electrons as reduced humus or as anthrahydroquinone-2,6-disulfonate . APH sediment was also able to use nitrate and amorphous manganese dioxide as terminal electron acceptors to support the anaerobic biodegradation of toluene . The addition of substoichiometric amounts of humic acids to bioassay reaction mixtures containing amorphous ferric oxyhydroxide as a terminal electron acceptor led to more than 65% conversion of toluene (1 mM) after 11 weeks of incubation, a result which paralleled the partial recovery of electron equivalents as acid-extractable Fe(II) . Negligible conversion of toluene and reduction of Fe(III) occurred in these bioassay reaction mixtures when humic acids were omitted . The present study provides clear quantitative evidence for the mineralization of an aromatic hydrocarbon by humus-respiring microorganisms . The results indicate that humic substances may significantly contribute to the intrinsic bioremediation of anaerobic sites contaminated with priority pollutants by serving as terminal electron acceptors.

Mar Environ Res, 2001 Sep, 52(3), 195 - 211
Phytoremediation of small-scale oil spills in fresh marsh environments: a mesocosm simulation; Dowty RA et al.; Research was conducted to assess the impact of oiling on fresh-marsh plant communities and to test the efficacy of techniques that may be used to enhance the bioremediation of crude oil spills in these environments while minimizing secondary anthropogenic impacts . To emulate field conditions, a mesocosm facility was used that houses 120 mesocosm vessels, each of 200-1 capacity . A five-way factorial treatment arrangement was used that included two substrates (inorganic, organic), two nutrient regimes (fertilized, not fertilized), two aeration levels (substrate aeration, no aeration), three oiling concentrations (0-, 5-, 10-1 m(-2) of South Louisiana Sweet Crude oil), and four vascular plant species (Alternanthera philoxeroides, Panicum hemitomon, Phragmites australis, Sagittaria lancifolia, and an unplanted control) . Under the 5- and 10-1 m(-2) oiling concentrations, S . lancifolia displayed a short-term response of increased productivity, whereas P . hemitomon had the highest biomass production and photosynthetic rates at the end of the 18-month experiment . Overall plant growth and productivity, as well as oil degradation, were significantly higher in the inorganic substrate, indicating that biodegradation of oil spills in organic substrates may require a longer time period . Time-released fertilizer also stimulated plant productivity and resulted in higher soil respiratory quotients, suggestive of greater microbial activity, particularly in aerated mesocosms . The amount of oil remaining after 18 months was lowest in aerated and fertilized mesocosms containing either P . hemitomon or S . lancifolia and a substrate of low organic matter content.

Biotechniques, 2001 Sep, 31(3), 598, 600, 602 - 4, passim
Detection of bacteria in environmental samples by direct PCR without DNA extraction; Fode-Vaughan KA et al.; Cultured cells and environmental samples were used directly in PCRs without the isolation of DNA . Serial dilution was used to eliminate the inhibitory effect of materials in natural samples . Primers specific for pmoA, which encodes a subunit of the particulate methane monooxygenase, were used to detect and quantify methanotrophic bacteria by direct most probable number PCR . Phototrophic bacteria were detected in environmental samples by direct PCR with primers specific for pufM, and members of the bacterial domain were detected with primers for 16S rDNA . Direct PCR provides a rapid, simple, and sensitive methodfor detecting and quantifying bacteria in environmental samples . Detection of methanotrophic bacteria can be applied to monitoring bioremediation.

Huan Jing Ke Xue, 2001 Jul, 22(4), 111 - 3
{Degradation of the herbicide dicamba under strictly anaerobic conditions}; Gu J et al.; Degradation of the herbicide dicamba was assayed under methane-producing condition using a coastal wetland soil as an inoculum . Benzene ring 14C labeled dicamba was employed and degradative process proceeds through demethoxylation yielding 3,6-dichlorosalicylic acid as the predominant intermediate . The data showed that the degradation rate of dicamba by the enrichment culture achieved 64%, 91% and 95% after 7, 16 and 27 days of incubation, respectively; only small quantities of CO2(0.74%) and CH4(0.11%) were recovered with insignificant radioactivity . The benzene ring of dicamba was not cleavaged to a significant extent . Future cleaning up of dicamba contaminated environment may require an effective bioremediation techniques.

Ann Chim, 2001 Jul-Aug, 91(7-8), 391 - 400
Pilot plant study of the microbial flora in a diesel fuel contaminated soil; Abbondanzi F et al.; This study focused on the impact of a recent soil pollution of diesel fuel on a site and its indigenous microbial flora . A pilot plant (0.5 m3) was set up and filled with a soil (about 700 kg), artificially and uniformly polluted with diesel fuel (7 g/kg) . This plant was then chemically and biologically monitored during the whole experiment (about two years) . During the monitoring, a morphological change of the microbial colonies was observed . This was probably due to the acclimation phenomena to the pollution . With batch kinetic studies (10 ml) and increasing the selective pressure of the pollutant, it was possible to select and isolate a microbial consortium and a single strain that developed the ability to use different diesel fuel fractions as carbon sources . GC-MS analytical techniques were used . Results showed that different fractions were degraded at different times . In the batch system, in 7 days, the microbial consortium degraded some aromatic hydrocarbons . The isolate strain, in 20 days, degraded linear hydrocarbons . After a two years acclimation, it was possible to obtain, from a pilot plant, a microbial consortium and a strain able to degrade diesel fuel, for a future bioremediation in situ process.

Appl Microbiol Biotechnol, 2001 Aug, 56(3-4), 555 - 9
Enhancing pyrene mineralization in contaminated soil by the addition of humic acids or composted contaminated soil; Haderlein A et al.; The addition of composted PAH-contaminated soil to PAH-contaminated soil spiked with 14C-labeled pyrene resulted in rapid mineralization of pyrene (more than 57% after 21 days compared with 3.4% in un-amended soil) . The addition of the humic acid fraction of the composted soil also increased the mineralization potential of the soil significantly, but to a lesser extent (37.5% mineralization after 106 days compared with 20.6% in unamended soil) . Increasing the humic acid concentration increased mineralization up to a maximum of more than three times the unamended rate, after which the rate of pyrene mineralization decreased, possibly due to inhibitory pH or concentrations of salts . The amendment of PAH-contaminated soil with materials containing humic acids or humic acid extracts is suggested as a method of bioremediation.

J Mol Microbiol Biotechnol, 2001 Oct, 3(4), 507 - 12
Secretion of mouse-metallothionein by engineered E . coli cells in metal-enriched culture media; Cols N et al.; Heterologous Escherichia coli expression systems were designed and assayed for the synthesis of functional mouse metallothionein (MT) as a secreted fusion protein . MT secretion was compared among different systems, and the optimum vector/host/medium combination was tested for metal removal . In this case, the Cu content of the medium decreased by up to 34% after growth of recombinant bacteria . The potential use of these genetically-engineered bacteria for water bioremediation is discussed as an alternative to cytoplasmic MT or membrane-bound MT heterologous expression systems.

Biomol Eng, 2001 Sep, 18(2), 49 - 56
Identification and characterization of Rhodopseudomonas spp., a purple, non-sulfur bacterium from microbial mats; Mehrabi S et al.; A species of facultative photo-organotrophic, purple, non-sulfur bacterium was isolated from mixed-species microbial mats, characterized and examined for metal tolerance and bioremediation potential . Contributing mats were natural consortia of microbes, dominated by cyanobacteria and containing several species of bacteria arranged in a laminar structure, stabilized within a gel matrix . Constructed microbial mats were used for bioremediation of heavy metals and organic chemical pollutants . Purple, non-sulfur bacteria are characteristically found in lower strata of intact mats, but their contributing function in mats survival and function by mediating the chemical environment has not been explored . The gram-negative rod-shaped bacterium, reported here, produced a dark red culture under phototrophic conditions, reproduced by budding and formed a lamellar intracytoplasmic membrane (ICM) system parallel to cytoplasmic membrane, which contained bacteriochlorophyll a and carotenoids . This strain was found to have multiple metal resistances and to be effective in the reductive removal of Cr(VI) and the degradation of 2,4,6-trichlorophenol . Based on the results obtained from morphology, nutrient requirements, major bacteriochlorophyll content, GC content, random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) profile and 16S-rDNA phylogenetic analysis, this member of the microbial mats may be identified as a new strain of the genus Rhodopseudomonas.

J Contam Hydrol, 2001 Sep, 51(1-2), 97 - 125
Modeling hydrocarbon biodegradation in tidal aquifers with water-saturation and heat inhibition effects; El-Kadi AI; A model is developed for hydrocarbon biodegradation, which includes saturated and unsaturated flow, multi-species transport, heat transport, and bacterial growth processes . Numerical accuracy of the model was tested against analytical solutions . The model was also verified against laboratory results for a saturated-flow problem and reasonable match was obtained . Expressions are proposed for inhibition due to water content and temperature fluctuations . Bioactivities under cyclic water content variation were studied under no-flow conditions . A quantitative approach was used to reconcile some of the apparent contradictory conclusions regarding the efficiency of biodegradation of soils under wetting and drying conditions . The efficiency depends on the nature of the oxygenation process . For cases involving the presence of dissolved oxygen and the absence of O2 vapor, subjecting the soil to constant water content close to its optimal value for degradation is most efficient . However, wetting and drying can enhance degradation if O2 is only provided through aeration or direct contact between air and the medium . Also presented are the results of a typical field application of the model and a discussion of the effects of tides, saturation inhibition, and heat inhibition . Other inhibition factors, such as pH or salinity, can be easily incorporated in the formulation . The quantitative approach developed here can be used in assessing bioremediation not only in tidal aquifers but also in areas where water-table or temperature effects are of significance . The approach can be useful in the design of remediation strategies under water-flow or no-flow conditions involving water content and temperature fluctuations.

Appl Microbiol Biotechnol, 2001 Jun, 55(6), 794 - 800
Isolation and characterization of psychotrophic bacteria from oil-reservoir water and oil sands; Kato T et al.; Four psychrotrophic strains, which grew at 4 degrees C but not at 37 degrees C, were isolated from Japanese oil-reservoir water (strains SIB1, SIC1, SIS1) and Canadian oil sands (strain CAB1) . Strains SIB1, SIS1, and CAB1 had a maximum growth rate at 20 degrees C and grew to the highest cell densities at the cultivation temperature of 0-4 degrees C . Strain SIS1 was capable of growing even at -5 degrees C . The growth profile of strain SIC1 was rather similar to that of a mesophilic bacterium . Strains SIB1, SIC1, and SIS1 were identified as members of the genus Shewanella, and strain CAB1 was a member of the genus Arthrobacter . All these strains exhibited weak degradation ability against catechol, a hydroxylated aromatic hydrocarbon, and tributyrin . These strains are expected to be of potential use in the in situ bioremediation technology of hazardous hydrocarbons and esters under low-temperature conditions.

Appl Microbiol Biotechnol, 2001 Jun, 55(6), 661 - 72
The use of transgenic plants in the bioremediation of soils contaminated with trace elements; Kramer U et al.; The use of plants to clean-up soils contaminated with trace elements could provide a cheap and sustainable technology for bioremediation . Field trials suggested that the rate of contaminant removal using conventional plants and growth conditions is insufficient . The introduction of novel traits into high biomass plants in a transgenic approach is a promising strategy for the development of effective phytoremediation technologies . This has been exemplified by generating plants able to convert organic and ionic forms of mercury into the less toxic, volatile, elemental mercury, a trait that occurs naturally only in some bacteria and not at all in plants . The engineering of a phytoremediator plant requires the optimization of a number of processes, including trace element mobilization in the soil, uptake into the root, detoxification and allocation within the plant . A number of transgenic plants have been generated in an attempt to modify the tolerance, uptake or homeostasis of trace elements . The phenotypes of these plants provide important insights for the improvement of engineering strategies . A better understanding, both of micronutrient acquisition and homeostasis, and of the genetic, biochemical and physiological basis of metal hyperaccumulation in plants, will be of key importance for the success of phytoremediation.

Chemosphere, 2001 Aug, 44(5), 925 - 34
Laboratory column studies for evaluating a barrier system for providing oxygen and substrate for TCE biodegradation; Kao CM et al.; The industrial solvent trichloroethylene (TCE) is among the most ubiquitous chlorinated compounds found in groundwater contamination . The objective of this study was to develop a biobarrier system containing oxygen-organic releasing material to enhance the aerobic cometabolism of TCE in situ . The oxygen-organic material, which contains calcium peroxide and peat, is able to release oxygen and primary substrates continuously upon contact with water . Batch experiments were conducted to design and identify the components of the oxygen-organic releasing material, and evaluate the oxygen and organic substrate (presented as COD equivalent) release from the designed oxygen-organic material . The observed oxygen and chemical oxygen demand (COD) release rates were approximately 0.0246 and 0.052 mg/d/g of material, respectively . A laboratory-scale column experiment was then conducted to evaluate the feasibility of this proposed system for the bioremediation of TCE-contaminated groundwater . This system was performed using a series of continuous-flow glass columns including a soil column, an oxygen-organic material column, followed by two consecutive soil columns . Aerobic acclimated sludges were inoculated in all three soil columns to provide microbial consortia for TCE biodegradation . Simulated TCE-contaminated groundwater with a flow rate of 0.25 l/day was pumped into this system . Effluent samples from each column were analyzed for TCE and other indicating parameters (e.g., pH, dissolved oxygen) . Results show that the decreases in TCE concentrations were observed over a 4-month operating period . Up to 99% of TCE removal efficiency was obtained in this passive system . Results indicate that the continuously released oxygen and organic substrates from the oxygen-organic materials enhanced TCE biotransformation . Thus, the biobarrier treatment scheme has the potential to be developed into an environmentally and economically acceptable remediation technology.

Chemosphere, 2001 Aug, 44(5), 1131 - 6
Bioremediation of coal tar PAH in soils using biodiesel; Taylor LT et al.; The addition of biodiesel together with nitrate and phosphate to soil containing coal tar, in laboratory and field experiments, resulted in degradation of coal tar polycyclic aromatic hydrocarbons (PAH) that was not apparent when the nutrients alone were added . The addition of motor diesel fuel instead of biodiesel was also tested . Over the 55 days of the field and laboratory experiments, the biodiesel resulted in an increased degradation of naphthalene in the coal tar by 52% and 85%, respectively, and motor diesel resulted in increased depletions of 85% and 96%, respectively . Other PAH containing up to four rings were depleted to lesser extents . The increases in PAH biodegradation by the diesel treatments were ascribed to tar solubilisation and dispersion thereby increasing the PAH bioavailability . The ready biodegradability and low phytotoxicity of biodiesel suggest that it may be suitable as a novel treatment for the bioremediation of coal tar contaminated soils.

Appl Microbiol Biotechnol, 2001 Jul, 56(1-2), 81 - 7
Microbial decolourisation and degradation of textile dyes; McMullan G et al.; Dyes and dyestuffs find use in a wide range of industries but are of primary importance to textile manufacturing . Wastewater from the textile industry can contain a variety of polluting substances including dyes . Increasingly, environmental legislation is being imposed to control the release of dyes, in particular azo-based compounds, into the environment . The ability of microorganisms to decolourise and metabolise dyes has long been known, and the use of bioremediation based technologies for treating textile wastewater has attracted interest . Within this review, we investigate the mechanisms by which diverse categories of microorganisms, such as the white-rot fungi and anaerobic bacterial consortia, bring about the degradation of dyestuffs.

Biodegradation, 2000, 11(5), 341 - 7
Surfactant inhibition of bacterial growth on solid anthracene; Chen P et al.; Surfactants have been proposed as a promising method to enhance bioremediation of hydrophobic compounds in contaminated soils . However, the results of effects of surfactants on bioremediation are not consistent . This study showed that Triton X-100 at low concentration (0.024 mM or 0.09 CMC) inhibited the rate of growth of either a Mycobacterium sp . or a Pseudomonas sp . on solid anthracene as sole carbon source . Recovery of microbial growth rate could be achieved by dilution of surfactants, while addition of more surfactant gave an immediate decrease in growth rate . No inhibition of growth by Triton X-100 was observed with growth on glucose . The surfactant sorbed onto the surfaces of both the cells and the anthracene particles, which could inhibit uptake of anthracene . The results were consistent with the hypothesis that inhibition of microbial adhesion of cells to anthracene was responsible for the inhibition of growth by Triton X-100.

Environ Technol, 2001 Jun, 22(6), 619 - 29
Nutrient stimulation of sulfolane biodegradation in a contaminated soil from a sour natural gas plant and in a pristine soil; Greene EA et al.; Natural gas in western Canada can contain up to 35% H2S . The Sulfinol process for sour gas treatment makes use of sulfolane and an amine to remove H2S and other sour components from natural gas . Sulfolane has leached into groundwaters at sour gas treatment plant sites, and poses a risk for off-site contamination . Sulfolane biodegradation was monitored in shake-flask cultures and air-sparged microcosms inoculated with uncontaminated topsoil or with sulfolane contaminated soil obtained near a Sulfinol process building at a sour gas treatment facility in western Canada . For both soils, supplementation with a source of fixed nitrogen stimulated sulfolane biodegradation . Topsoil cultures and microcosms were only slightly affected by the addition of phosphate . Contaminated soil microcosms and cultures were stimulated by phosphate addition, but not to the same degree as by the addition of nitrogen . For these cultures and microcosms, amendment with both fixed nitrogen and phosphate produced an additive effect . It was possible to predict the nutrient requirements of air-sparged microcosms inoculated with each soil type using shake-flask cultures . Shake-flask cultures require less time and effort and fewer materials than the more complex air-sparged soil microcosms, and will be useful for large-scale experiments to predict the nutrient supplements required for bioremediation of sulfolane-contaminated sites.

J Environ Qual, 2001 Jul-Aug, 30(4), 1134 - 43
In situ bioremediation through mulching of soil polluted by a copper-nickel smelter; Kiikkila O et al.; Bioremediation of a heavy metal-polluted soil was investigated in a 3-yr field experiment by adding mulch to a polluted forest floor . The mulch consisted of a mixture of compost and woodchips . The remediation treatment decreased the toxicity of the soil solution to bacteria as determined by the {3H}-thymidine incorporation technique, that is, by measuring the growth rate of soil bacteria extracted from unpolluted humus after exposing them to soil solution containing heavy metals from the experimental plots . Canonical correlation analysis was performed in order to identify the chemical and microbiological changes in the soil . The pH of the mulched organic layer increased by one unit . The concentration of complexed Cu increased and that of free Cu2+ decreased in the soil solution from the mulch treatment . According to basal respiration and litter decomposition, microbial activity increased during the 3 yr following the remediation treatment . The {3H}-thymidine incorporation technique was also used to study the growth rate and tolerance of bacteria to Cu . The bacterial growth rate increased and the Cu tolerance decreased on the treated plots . The structure of the microbial community, as determined by phospholipid fatty acid (PLFA) analysis, remained unchanged . The results indicate that remediation of the polluted soil had occurred, and that adding a mulch to the forest floor is a suitable method for remediating heavy metal-polluted soil.

Lett Appl Microbiol, 2001 Aug, 33(2), 164 - 8
Effect of copper on the degradation of phenanthrene by soil micro-organisms; Sokhn J et al.; AIMS: The effect of copper on the degradation by soil micro-organisms of phenanthrene, a polycyclic aromatic hydrocarbon, was investigated . METHODS AND RESULTS: Inert nylon filters were incubated in the soil for 28 days at 25 degrees C . Each filter was inoculated with a soil suspension, phenanthrene (400 ppm), copper (0, 70, 700 or 7000 ppm) and nitrogen/phosphorus sources . The filters were assessed for phenanthrene degradation, microbial respiration and colonization . Phenanthrene degradation proceeded even at toxic copper levels (700/7000 ppm), indicating the presence of phenanthrene-degrading, copper-resistant and/or -tolerant microbes . However, copper at these high levels reduced microbial activity (CO2 evolution) . CONCLUSION: High levels of copper caused an incomplete mineralization of phenanthrene and possible accumulation of its metabolites . SIGNIFICANCE AND IMPACT OF THE STUDY: The presence of heavy metals in soils could seriously affect the bioremediation of PAH-polluted environments.

Environ Microbiol, 2001 Jun, 3(6), 407 - 16
Methyl tert-butyl ether (MTBE) degradation by a microbial consortium; Fortin NY et al.; The widespread use of methyl tert-butyl ether (MTBE) as a gasoline additive has resulted in a large number of cases of groundwater contamination . Bioremediation is often proposed as the most promising alternative after treatment . However, MTBE biodegradation appears to be quite different from the biodegradation of usual gasoline contaminants such as benzene, toluene, ethyl benzene and xylene (BTEX) . In the present paper, the characteristics of a consortium degrading MTBE in liquid cultures are presented and discussed . MTBE degradation rate was fast and followed zero order kinetics when added at 100 mg l(-1) . The residual MTBE concentration in batch degradation experiments ranged from below the detection limit (1 microg l(-1)) to 50 microg l(-1).The specific activity of the consortium ranged from 7 to 52 mgMTBE g(dw)(-1) h(-1) (i.e . 19-141 mgCOD g(dw) (-1) h(-1)) . Radioisotope experiments showed that 79% of the carbon-MTBE was converted to carbon-carbon dioxide . The consortium was also capable of degrading a variety of hydrocarbons, including tert-butyl alcohol (TBA), tert-amyl methyl ether (TAME) and gasoline constituents such as benzene, toluene, ethylbenzene and xylene (BTEX) . The consortium was also characterized by a very slow growth rate (0.1 d(-1)), a low overall biomass yield (0.11 gdw g(-1)MTBE; i.e . 0.040 gdw gCOD(-1)), a high affinity for MTBE and a low affinity for oxygen, which may be a reason for the slow or absence of MTBE biodegradation in situ . Still, the results presented here show promising perspectives for engineering the in situ bioremediation of MTBE.

Curr Drug Metab, 2001 Jun, 2(2), 117 - 37
Analysis of mammalian cytochrome P450 structure and function by site-directed mutagenesis; Domanski TL et al.; Over the past decade, site-directed mutagenesis has become an essential tool in the study of mammalian cytochrome P450 structure-function relationships . Residues affecting substrate specificity, cooperativity, membrane localization, and interactions with redox partners have been identified using a combination of amino-acid sequence alignments, homology modeling, chimeragenesis, and site-directed mutagenesis . As homology modeling and substrate docking technology continue to improve, the ability to predict more precise functions for specific residues will also advance, making it possible to utilize site-directed mutagenesis to test these predictions . Future studies will employ site-directed mutagenesis to learn more about cytochrome P450 substrate access channels, to define the role of residues that do not lie within substrate recognition sites, to engineer additional soluble forms of microsomal cytochromes P450 for x-ray crystallography, and to engineer more efficient enzymes for drug activation and/or bioremediation.

J Ind Microbiol Biotechnol, 2001 Apr, 26(4), 210 - 5
Chromium accumulation by two Streptomyces spp . isolated from riverine sediments; Amoroso MJ et al.; Strains designated R22 and R25, isolated from Sali River sediments, Argentina, were highly resistant to chromium . These strains were shown by 16S rRNA sequencing studies to be Streptomyces spp.; this affiliation was consistent with morphological and chemical characteristics . Growth of strains R22 and R25 in medium containing 100 mg l(-1) chromate was reduced by only 23% and 34%, respectively, compared with growth in medium without added chromium . Streptomyces sp . strains R22 and R25 both accumulated chromium with yields of 10.0 and 5.6 mg Cr g(-1) of dry weight, respectively, and a chromate concentration of 50 mg ml(-1) . Cell fractionation studies with strain R22 showed that the great majority of the chromium were associated with the cell wall fraction . Streptomyces strains R22 and R25 may have applications in bioremediation of chromium contamination.

Sci Total Environ, 2001 Jul 2, 274(1-3), 137 - 49
Towards environmental toxicogenomics -- development of a flow-through, high-density DNA hybridization array and its application to ecotoxicity assessment; Fredrickson HL et al.; Assessment of the environmental hazard posed by soils/sediments containing low to moderate levels of contaminants using standard analytical chemical methods is uncertain due (in part) to a lack of information on contaminant bioavailability, the unknown interactive effects of contaminant mixtures, our inability to determine the species of a metal in an environmental matrix, and the relative sensitivity of bioassay species . Regulatory agencies compensate for this uncertainty by lowering cleanup goals, but in this process they effectively exclude otherwise attractive cleanup options (i.e . bioremediation) . Direct evaluations of soil and sediment toxicity preclude uncertainty from most of these sources . However, the time and cost of chronic toxicity tests limits their general application to higher levels of tiered toxicity assessments . Transcriptional level (mRNA) toxicity assessments offer great advantages in terms of speed, cost and sample throughput . These advantages are currently offset by questions about the environmental relevance of molecular level responses . To this end a flow-through, high-density DNA hybridization array (genosensor) system specifically designed for environmental risk assessment was developed . The genosensor is based on highly regular microchannel glass wafers to which gene probes are covalently bound at discrete (200-microm diameter spot) and addressable (250-microm spot pitch) locations . The flow-through design enables hybridization and washing times to be reduced from approximately 18 h to 20 min . The genosensor was configured so that DNA from 28 environmental samples can be simultaneously hybridized with up to 64 different gene probes . The standard microscopic slide format facilitates data capture with most automated array readers and, thus high sample throughput (> 350 sample/h) . In conclusion, hardware development for molecular analysis is enabling very tractable means for analyzing RNA and DNA . These developments have underscored the need for further developmental work in probe design software, and the need to relate transcriptional level data to whole-organism toxicity indicators.

Crit Rev Microbiol, 2001, 27(2), 133 - 66
Enzymes and operons mediating xenobiotic degradation in bacteria; Mishra V et al.; Aromatic hydrocarbons constitute a major group of environmental pollutants . Bioremediation appears to be the only viable alternative for large-scale decontamination . A number of bacteria have been identified that can degrade a variety of xenobiotics . Extensive studies of the enzymes and genes involved in degradation of aromatic hydrocarbons have revealed that the degradative enzymes could be broadly grouped into two major categories, peripheral and ring-cleavage enzymes . The peripheral enzymes are the ones that catabolize the pollutants initially to a metabolite that is further degraded . A majority of peripheral enzymes are oxygenases that hydroxylate the aromatic compounds, rendering them susceptible to the enzymes of ring-cleavage pathway . The genes of ring-cleavage enzymes have been shown to be highly conserved between different bacterial species . Presently, a number of constraints limit the use of available strains for efficient bioremediation . This review describes the enzymes and genes involved in xenobiotic degradation and underscores the importance of understanding the expression and regulation of genes encoding peripheral enzymes and their intelligent manipulation using recombinant DNA technology for efficient degradation of aromatic compounds.

Arch Environ Contam Toxicol, 2001 Apr, 40(3), 311 - 7
Immunotoxicity of explosives-contaminated soil before and after bioremediation; Beltz LA et al.; Soils from the Yorktown Naval Base contaminated with trinitrotoluene (TNT) and other explosives were used to prepare eluates before and after bioremediation using microbial growth amendments in the presence (P1 eluates) or absence (P2 eluates) of exogenous white rot fungus . Effectiveness of bioremediation was examined by several immunotoxicity assays-viability/growth of lymphocytes, cytokine production, and expression of the interleukin-2 (IL-2) receptor-using human peripheral blood mononuclear cells exposed to the eluates . Although TNT concentrations decreased in both P1 and P2 eluates relative to untreated baseline soil (BL) eluates, a recovery in lymphocyte growth/viability and IL-2 secretion was seen with P2 but not P1 eluates relative to BL eluates . IL-2 receptor levels were higher in cells exposed to BL and P2 eluates than when exposed to P1 eluates . Interferon-gamma, tumor necrosis factor-beta, and IL-10 levels were highest in BL and P2 eluates and lowest in P1 eluates . Taken together, these results suggest that treatment of the soil with microbial growth amendments in the absence but not the presence of exogenous white rot fungi lead to partial bioremediation as assessed by lymphocyte functions.

Biodegradation, 2000, 11(2-3), 171 - 86
Aerobic MTBE biodegradation: an examination of past studies, current challenges and future research directions; Deeb RA et al.; With the current practice of amending gasoline with up to 15% by volume MTBE, the contamination of groundwater by MTBE has become widespread . As a result, the bioremediation of MTBE-impacted aquifers has become an active area of research . A review of the current literature on the aerobic biodegradation of MTBE reveals that a number of cultures from diverse environments can either partially degrade or completely mineralize MTBE . MTBE is either utilized as a sole carbon and energy source or is degraded cometabolically by cultures grown on alkanes . Reported degradation rates range from 0.3 to 50 mg MTBE/g cells/h while growth rates (0.01-0.05 g MTBE/g cells/d) and cellular yields (0.1-0.2 g cells/g MTBE) are generally low . Studies on the mechanisms of MTBE degradation indicate that a monooxygenase enzyme cleaves the ether bond yielding tert-butyl alcohol (TBA) and formaldehyde as the dominant detectable intermediates . TBA is further degraded to 2-methyl-2-hydroxy-1-propanol, 2-hydroxyisobutyric acid, 2-propanol, acetone, hydroxyacteone and eventually, carbon dioxide . The majority of these intermediates are also common to mammalian MTBE metabolism . Laboratory studies on the degradation of MTBE in the presence of gasoline aromatics reveal that while degradation rates of other gasoline components are generally not inhibited by MTBE, MTBE degradation could be inhibited in the presence of more easily biodegradable compounds . Controlled field studies are clearly needed to elucidate MTBE degradation potential in co-contaminant plumes . Based on the reviewed studies, it is likely that a bioremediation strategy involving direct metabolism, cometabolism, bioaugmentation, or some combination thereof, could be applied as a feasible and cost-effective treatment method for MTBE contamination.

Biodegradation, 2000, 11(2-3), 125 - 39
Metabolic indicators for detecting in situ anaerobic alkylbenzene degradation; Beller HR; Monitoring programs for intrinsic bioremediation of fuel hydrocarbons require indicators that can convincingly demonstrate in situ metabolism . In this evaluation of potential indicators of in situ anaerobic alkylbenzene metabolism, laboratory and field data are reviewed for two classes of aromatic acids: (i) benzylsuccinate, E-phenylitaconate, and their methyl homologs, and (ii) benzoate, and methyl-, dimethyl-, and trimethylbenzoates . The review includes previously unpublished field data from a hydrocarbon-contaminated site in Fallon (Nevada), at which both classes of metabolites were detected in groundwater . The two classes of compounds were evaluated with respect to specificity (i.e., unique biochemical relationship to a specific alkylbenzene), stability, and generation as degradation intermediates versus dead-end products; recent developments in the biochemistry of anaerobic toluene and xylene degradation were incorporated in this evaluation . In general, benzylsuccinates/E-phenylitaconates are superior to benzoates in terms of their very high specificity to their parent hydrocarbons and their lack of commercial and industrial sources . They are also uniquely indicative of anaerobic conditions . All of the benzoates, benzylsuccinates, and E-phenylitaconates are relatively stable chemically and (with the exception of benzoate) biologically under anaerobic conditions, based on the limited data available . Although benzoate, benzylsuccinate, and E-phenylitaconate are intermediates of anaerobic toluene mineralization to carbon dioxide, their methyl homologs can be either mineralization intermediates or cometabolic dead-end products of alkylbenzenes, depending on the bacteria involved . Benzoates are far more commonly reported in field studies of hydrocarbon-contaminated aquifers than are benzylsuccinates and E-phenylitaconates, although it is not clear whether this is an accurate representation of the relative occurrence of these metabolites at contaminated sites, or whether it instead reflects the limited range of target analytes used in most field studies to date.

Angew Chem Int Ed Engl, 2001 Jun 18, 40(12), 2204 - 2222
Protein Crystals as Novel Catalytic Materials; Margolin AL et al.; In this era of molecular biology, protein crystallization is often considered to be a necessary first step in obtaining structural information through X-ray diffraction analysis . In a different light, protein crystals can also be thought of as materials, whose chemical and physical properties make them broadly attractive and useful across a larger spectrum of disciplines . The full potential of these protein crystalline materials has been severely restricted in practice, however, both by their inherent fragility, and by strongly held skepticism concerning their routine and predictable growth, formulation, and practical application . Fortunately, these problems have turned out to be solvable . A systematic exploration of the biophysics and biochemistry of protein crystallization has shown that one can dependably create new protein crystalline materials more or less at will . In turn, these crystals can be readily strengthened, both chemically and mechanically, to make them suitable for practical commercialization . Today, these novel materials are used as industrial catalysts on a commercial scale, in bioremediation and "green chemistry" applications, and in enantioselective chromatography of pharmaceuticals and fine chemicals . In the near future, their utility will expand, to include the purification of protein drugs, formulation of direct protein therapeutics, and development of adjuvant-less vaccines.

J Environ Monit, 2001 Jun, 3(3), 274 - 80
Bioremediation of an area contaminated by a fuel spill; Vallejo B et al.; In order to decontaminate a large area of restricted access contaminated by a fuel spill, laboratory and field studies were developed in two steps: (a) monitoring of the laboratory experiment on bacterial growth under aerobic and anaerobic conditions with and without addition of nutrients; and (b) use of the best conditions obtained in (a) for the decontamination of the soil . A hydraulic barrier was installed both to clean the aquifer and to avoid migration of hydrocarbons as a consequence of their solution in the groundwater and subsequent displacement . The objective was to create an ideal environment for the treatment of the affected area that favoured the growth of the indigenous bacteria (Pseudomonas and Arthrobacter) that biodegrade the hydrocarbons . Monitoring of the changes in the total concentration of petroleum hydrocarbons in the soil subjected to bacterial action was performed by gas chromatography . In a field study, the progress of biodegradation of hydrocarbons was evaluated in situ by changes in subsurface CO2/O2 levels by means of an analyser equipped with an infrared detector . Biostimulation and oxygen were the most influential factors for the biodegradation of the hydrocarbons . The use of bioventing of the soil was shown as an excellent technology to promote in situ bioremediation of the polluted area.

J Environ Monit, 2001 Jun, 3(3), 267 - 73
Environmental monitoring in soil contamination and remediation programs: how practitioners are using the Internet to share knowledge; Guerin TF; Internet listservers provide a means for professionals from all sectors of the industry and profession, to communicate and collaborate with each other, as well as other stakeholders (e.g., suppliers, academics, the general public and community members) in real time . This article highlights key Internet listservers in the field of environmental monitoring in soil contamination and remediation and how to subscribe to them . The most active and relevant listservers for environmental scientists, technologists and professionals in the soil contamination and remediation profession are the Bioremediation Discussion Group (BioGroup), Phytonet, Phytoremediation listserver, Groundwater listserver and Environmental Forensics listserver . Other observations and lessons so far from the use of Internet listservers are: (i) that moderators provide an important role in maintaining the level of quality and participation, (ii) do not underestimate the knowledge base held within these, and (iii) if not selected and managed properly, e-mail from listservers can generate an excess of e-mail and waste time.

Huan Jing Ke Xue, 2001 Mar, 22(2), 101 - 5
{Modeling research about bioremediation of organic pollutants in soil-water-microbes system}; Liu L et al.; A new Theory, organic pollutant sequestration inside soil particles, was applied in the research in order to explain the persistence of residual chemicals in remediation sites . Based on this theory, a mathematical model which simulates organic pollutant bioremediation process in soil-water-microbes system was developed . In the model, diffusion is represented by Fick's second law, reversible sorption-desorption by a linear isotherm, irreversible sequestration by a pseudo-first order kinetics, and biodegradation by Monod kinetics . Model results match successfully with experimental data . Model simulations are performed in the study . It is noteworthy that the mathematical model will be useful in quantitatively predicting the time and degradation extend of organic pollutant in remediation sites.

Yi Chuan Xue Bao, 2001, 28(6), 583 - 8
{Cloning and fusion expression of detoxifying gene in Escherichia coli}; Huang J et al.; In insects, esterases play an important role in the degradation of organophosphate (OP) and Carbamate (CB) insecticides . The ability of esterase B1 to degrading OP and CB insecticides opens broad prospect of using it in programs to the insecticide pollution . OPs can be detoxified by hydrolysis of their phosphoester bonds, pyrethroids and some OPs like malathion, by hydrolysis of their carboxylester bonds, and diverse carbamate insecticides, herbicides and fungicides by hydrolysis of amide or other similar bonds . Most of the candidate bioremediation enzymes identified to date have been hydrolases . In recent years, we have focused our work on the transfer of a detoxifying esterase B1 gene from mosquito into E . coli and explored the possibility of using the detoxified enzymes in environmental protection . 5' initial of esterase B1 cDNA was cloned by RT-PCR and sequenced consequently . After the combination of 5' initial and 3' terminal fragment of esterase B1 cDNA, the recombinant vector pET-ESTB1 was constructed and transformed into E . coli BL21 . A 60 kD protein was induced by IPTG and its expression was temperature-dependent . After 12 h induction, the target protein occupied 27% of the total protein . A pure recombinant protein was obtained by purification, and was detected with 10% SDS-PAGE . The results showed that 22.1% of malathion was degraded by crude detoxification enzyme in 15 mins, demonstrated a high degradation property . This research provides a novel approach, which takes the advantages of eucaryotes for bioremediation of pesticide pollutions.

Cytometry, 2001 Jul 1, 44(3), 179 - 87
An industrial application of multiparameter flow cytometry: assessment of cell physiological state and its application to the study of microbial fermentations; Hewitt CJ et al.; BACKGROUND: When using traditional microbiological techniques to monitor cell proliferation and viability, stressed, sublethally injured, or otherwise "viable but nonculturable" cells often go undetected . Because of this, such cells often are not considered by mathematical models used to predict bioprocess performance on scale-up and inaccuracies result . Therefore, analytical techniques, decoupled from postsampling growth, are desirable to rapidly monitor individual cell physiologic states during microbial fermentations . METHODS: Microbial cells, including Escherichia coli, Rhodococus sp., and Sacharomyces cerevisiae, were taken at various stages from a range of fermentation processes and stained with one of three mixtures of fluorescent stains: rhodamine 123/propidium iodide, bis-oxonol/propidium iodide, or bis-oxonol/ethidium bromide/propidium iodide . An individual cell's physiologic state was assessed with a Coulter Epics Elite analyzer based on the differential uptakes of these fluorescent stains . RESULTS: It was possible to resolve an individual cell's physiologic state beyond culturability based on the functionality of dye extrusion pumps and the presence or absence of an intact polarized cytoplasmic membrane, enabling assessment of population heterogeneity . This approach allows the simultaneous differentiation of at least four functional subpopulations in microbial populations . CONCLUSIONS: Fluorescent staining methods used in our laboratories have led to a functional classification of the physiological state of individual microbial cells based on reproductive activity, metabolic activity, and membrane integrity . We have used these techniques extensively for monitoring the stress responses of microorganisms in such diverse areas as bioremediation, biotransformation, food processing, and microbial fermentation; microbial fermentation is discussed in this article .

Appl Environ Microbiol, 2001 Jul, 67(7), 3180 - 7
Development of a genetic system for Geobacter sulfurreducens; Coppi MV et al.; Members of the genus Geobacter are the dominant metal-reducing microorganisms in a variety of anaerobic subsurface environments and have been shown to be involved in the bioremediation of both organic and metal contaminants . To facilitate the study of the physiology of these organisms, a genetic system was developed for Geobacter sulfurreducens . The antibiotic sensitivity of this organism was characterized, and optimal conditions for plating it at high efficiency were established . A protocol for the introduction of foreign DNA into G . sulfurreducens by electroporation was also developed . Two classes of broad-host-range vectors, IncQ and pBBR1, were found to be capable of replication in G . sulfurreducens . In particular, the IncQ plasmid pCD342 was found to be a suitable expression vector for this organism . When the information and novel methods described above were utilized, the nifD gene of G . sulfurreducens was disrupted by the single-step gene replacement method . Insertional mutagenesis of this key gene in the nitrogen fixation pathway impaired the ability of G . sulfurreducens to grow in medium lacking a source of fixed nitrogen . Expression of the nifD gene in trans complemented this phenotype . This paper constitutes the first report of genetic manipulation of a member of the Geobacter genus.

Appl Environ Microbiol, 2001 Jul, 67(7), 3149 - 60
Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site; Chang YJ et al.; Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites . To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites . In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated . Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis . A remarkable diversity among the DSR sequences was revealed, including sequences from delta-Proteobacteria, gram-positive organisms, and the Nitrospira division . PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0 . Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected . Those belonging to SRB within delta-Proteobacteria were mainly recovered from low-uranium (< or =302 ppb) samples . One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites . Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001) . This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium . The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research.

Appl Environ Microbiol, 2001 Jul, 67(7), 3127 - 33
Bioremediation (natural attenuation and biostimulation) of diesel-oil-contaminated soil in an alpine glacier skiing area; Margesin R et al.; We investigated the feasibility of bioremediation as a treatment option for a chronically diesel-oil-polluted soil in an alpine glacier area at an altitude of 2,875 m above sea level . To examine the efficiencies of natural attenuation and biostimulation, we used field-incubated lysimeters (mesocosms) with unfertilized and fertilized (N-P-K) soil . For three summer seasons (July 1997 to September 1999), we monitored changes in hydrocarbon concentrations in soil and soil leachate and the accompanying changes in soil microbial counts and activity . A significant reduction in the diesel oil level could be achieved . At the end of the third summer season (after 780 days), the initial level of contamination (2,612 +/- 70 microg of hydrocarbons g {dry weight} of soil(-1)) was reduced by (50 +/- 4)% and (70 +/- 2)% in the unfertilized and fertilized soil, respectively . Nonetheless, the residual levels of contamination (1,296 +/- 110 and 774 +/- 52 microg of hydrocarbons g {dry weight} of soil(-1) in the unfertilized and fertilized soil, respectively) were still high . Most of the hydrocarbon loss occurred during the first summer season ({42 +/- 6}% loss) in the fertilized soil and during the second summer season ({41 +/- 4}% loss) in the unfertilized soil . In the fertilized soil, all biological parameters (microbial numbers, soil respiration, catalase and lipase activities) were significantly enhanced and correlated significantly with each other, as well as with the residual hydrocarbon concentration, pointing to the importance of biodegradation . The effect of biostimulation of the indigenous soil microorganisms declined with time . The microbial activities in the unfertilized soil fluctuated around background levels during the whole study.

J Ind Microbiol Biotechnol, 1999 Oct, 23(4-5), 347 - 352
5-Chloropicolinic acid is produced by specific degradation of 4-chlorobenzoic acid by Sphingomonas paucimobilis BPSI-3; Davison AD et al.; We have previously shown that the bacterium Sphingomonas paucimobilis BPSI-3, isolated from PCB-contaminated soil, can degrade halogenated biphenyls, naphthalenes, catechols and benzoic acids . However, before such an organism can be used in bioremediation, it is important to characterise the degradation products and determine the degradation pathways to ensure that compounds more toxic or mobile than the original contaminants are not produced . In the degradation of 4-chlorobiphenyl, S . paucimobilis BPSI-3 produces a novel chlorinated picolinic acid . In this paper, we show that 4-chlorobenzoate is an intermediate in this degradation and, through (15)N-labelling, that 5-chloropicolinate is the only nitrogenous metabolite isolated under the extraction conditions used . The position of the chlorine indicates that degradation of 4-chlorocatechol occurs exclusively via a 2,3-extradiol cleavage . These data allow us to postulate a more definitive catabolic pathway for the biodegradation of 4-chlorobiphenyl to 5-chloro-2-hydroxymuconic acid semialdehyde via 4-chlorobenzoate in S . paucimobilis BPSI-3.

Curr Opin Biotechnol, 2001 Jun, 12(3), 237 - 41
Microorganisms relevant to bioremediation; Watanabe K; Naturally occurring microbial consortia have been utilized in a variety of bioremediation processes . Recent developments in molecular microbial ecology offer new tools that facilitate molecular analyses of microbial populations at contaminated and bioremediated sites . Information provided by such analyses aids in the evaluation of the effectiveness of bioremediation and the formulation of strategies that might accelerate bioremediation.

Appl Microbiol Biotechnol, 2001 May, 55(4), 510 - 4
Decolorization of molasses spent wash by the white-rot fungus Flavodon flavus, isolated from a marine habitat; Raghukumar C et al.; Flavodon flavus (Klotzsch) Ryvarden, a basidiomycete (NIOCC strain 312) isolated from decomposing leaves of a sea grass, decolorized pigments in molasses spent wash (MSW) by 80% after 8 days of incubation, when used at concentrations of 10% and 50% . Decolorizing activity was also present in media prepared with half-strength seawater (equivalent to 15 ppt salinity) . Decolorizing activity was seen in low-nitrogen medium, nutrient-rich medium and in sugarcane bagasse medium . The percentage decolorization of MSW was highest when glucose or sucrose was used as the carbon source in the low-nitrogen medium . The production of lignin-modifying enzymes, manganese-dependent peroxidase (MNP) and laccase decreased in a medium containing MSW . MNP production and MSW decolorization were inversely correlated, suggesting no role for MNP in MSW decolorization . The decolorization of MSW was not effective when F . flavus was immobilized in calcium alginate beads . Decolorization was achieved best in oxygenated cultures . Besides color, total phenolics and chemical oxygen demand were reduced by 50% in MSW treated with F . flavus, suggesting its potential in the bioremediation of effluents.

Environ Int, 2001 May, 26(5-6), 409 - 11
Bioremediation of oil sludge-contaminated soil; Vasudevan N et al.; Bioremediation has become an important method for the restoration of oil-polluted environments by the use of indigenous or selected microbial flora . Several factors such as aeration, use of inorganic nutrients or fertilizers and the type of microbial species play a major role in the remediation of oil-contaminated sites . Experiments were undertaken for bioremediation of oil sludge-contaminated soil in the presence of a bacterial consortium, inorganic nutrients, compost and a bulking agent (wheat bran) . Experiments were conducted in glass troughs for the 90-day period . Bulked soil showed more rapid degradation of oil compared to all other amendments . During the experimental period, wheat bran-amended soil showed 76% hydrocarbon removal compared to 66% in the case of inorganic nutrients-amended soil . A corresponding increase in the number of bacterial populations was also noticed . Addition of the bacterial consortium in different amendments significantly enhanced the removal of oil from the petroleum sludge from different treatment units.

Water Sci Technol, 2001, 43(5), 341 - 8
Effects of subsurface heterogeneity on natural bioremediation at a gasoline spill site; Kao CM et al.; A test cell of 3-m by 6-m located at the mid-point of a gasoline spill site was selected to test the hypothesis that the rate of hydrocarbon biodegradation is influenced by the spatial distribution of the electron acceptors, aqueous geochemistry, and microbial population . Multilevel samplers (MLSs) were installed at four corners of the test cell for groundwater sampling . Sampling ports were placed at 0.3-m intervals from 1.5 to 4.8 m below land surface (bls) . A 0.91-m by 12.7-cm sediment core (from 3.3 to 4.2 m bls) in the center of the MLSs was collected . The core was cut into 7 sections, and each was used for sediment extractions, microbial enumeration, grain size distribution, and microcosm studies . Groundwater analytical results indicate that iron reduction was the dominant biodegradation process within this test cell . Iron-reducing process caused the preferential removal of certain compounds . Microbial enumeration results show that the distribution of microbial population varied with depth and sediment materials . Lower microbial population was observed in those sections with higher portion of clayey materials . The less permeable materials would limit the bacterial transport, decrease the bioavailability of Fe(III) to iron-reducing bacteria, and thus cause the low biodegradation activity . Results suggest that using blended sediments for biodegradation rate measurements may provide misleading results.

Curr Opin Microbiol, 2001 Jun, 4(3), 307 - 12
Microbial nitrogen cycles: physiology, genomics and applications; Ye RW et al.; Genes and pathways involved in inorganic nitrogen cycles have been found in traditional as well as unusual microorganisms . These pathways or enzymes play a very important role in the adaptation or survival of these microorganisms under a variety of environmental conditions . Microbial nitrogen metabolism has industrial applications ranging from wastewater treatment to bioremediation and potential future use in biocatalysis for chemical production.

Chemosphere, 2001 Jun, 43(8), 1085 - 94
Prediction of complete bioremediation periods for PAH soil pollutants in different physical states by mechanistic models; Mulder H et al.; Mass-transfer models and biodegradation models were developed for three theoretical physical states of polycyclic aromatic hydrocarbons (PAHs) in soil . These mechanistic models were used to calculate the treatment periods necessary for complete removal of the PAH pollutants from the soil under batch conditions . Results indicate that the bioremediation of PAHs in such systems is mainly mass-transfer limited . The potential for bioremediation as a treatment technique for PAH contaminated soils is therefore mainly determined by the mass-transfer dynamics of PAHs . Under mass-transfer limited conditions simplified mathematical models, based on the assumption of a zero dissolved PAH concentrations, can be used to predict the period of time needed for complete bioremediation.

Water Res, 2001 Jun, 35(9), 2145 - 52
A field evaluation of in situ biodegradation of trichloroethylene through methane injection; Eguchi M et al.; A field study of biodegradation of trichloroethylene (TCE) through methane injection was conducted at the yard of a home in Japan . Methane was selected as the safest substrate for injection into groundwater . Methane, oxygen, nitrate, and phosphate were introduced into groundwater contaminated with 220 microg/L of TCE . After a week of biostimulation, methane concentrations gradually decreased below the detection limit . Methane oxidizing bacterial numbers increased from 10 to 10(4) cells/mL with methane consumptions . During methane injection . 10-20% of TCE removal was observed . The biotransformation yield was 3-13 mgTCE/gCH4 in this field test . After methane injections were stopped, TCE removal was not observed . These results indicated that bioremediation using methane was useful as a safe technology for a TCE-contaminated area near homes.

FEMS Microbiol Rev, 2001 May, 25(3), 335 - 47
Interactions of chromium with microorganisms and plants; Cervantes C et al.; Chromium is a highly toxic non-essential metal for microorganisms and plants . Due to its widespread industrial use, chromium (Cr) has become a serious pollutant in diverse environmental settings . The hexavalent form of the metal, Cr(VI), is considered a more toxic species than the relatively innocuous and less mobile Cr(III) form . The presence of Cr in the environment has selected microbial and plant variants able to tolerate high levels of Cr compounds . The diverse Cr-resistance mechanisms displayed by microorganisms, and probably by plants, include biosorption, diminished accumulation, precipitation, reduction of Cr(VI) to Cr(III), and chromate efflux . Some of these systems have been proposed as potential biotechnological tools for the bioremediation of Cr pollution . In this review we summarize the interactions of bacteria, algae, fungi and plants with Cr and its compounds.

Environ Sci Technol, 2001 Apr 1, 35(7), 1420 - 4
Enhancement of orimulsion biodegradation through the addition of natural marine carbon substrates; Proctor LM et al.; Orimulsion is a bitumen-based heavy fuel that is a less expensive alternative to traditional fuel oils . However, because its density is intermediate between that of freshwater and seawater, in the event of a spill, the fuel could strand in the sediments . Previous work indicated that only 0.6-2.7% of the bitumen would degrade in long incubations of marine sediments . We added various natural carbon substrates to stimulate the degradation of bitumen by native populations of benthic bacteria . The concentration and carbon isotopic signature of the respired carbon dioxide was measured to partition the substrates that supported bacterial respiration . We found that the addition of seagrass and pinfish stimulated the degradation of bitumen by as much as 2-9-fold relative to incubations without these substrates . Biodegradation of bitumen may be enhanced by the addition of natural marine carbon substrates and may be a useful approach for bioremediation . Preadaptation of the bacteria to bitumen did not significantly enhance their ability to degrade it.

Environ Sci Technol, 2001 Jan 15, 35(2), 261 - 9
Stable carbon isotope evidence for intrinsic bioremediation of tetrachloroethene and trichloroethene at area 6, Dover Air Force Base; Sherwood Lollar B et al.; Area 6 at Dover Air Force Base (Dover, DE) has been the location of an in-depth study by the RTDF (Remediation Technologies Development Forum Bioremediation of Chlorinated Solvents Action Team) to evaluate the effectiveness of natural attenuation of chlorinated ethene contamination in groundwater . Compound-specific stable carbon isotope measurements for dissolved PCE and TCE in wells distributed throughout the anaerobic portion of the plume confirm that stable carbon isotope values are isotopically enriched in 13C consistent with the effects of intrinsic biodegradation . During anaerobic microbial reductive dechlorination of chlorinated hydrocarbons, the light (12C) versus heavy isotope (13C) bonds are preferentially degraded, resulting in isotopic enrichment of the residual contaminant in 13C . To our knowledge, this study is the first to provide definitive evidence for reductive dechlorination of chlorinated hydrocarbons at a field site based on the delta13C values of the primary contaminants spilled at the site, PCE and TCE . For TCE, downgradient wells show delta13C values as enriched as -18.0/1000 as compared to delta13C values for TCE in the source zone of -25.0 to -26.0/1000 . The most enriched delta13C value on the site was observed at well 236, which also contains the highest concentrations of cis-DCE, VC, and ethene, the daughter products of reductive dechlorination . Stable carbon isotope signatures are used to quantify the relative extent of biodegradation between zones of the contaminant plume . On the basis of this approach, it is estimated that TCE in downgradient well 236 is more than 40% biodegraded relative to TCE in the proposed source area.

Ground Water, 2001 May-Jun, 39(3), 422 - 32
Travel-time based model of bioremediation using circulation wells; Cirpka OA et al.; Vertical circulation wells can efficiently provide microorganisms with substrates needed for enhanced bioremediation . We present a travel-time based approach for modeling bioreactive transport in a flow field caused by a series of circulation wells . Mixing within the aquifer is due to the differences in sorption behavior of the reactants . Neglecting local dispersion, transport simplifies to a single one-dimensional problem with constant coefficients for each well . Recirculation is characterized by the discharge densities over travel time . We apply the model to the stimulation of cometabolic dechlorination of trichloroethene (TCE) by alternate injection of oxygen and toluene into the circulation wells . Mixing within the wells can be minimized by interposing sufficiently long breaks between the oxygen and toluene pulses . In our simulation, the proposed injection scheme stimulates biomass growth without risking biofouling of the aquifer.

Environ Toxicol Chem, 2001 May, 20(5), 965 - 71
Potential of activated carbon to decrease 2,4,6-trinitrotoluene toxicity and accelerate soil decontamination; Vasilyeva GK et al.; Activated carbon can be used to decrease 2,4,6-trinitrotoluene (TNT) toxicity and promote bioremediation of highly contaminated soil . Adding activated carbon at 0.25, 0.75, and 1.0% (w/w) to Sharpsburg soil contaminated with 500, 1,000, and 2,000 mg TNT/kg decreased concentrations of TNT and its transformation products in soil solution to 5 mg/L or less, resulting in low toxicity to corn plants (Zea mays L.) and soil microorganisms . As much as 50% of the added TNT was rapidly bound to the soil-activated carbon matrix . Simultaneous accumulation of 2,4,6-trinitrobenzaldehyde (TNBAld) indicated that the activated carbon promoted oxidation of TNT . Some of the TNBAld was further oxidized to 1,3,5-trinitrobenzene, followed by reduction to 3,5-dinitroaniline . Reversibly bound TNT was gradually transformed to 2-amino-4,6-dinitrotoluene and 4-amino-2,6-dinitrotoluene, and both were bound to the soil-activated carbon matrix . The transformation and binding of TNT to soil were further promoted by incorporating shredded corn plants after growing for 52 d in the activated carbon-amended soil . After 120 d, these amendments reduced extractable TNT and transformation products by 91% in soil containing 2,000 mg TNT/kg, compared to 55% in unamended soil . These results demonstrate the potential use of activated carbon in combination with plants to promote in situ bioremediation of soils highly contaminated with explosives.

Water Res, 2001 Jun, 35(8), 1951 - 60
Application of microbial enumeration technique to evaluate the occurrence of natural bioremediation; Kao CM et al.; Natural bioremediation is believed to be the major processes that account for both containment of the petroleum-hydrocarbon plume and reduction of the contaminant concentrations . In this study, the feasibility of applying the microbial enumeration technique was assessed for natural biodegradation evaluation at three selected gasoline spill sites . At each site, two monitor wells were installed along the groundwater flow, and one multilevel sampler (MLS) was installed to delineate the vertical distribution of the contaminant plume . Two continuous soil cores were collected at each site to evaluate the horizontal distribution of the microbial activity . Soil samples were used for microbial enumeration, grain-size distribution analysis, and sediment extraction . In situ tracer study was performed using 1,2,4-trimethylbenzene (1,2,4-TMB) as the tracer to study the efficiency of contaminant biodegradation . Investigation results demonstrate the agreement between microbial enumeration and other evaluation techniques for natural bioremediation (e.g., geochemical indicator analysis, tracer study) . Results suggest that the microbial enumeration is useful in assessing the occurrence, efficiency, and status of the bioremediation . Because this technique provides insight into factors controlling contaminant biodegradation, it could be performed as the supplemental method for natural bioremediation evaluation at petroleum-hydrocarbon spill sites.

Appl Microbiol Biotechnol, 2001 Mar, 55(2), 248 - 53
Diversity in kinetics of trichloroethylene-degrading activities exhibited by phenol-degrading bacteria; Futamata H et al.; Whole-cell kinetics of phenol- and trichloroethylene (TCE)-degrading activities expressed by 13 phenol-degrading bacteria were analyzed . The Ks (apparent affinity constant in Haldane's equation) values for TCE were unexpectedly diverse, ranging from 11 microM to over 800 microM . The Vmax/Ks values for phenol were three orders of magnitude higher than the values for TCE in all bacteria analyzed, suggesting that these bacteria preferentially degrade phenol rather than TCE . A positive correlation between Ks for phenol and Ks for TCE was found, i.e., bacteria exhibiting high Ks values for phenol showed high Ks values for TCE, and vice versa . A comparison of the Ks values allowed grouping of these bacteria into three types, i.e., low-, moderate- and high-Ks types . Pseudo-first-order degradation-rate constants for TCE at 3.8 microM were found to be adequate to rapidly discriminate among the three types of bacteria . When bacteria were grown on phenol at the initial concentration of 2 mM, Comamonas testosteroni strain R5, a representative of low-Ks bacteria, completely degraded TCE at 3.8 microM, while strain P-8, a representative of high-Ks bacteria, did not . A mixed culture of these two bacteria poorly degraded TCE under the same conditions, where P-8 outgrew R5 . These results suggest that low-Ks bacteria should be selectively grown for effective bioremediation of TCE-contaminated groundwater.

Lett Appl Microbiol, 2001 May, 32(5), 340 - 5
Application of resazurin for estimating abundance of contaminant-degrading micro-organisms; Guerin TF et al.; AIMS: The aim of the current study was to test whether resazurin changed colour when incubated with a range of organic chemicals used as growth substrates in bioremediation studies and to determine whether resazurin was more effective in estimating microbial growth than turbidity alone (i.e . no resazurin) or use of the dye, methylene blue . METHODS AND RESULTS: Resazurin was incubated with a range of organic chemicals that were used as substrates in an MPN assay . Only 1,2-dichlorobenzene, 2,4-D, glycol sulphite and sulphinol reacted to generate false positives . Resazurin was also used to estimate micro-organisms in a series of bioremediation studies . CONCLUSION: The results showed that resazurin was more sensitive than methylene blue or turbidity alone as an indicator of microbial growth . SIGNIFICANCE AND IMPACT OF THE STUDY: The significance of the current study is that resazurin should be used in MPN assays for estimating contaminant-degrading micro-organisms instead of turbidity alone or other dyes such as methylene blue.

Environ Microbiol, 2001 Mar, 3(3), 187 - 93
Bacterial populations occuring in a trichloroethylene-contaminated aquifer during methane injection; Baker P et al.; Soil core samples were obtained from a trichloroethylene (TCE)-contaminated aquifer before and after the start of methane biostimulation . DNA was extracted directly from the soil samples, and denaturing gradient gel electrophoresis (DGGE) was used to analyse bacterial 16S ribosomal DNA fragments that were PCR amplified from these DNA samples . This analysis consistently detected two phylotypes in the methane-injected samples . These phylotypes were closely related to Methylobacter and Methylomonas, both belonging to type I methanotrophs . A competitive DGGE analysis using Methylosinus trichosporium OB3b cells as an internal quantitative standard showed that these populations accounted for 10(8)-10(9) cells g(-1) soil . These results showed that type I methanotrophs formed a significant proportion of the bacterial community during methane biostimulation . The implications of this finding for TCE bioremediation were discussed.

Appl Environ Microbiol, 2001 May, 67(5), 2139 - 44
Effects of alkylphosphates and nitrous oxide on microbial degradation of polycyclic aromatic hydrocarbons; Bogan BW et al.; We conducted a series of liquid-culture experiments to begin to evaluate the abilities of gaseous sources of nitrogen and phosphorus to support biodegradation of polycyclic aromatic hydrocarbons (PAHs) . Nutrients examined included nitrous oxide, as well as triethylphosphate (TEP) and tributylphosphate (TBP) . Cultures were established using the indigenous microbial populations from one manufactured gas plant (MGP) site and one crude oil-contaminated drilling field site . Mineralization of phenanthrene was measured under alternative nutrient regimes and was compared to that seen with ammoniacal nitrogen and PO(4) . Parallel cultures were used to assess removal of a suite of three- to five-ring PAHs . In summary, the abilities of the different communities to degrade PAH when supplemented with N(2)O, TEP, and TBP were highly variable . For example, in the MGP soil, organic P sources, especially TBP, supported a considerably higher degree of removal of low-molecular-weight PAHs than did PO(4); however, loss of high-molecular-weight compounds was impaired under these conditions . The disappearance of most PAHs was significantly less in the oil field soil when organophosphates were used . These results indicate that the utility of gaseous nutrients for PAH bioremediation in situ may be limited and will very likely have to be assessed on a case-by-case basis.

Folia Biol (Krakow), 2000, 48(3-4), 143 - 7
Microorganisms resistant to heavy metals and toxic chemicals as indicators of environmental pollution and their use in bioremediation; Riaz-ul-Haq et al.; Microorganisms present in water samples from various industrial effluents were analysed for their resistance to lead, chromium, and cadmium . The ability of these microorganisms to grow on or metabolize toxic hydrocarbons and pesticides was also checked . Microorganisms in samples from the steel and tanning industries were generally resistant to metal ions but were not capable of metabolizing toxic hydrocarbons . Conversely, microorganisms found in samples of pesticide and from the chemical industry were capable of metabolizing hydrocarbons and pesticides but were not much resistant to metal ions . Microorganisms from effluents of the paint industry and urban wastes were resistant to lead . A correlation between the population of microorganisms and the type of pollution was observed . Indigenous microorganism could be regarded as indicators of pollution and be used in various operations to resist, process, metabolize, and detoxify toxic industrial wastes.

J Contam Hydrol, 2001 Mar, 48(1-2), 1 - 21
Model coupling intraparticle diffusion/sorption, nonlinear sorption, and biodegradation processes; Karapanagioti HK et al.; Diffusion, sorption and biodegradation are key processes impacting the efficiency of natural attenuation . While each process has been studied individually, limited information exists on the kinetic coupling of these processes . In this paper, a model is presented that couples nonlinear and nonequilibrium sorption (intraparticle diffusion) with biodegradation kinetics . Initially, these processes are studied independently (i.e., intraparticle diffusion, nonlinear sorption and biodegradation), with appropriate parameters determined from these independent studies . Then, the coupled processes are studied, with an initial data set used to determine biodegradation constants that were subsequently used to successfully predict the behavior of a second data set . The validated model is then used to conduct a sensitivity analysis, which reveals conditions where biodegradation becomes desorption rate-limited . If the chemical is not pre-equilibrated with the soil prior to the onset of biodegradation, then fast sorption will reduce aqueous concentrations and thus biodegradation rates . Another sensitivity analysis demonstrates the importance of including nonlinear sorption in a coupled diffusion/sorption and biodegradation model . While predictions based on linear sorption isotherms agree well with solution concentrations, for the conditions evaluated this approach overestimates the percentage of contaminant biodegraded by as much as 50% . This research demonstrates that nonlinear sorption should be coupled with diffusion/sorption and biodegradation models in order to accurately predict bioremediation and natural attenuation processes . To our knowledge this study is unique in studying nonlinear sorption coupled with intraparticle diffusion and biodegradation kinetics with natural media.

J Air Waste Manag Assoc, 2000 Oct, 50(10), 1818 - 30
The fate of hydrogen peroxide as an oxygen source for bioremediation activities within saturated aquifer systems; Zappi M et al.; In situ bioremediation is an innovative technique for the remediation of contaminated aquifers that involves the use of microorganisms to remediate soils and groundwaters polluted by hazardous substances . During its application, this process may require the addition of nutrients and/or electron acceptors to stimulate appropriate biological activity . Hydrogen peroxide has been commonly used as an oxygen source because of the limited concentrations of oxygen that can be transferred into the groundwater using above-ground aeration followed by reinjection of the oxygenated groundwater into the aquifer or subsurface air sparging of the aquifer . Because of several potential interactions of H2O2 with various aquifer material constituents, its decomposition may be too rapid, making effective introduction of the H2O2 into targeted treatment zones extremely difficult and costly . Therefore, a bench-scale study was conducted to determine the fate of H2O2 within subsurface aquifer environments . The purpose of this investigation was to identify those aquifer constituents, both biotic and abiotic, that are most active in controlling the fate of H2O2 . The decomposition rates of H2O2 were determined using both equilibrated water samples and soil slurries . Results showed H2O2 decomposition to be effected by several commonly found inorganic soil components; however, biologically mediated catalytic reactions were determined to be the most substantial.

J Environ Qual, 2001 Mar-Apr, 30(2), 418 - 26
Removal of herbicides from liquid media by fungi isolated from a contaminated soil; Bordjiba O et al.; Fungi were isolated from soil samples corresponding to pesticide-contaminated soil (CS) and noncontaminated soil (NCS) in the Annaba vicinity (Algeria) and identified . The number of isolates obtained from CS and NCS were 263 and 288, respectively . The most frequent species (Aspergillus fumigatus, A . niger, A . terreus, Absidia corymbifera, and Rhizopus microsporus var microsporus) were not sensitive to the pesticides . The growth of the genus Trichoderma was inhibited by the pesticides, while genera Absidia and Fusarium were stimulated . The 53 species isolated were assayed for their ability to remove metribuzin from liquid medium . Only Botrytis cinerea from NCS and Sordaria superba and Absidia fusca from CS removed more than 50% of the compound after 5 d . Metamitron was very resistant . Among the 21 species tested, only Alternaria solani (from NCS), Drechslera australiensis (from CS and NCS), and Absidia fusca (from CS) reduced the concentration in the medium more than 10% (10-16%) . Twelve species were grown with linuron, seven of them were inefficient in removing this compound . The two strains of Sordaria macrospora yielded 22 to 25% depletion, while Botrytis cinerea depleted linuron almost completely . Among the 31 species assayed for their ability to eliminate metobromuron, Botrytis cinerea (from CS and NCS) depleted almost completely the chemical from the medium . Rhizopus oryzae and Absidia fusca from CS removed 40 and 47% of the compound, respectively . No systematic relationships were observed between the soil contamination and herbicide elimination capacities of soil fungi . Absidia fusca and Botrytis cinerea were particularly interesting for bioremediation purposes because they were able to transform efficiently three of the four compounds assayed.

Bioresour Technol, 2001 May, 78(1), 37 - 45
Three-dimensional outgrowth of a wood-rotting fungus added to a contaminated soil from a former gasworks site; Andersson BE et al.; The capability of wood-rotting fungi (WRF) to colonise contaminated soil is an important fungal characteristic in the development of WRF-based soil bioremediation, it is also important to have methods that monitor the presence of the WRF in the soil . In this lab-scale study, it was shown that it was possible to re-capture, localise and identify a brown-rot fungus, Antrodia vaillantii, after it has been inoculated into, and grown in, a contaminated soil from a former gasworks site . The three-dimensional outgrowth of A . vaillantii was monitored by allowing it to grow into fungicide-treated wood baits, temporarily placed in the soil . After two weeks, the baits were withdrawn from the soil and surface sterilised with hydrogen peroxide to favour fungi growing inside baits, i.e., A . vaillantii . After subsequent plating of baits on selective agar medium the presence of A . vaillantii was confirmed with PCR/RFLP . A . vaillantii was found to be viable throughout the 54 days long study and exhibited a surface growth pattern similar to other well-known cord-forming basidiomycetes . Firstly, the upper part of the soil closest to the place of inoculation was colonised, however, over a period of time, the area of colonisation spread deeper into the soil . The detection method employed in the current study gave a conservative estimate of the fungal proliferation and did not require extensive sampling . Its use could be applicable in both applied research, such as soil bioremediation, and in pure microbial ecology studies.

Biochemistry, 2001 Mar 6, 40(9), 2712 - 22
High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta; Benning MM et al.; Phosphotriesterase, isolated from the soil-dwelling bacterium Pseudomonas diminuta, catalyzes the detoxification of organophosphate-based insecticides and chemical warfare agents . The enzyme has attracted significant research attention in light of its possible employment as a bioremediation tool . As naturally isolated, the enzyme is dimeric . Each subunit contains a binuclear zinc center that is situated at the C-terminal portion of a "TIM" barrel motif . The two zincs are separated by approximately 3.4 A and coordinated to the protein via the side chains of His 55, His 57, His 201, His 230, Asp 301, and a carboxylated Lys 169 . Both Lys 169 and a water molecule (or hydroxide ion) serve to bridge the two zinc ions together . Interestingly, these metals can be replaced with cadmium or manganese ions without loss of enzymatic activity . Here we describe the three-dimensional structures of the Zn(2+)/Zn(2+)-, Zn(2+)/Cd(2+)-, Cd(2+)/Cd(2+)-, and Mn(2+)/Mn(2+)-substituted forms of phosphotriesterase determined and refined to a nominal resolution of 1.3 A . In each case, the more buried metal ion, referred to as the alpha-metal, is surrounded by ligands in a trigonal bipyramidal ligation sphere . For the more solvent-exposed or beta-metal ion, however, the observed coordination spheres are either octahedral (in the Cd(2+)/Cd(2+)-, Mn(2+)/Mn(2+)-, and the mixed Zn(2+)/Cd(2+)-species) or trigonal bipyramidal (in the Zn(2+)/Zn(2+)-protein) . By measuring the anomalous X-ray data from crystals of the Zn(2+)/Cd(2+)-species, it has been possible to determine that the alpha-metal ion is zinc and the beta-site is occupied by cadmium.

J Environ Monit, 2001 Feb, 3(1), 49 - 60
The relevance of speciation in the remediation of soils and sediments contaminated by metallic elements--an overview and examples from Central Scotland, UK; Hursthouse AS; The environmental impact of metallic contaminants in soils and sediments is dependent both on the chemical speciation of the metal and the response of the matrix to biological and physicochemical conditions . These factors are responsible for the mobilisation of the metal from the solid into the aquatic phase and hence transport within the immediate vicinity, impacting on the rate of dispersal, dilution, uptake and transfer into living systems . The impact of changing environmental conditions on the contaminant inventory can be to enhance or moderate these phenomena, with subsequent consequences for the broader risk assessment of the contaminants . Remediation of metallic contaminants can only be brought about by their removal from the site or by establishing conditions which favour their retention in the solid phase . A wide range of in situ and ex situ approaches are available and a summary overview is presented . The examples show assessment at both the field and laboratory scale and demonstrate an equally wide range of success in achieving remediation targets . This can be attributed to limitations in ensuring that the desired conditions for the initial removal or immobilisation process are met and maintained over a suitable period of time . Three areas are reviewed which include: the transport and release of metallic contaminants in estuarine sediments and the assessment of their potential to impact on biota; terrestrial contamination systems involving the release of chromium from waste ore contaminating urban environments; the response of metal-contaminated wastes to changing environmental conditions and the impact of natural bioremediation . The focus of the discussion is to highlight the generation of reliable speciation information and the problems associated with impact and risk assessment . Particular issues of concern are the laboratory to field scale evaluation of contaminant behaviour and the approach used to assess the reliability of remediation options . In conclusion, part of a recent initiative in risk assessment and the development of pilot scale experimental systems to study long-term behaviour are addressed as future goals to fill gaps in current research.

Mol Biotechnol, 2000 Nov, 16(3), 211 - 9
Cytoplasmic expression of a soluble synthetic mammalian metallothionein-alpha domain in Escherichia coli . Enhanced tolerance and accumulation of cadmium; Li Y et al.; Bacteria are commonly used for bioremediation of heavy metal pollution and strategies to improve their performance in this respect are desirable . In this study, an Escherichia coli strain was engineered to express a common metallothionein-alpha domain . The metallothionein-alpha domain was over-expressed in the cytoplasm of E . coli as a fusion to the carboxyl terminal of maltose binding protein . The fusion protein was highly soluble in the cytoplasm of E . coli . When grown in the presence of cadmium, cells expressing the metallothionein-alpha fusion protein showed increased viability compared with control cells . Cells expressing the metallothionein-alpha also demonstrated increased accumulation of cadmium.

FEMS Microbiol Ecol, 2001 Mar, 35(1), 75 - 84
Enhanced degradation of phenoxyacetic acid in soil by horizontal transfer of the tfdA gene encoding a 2,4-dichlorophenoxyacetic acid dioxygenase; de Lipthay JR et al.; Few studies have investigated the possible impact of in situ gene transfer on the degradation of xenobiotic compounds in natural environments . In this work we showed that horizontal transfer of the tfdA gene, carried on plasmid pRO103, to phenol degrading recipient strains significantly increased the degradation rate of phenoxyacetic acid in sterile and non-sterile soil microcosms . The tfdA gene encodes a 2,4-dichlorophenoxyacetic acid/2-oxoglutarate dioxygenase and by complementation with the phenol degradation pathway an expanded catabolic substrate range, now including phenoxyacetic acid, is evolved . Presence of selective pressure had a positive effect on the emergence of transconjugants . However, even in the absence of phenoxyacetic acid transconjugant populations were detected and were kept at a constant level throughout the experimental period . The residuesphere (interface between decaying plant material and soil matrix) of dry leaves of barley was shown to be a hot-spot for gene transfer and presence of barley straw increased the conjugation frequencies in soil microcosms to the same extent as presence of organic nutrients . The results of this study indicate that dissemination of catabolic plasmids is a possible mechanism of genetic adaptation to degradation of xenobiotic compounds in natural environments, and that complementation of catabolic pathways possibly plays an important role in the evolution of new degradative capabilities . The application of horizontal gene transfer as a possible tool in bioremediation of contaminated sites is discussed.

J Microbiol Methods, 2001 Apr, 44(3), 271 - 81
Utility of high performance liquid chromatography/electrospray/mass spectrometry of polar lipids in specifically Per-13C labeled Gram-negative bacteria DA001 as a tracer for acceleration of bioremediation in the subsurface; Lytle CA et al.; Specific fatty acids from phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) recovered from a per 13C-labeled bacteria can be detected in environmental samples and used as measures of bacterial transport in the subsurface . Detection of palmitic acid (16:0) and oleic acid (18:1) at m/z 271 (255+16) and 299 (281+18) as negative ions in PG and PE separated by high performance liquid chromatography (HPLC) and detected after up-front collisionally induced dissociation (CID) utilizing electrospray (ES) mass spectrometry (MS) provided sufficient sensitivity and specificity for detection in the presence of the indigenous microbiota . Application of tandem mass spectrometry (MS/MS) in the multiple reaction monitoring (MRM) was use to monitor selected transitions . MRM can increase the sensitivity so that polar lipids recovered from cell densities currently at about 10(4) cells/sample can be detected . This technology provides a non-intrusive mechanism for monitoring the distribution of bacteria added to accelerate in situ bioremediation of subsurface sediments.

Microbiol Mol Biol Rev, 2001 Mar, 65(1), 44 - 79
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics; Makarova KS et al.; The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens . D . radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation . These characteristics were the impetus for sequencing the genome of D . radiodurans and the ongoing development of its use for bioremediation of radioactive wastes . Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood . In this work we present an extensive comparative sequence analysis of the Deinococcus genome . Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group . Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages . Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins . Analysis of paralogs in Deinococcus has revealed several unique protein families . In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected . Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail . Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria . For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance . Compared to other bacteria, the D . radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats . In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.

Environ Microbiol, 2000 Aug, 2(4), 383 - 8
Remarkably low temperature optima for extracellular enzyme activity from Arctic bacteria and sea ice; Huston AL et al.; Extracellular degradative enzymes released by psychrophilic marine bacteria (growing optimally at or below 15 degrees C and maximally at 20 degrees C) typically express activity optima at temperatures well above the upper growth limit of the producing strain . In the present study, we investigated whether or not near-zero Arctic environments contain extracellular enzymes with activity optimized to temperatures lower than previously reported . By applying fluorescently tagged substrate analogues to measure leucine-aminopeptidase and chitobiase activity, the occurrence of extracellular enzymatic activity (EEA) with remarkably low temperature optima (15 degrees C) was documented in sea-ice samples . An extremely psychrophilic bacterial isolate, strain 34H, yielded an extract of cell-free protease with activity optimized at 20 degrees C, the lowest optimum yet reported for cell-free EEA from a pure culture . The use of zymogram gels revealed the presence of three proteolytic bands (between 37 and 45 kDa) in the extract and the release of the greatest quantities of the proteases when the strain was grown at -1 degrees C, suggesting a bacterial strategy for counteracting the effects of very cold temperatures on the catalytic efficiency of released enzymes . The detection of unusually cold-adapted EEA in environmental samples has ramifications not only to polar ecosystems and carbon cycling but also to protein evolution, biotechnology and bioremediation.

Prikl Biokhim Mikrobiol, 2001 Jan-Feb, 37(1), 77 - 9
{A new oil-oxidizing micromycete Fusarium sp.}; Iagafarova GG et al.; The strain Fusarium sp . No . 56 isolated from natural oil-containing soil samples taken near the city of Oktyabr'skii, Republic of Bashkortostan, displayed a pronounced capability of biotransforming oil and its light and heavy fractions . This micromycete is nonpathogenic and can grow at 10 degrees C . The latter property is of practical significance for its uses in soil and water bioremediation under cold climatic conditions of Bashkortostan and other regions.

Environ Microbiol, 2000 Oct, 2(5), 564 - 71
Artificial selection of microbial ecosystems for 3-chloroaniline biodegradation; Swenson W et al.; We present a method for selecting entire microbial ecosystems for bioremediation and other practical purposes . A population of ecosystems is established in the laboratory, each ecosystem is measured for a desired property (in our case, degradation of the environmental pollutant 3-chloroaniline), and the best ecosystems are used as 'parents' to inoculate a new generation of 'offspring' ecosystems . Over many generations of variation and selection, the ecosystems become increasingly well adapted to produce the desired property . The procedure is similar to standard artificial selection experiments except that whole ecosystems, rather than single individuals, are the units of selection . The procedure can also be understood in terms of complex system theory as a way of searching a vast combinatorial space (many thousands of microbial species and many thousands of genes within species) for combinations that are especially good at producing the desired property . Ecosystem-level selection can be performed without any specific knowledge of the species that comprise the ecosystems and can select ensembles of species that would be difficult to discover with more reductionistic methods . Once a 'designer ecosystem' has been created by ecosystem-level selection, reductionistic methods can be used to identify the component species and to discover how they interact to produce the desired effect.

Environ Microbiol, 2001 Jan, 3(1), 32 - 42
Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of Arthrobacter chlorophenolicus A6 cells during degradation of 4-chlorophenol in soil; Elvang AM et al.; The recently isolated novel species Arthrobacter chlorophenolicus A6 is capable of growth on and degradation of high concentrations of 4-chlorophenol (up to 350 microg ml(-1)) as the sole carbon and energy source . This strain shows promise for bioremediation of environmental sites contaminated with high levels of chlorophenols . In this study, green fluorescent protein (gfp) or luciferase (luc) genes were used as biomarkers for monitoring cell number and activity, respectively, during degradation of 4-chlorophenol by A . chlorophenolicus cells . The individual marked strains, Arthrobacter chlorophenolicus A6L (luc-tagged) and Arthrobacter chlorophenolicus A6G (gfp-tagged), were monitored during degradation of 250 microg ml(-1) 4-chlorophenol in pure culture and 175 microg g(-1) 4-chlorophenol in soil microcosms . Both gene-tagged strains were capable of cleaning up the contaminated soil during 9 d incubation . During the bioremediation experiments, the luc-tagged cells were monitored using luminometry and the gfp-tagged cells using flow cytometry, in addition to selective plate counting for both strains . The cells remained at high population levels in the soil (evidenced by GFP-fluorescent cell counts) and the A . chlorophenolicus A6L population was metabolically active (evidenced by luciferase activity measurements) . These results demonstrate that the Arthrobacter chlorophenolicus A6 inoculum is effective for cleaning-up soil containing high concentrations of 4-chlorophenol.

Anal Chem, 2001 Feb 1, 73(3), 703 - 7
Determination of naphthenic acids in crude oils using nonaqueous ion exchange solid-phase extraction; Jones DM et al.; A method is presented for the routine, rapid, and quantitative analysis of aliphatic and naphthenic acids in crude oils, based on their isolation using nonaqueous ion exchange solid-phase extraction cartridges . The isolated acid fractions are methylated and analyzed by gas chromatography and gas chromatography/mass spectrometry . The method is effective on both light and heavy oils and is capable of providing mechanistic information of geochemical significance on the origin of the acids in the oils . Analysis of oils that were solvent extracted from laboratory and field mesocosm marine sediment oil degradation studies indicate that this new method of analyzing the products of hydrocarbon biodegradation may be a useful tool for monitoring the progress of bioremediation of oil spills in the environment.

Bioresour Technol, 2001 Mar, 77(1), 41 - 9
Aspergillus niger absorbs copper and zinc from swine wastewater; Price MS et al.; Wastewater from swine confined-housing operations contains elevated levels of copper and zinc due to their abundance in feed . These metals may accumulate to phytotoxic levels in some agricultural soils of North Carolina due to land application of treated swine effluent . We evaluated fungi for their ability to remove these metals from wastewater and found Aspergillus niger best suited for this purpose . A . niger was able to grow on plates amended with copper at a level five times that inhibitory to the growth of Saccharomyes cerevisiae . We also found evidence for internal absorption as the mechanism used by A . niger to detoxify its environment of copper, a property of the fungus that has not been previously exploited for metal bioremediation . In this report, we show that A . niger is capable of removing 91% of the copper and 70% of the zinc from treated swine effluent.

Folia Microbiol (Praha), 2000, 45(1), 35 - 40
Effect of the carbon source on assessment of degrading bacteria with the spread-plating technique during in situ bioremediation; Damborsky J et al.; Spread-plating belongs to traditional microbiological methods employed for quantification of subsurface microflora during bioremediation projects in the Czechia . Concentration of degrading organisms is estimated from the number of colonies grown on agar plates supplied with contaminant as the sole carbon source . The data obtained during in situ bioremediation of the Dacice site contaminated by cutting oil suggests that changes in the composition of the carbon source in the subsurface may cause a discrepancy between laboratory data and situation in subsurface.

Biodegradation, 2000, 11(1), 1 - 9
Combined ozonation and biodegradation for remediation of mixtures of polycyclic aromatic hydrocarbons in soil; Nam K et al.; A study was conducted to investigate the feasibility of a combined treatment (i.e., ozonation and biodegradation) to overcome the inherent bacterial bioavailability limitation, and hence bioremediation limitation, of polycyclic aromatic hydrocarbons in soil . Ozonation was very efficient in the removal of naphthalene, fluorene, phenanthrene, and anthracene, but not for pyrene, chrysene, and benzo(a)pyrene from soil freshly spiked with the hydrocarbons . A similar result was obtained from coal tar-contaminated soil . Elimination of polycyclic aromatic hydrocarbons increased appreciably in sand containing 0.03% organic carbon, indicating the adverse effect of organic carbon on the efficiency of ozone treatment . In spiked and coal tar-contaminated soils, ozonation followed by biodegradation significantly increased the degradation of various polycyclic aromatic hydrocarbons including chrysene and benzo(a)pyrene which were not degraded by the test bacterial consortium alone . In particular, the effect of the combined treatment was more pronounced in coal tar-contaminated soil than in sterile soil spiked with hydrocarbons, probably due to the augmented biological activity of the introduced consortium . The results suggest that a combined treatment including ozonation and biodegradation may be a promising bioremediation technology in soil contaminated with mixtures of polycyclic aromatic hydrocarbons such as former manufactured gas plant sites.

Res Microbiol, 2000 Dec, 151(10), 807 - 14
Cultivation-independent techniques for studying methanotroph ecology; Murrell JC et al.; Methane-oxidizing bacteria (methanotrophs) have attracted considerable attention over the past 30 years . They have the unique ability to use methane as sole carbon and energy source, they are found in a wide variety of environments and play a crucial role in the global methane cycle . Methanotrophs also show considerable potential for bioremediation processes such as degradation of ground water pollutants, and for production of bulk chemicals from cheap substrates . We review here the cultivation-independent molecular biological methods that are available for the detection and characterization of methanotrophs in the natural environment.

J Biotechnol, 2001 Feb 13, 85(2), 81 - 102
Formation and detoxification of reactive intermediates in the metabolism of chlorinated ethenes; van Hylckama Vlieg JE et al.; Short-chain halogenated aliphatics, such as chlorinated ethenes, constitute a large group of priority pollutants . This paper gives an overview on the chemical and physical properties of chlorinated aliphatics that are critical in determining their toxicological characteristics and recalcitrance to biodegradation . The toxic effects and principle metabolic pathways of halogenated ethenes in mammals are briefly discussed . Furthermore, the bacterial degradation of halogenated compounds is reviewed and it is described how product toxicity may explain why most chlorinated ethenes are only degraded cometabolically under aerobic conditions . The cometabolic degradation of chlorinated ethenes by oxygenase-producing microorganisms has been extensively studied . The physiology and bioremediation potential of methanotrophs has been well characterized and an overview of the available data on these organisms is presented . The sensitivity of methanotrophs to product toxicity is a major limitation for the transformation of chlorinated ethenes by these organisms . Most toxic effects arise from the inability to detoxify the reactive chlorinated epoxyethanes occurring as primary metabolites . Therefore, the last part of this review focuses on the metabolic reactions and enzymes that are involved in the detoxification of epoxides in mammals . A key role is played by glutathione S-transferases . Furthermore, an overview is presented on the current knowledge about bacterial enzymes involved in the metabolism of epoxides . Such enzymes might be useful for detoxifying chlorinated ethene epoxides and an example of a glutathione S-transferase with activity for dichloroepoxyethane is highlighted.

Trends Biotechnol, 2001 Feb, 19(2), 67 - 73
Metal-binding proteins and peptides in bioremediation and phytoremediation of heavy metals; Mejare M et al.; The expression of metal-binding proteins or peptides in microorganisms and plants in order to enhance heavy metal accumulation and/or tolerance has great potential . Several different peptides and proteins have been explored . This review focuses on cadmium (Cd) because of the significant importance of this metal and because of its global presence in many food materials.

Appl Microbiol Biotechnol, 2000 Dec, 54(6), 850 - 3
Irpex lacteus, a white rot fungus applicable to water and soil bioremediation; Novotny C et al.; Growth parameters, ligninolytic enzyme activities and ability to degrade polycyclic aromatic hydrocarbons by the fungus Irpex lacteus were characterized and compared with those of other white rot fungi capable of rapid decolorization of poly R-478 and Remazol Brilliant Blue R dyes . I . lacteus was able to grow on mineral and complex media and efficiently colonized sterile and non-sterile soil by exploratory mycelium growing from a wheat straw inoculum . In shallow stationary cultures growing on high nitrogen mineral medium containing 45 mM ammonium as nitrogen source, the fungus produced lignin peroxidase (LIP), Mn-dependent peroxidase (MnP) and laccase simultaneously, the respective maximal activities of 70, 970 and 36 U/l being attained around day 18 . Growing in nitrogen-limited medium (2.4 mM ammonium), no LIP was formed and levels of MnP and laccase decreased significantly . During growth in sterile soil, the fungus synthesized LIP and laccase but not MnP . I . lacteus efficiently removed three- and four-ringed PAHs from liquid media and artificially spiked soil . The variety of ligninolytic enzymes, robust growth, capability of soil colonization and resistance to inhibitory action of soil bacteria make I . lacteus a suitable fungal organism for use in bioremediation.

Appl Microbiol Biotechnol, 2000 Dec, 54(6), 838 - 43
Bioremediation of polychlorinated biphenyl-contaminated soil using carvone and surfactant-grown bacteria; Singer AC et al.; Partial bioremediation of polychlorinated biphenyl (PCB)-contaminated soil was achieved by repeated applications of PCB-degrading bacteria and a surfactant applied 34 times over an 18-week period . Two bacterial species, Arthrobacter sp . strain B1B and Ralstonia eutrophus H850, were induced for PCB degradation by carvone and salicylic acid, respectively, and were complementary for the removal of different PCB congeners . A variety of application strategies was examined utilizing a surfactant, sorbitan trioleate, which served both as a carbon substrate for the inoculum and as a detergent for the mobilization of PCBs . In soil containing 100 microg Aroclor 1242 g(-1) soil, bioaugmentation resulted in 55-59% PCB removal after 34 applications . However, most PCB removal occurred within the first 9 weeks . In contrast, repeated addition of surfactant and carvone to non-inoculated soil resulted in 30-36% PCB removal by the indigenous soil bacteria . The results suggest that bioaugmentation with surfactant-grown, carvone-induced, PCB-degrading bacteria may provide an effective treatment for partial decontamination of PCB-contaminated soils.

Appl Microbiol Biotechnol, 2000 Dec, 54(6), 751 - 8
Enzymology of Phanerochaete chrysosporium with respect to the degradation of recalcitrant compounds and xenobiotics; Cameron MD et al.; The archetypal white-rot fungus Phanerochaete chrysosporium has been shown to degrade a variety of persistent environmental pollutants . Many of the enzymes responsible for pollutant degradation, which are normally involved in the degradation of wood, are extracellular . Thus, P . chrysosporium is able to degrade toxic or insoluble chemicals more efficiently than other microorganisms . P . chrysosporium has a range of oxidative and reductive mechanisms and uses highly reactive, nonspecific redox mediators which increase the number of chemicals that can be effectively degraded . This review gives an overview of the enzymes that are believed to be important for bioremediation and briefly discusses the degradation of some individual chemicals.

FEMS Microbiol Lett, 2001 Jan 1, 194(1), 39 - 45
The predatory soil flagellate Heteromita globosa stimulates toluene biodegradation by a Pseudomonas sp; Mattison RG et al.; A model food chain was established to investigate the influence of grazing by flagellates on bacteria degrading toluene in batch culture . The rate of toluene consumed by a Pseudomonas sp . strain PS+ (max . 0.37 fmol cell(-1) h(-1)) was significantly higher in the presence of the bacterivorous flagellate Heteromita globosa (max . 1.38 fmol cell(-1) h(-1)) . A maximum increase of up to 7.5 times was observed in the rate of toluene consumed by these bacteria during exponential growth of this flagellate . Carbon conversion efficiency (CCE) of bacteria to flagellate biomass was estimated to be 33.4% based on measured biovolumes and published values for carbon contents . However, the CCE for toluene-derived carbon was lower (max . 4.9%) when calculations were based on incorporation of {ring-U-(14)C}toluene into biomass of flagellates grazing on labelled bacteria . The findings suggest a potential role for flagellates in bioremediation processes.

Enzyme Microb Technol, 2000 Dec, 27(10), 812 - 820
Halorespiring bacteria-molecular characterization and detection; Smidt H et al.; Recently, a rapidly increasing number of bacteria has been isolated that is able to couple the reductive dehalogenation of various halogenated aromatic and aliphatic compounds like chlorophenols and tetrachloroethene to energy conservation by electron-transport-coupled phosphorylation . The potential of these halorespiring bacteria for innovative clean-up strategies of polluted anoxic environments has greatly stimulated efforts to unravel the molecular basis of the novel respiratory chains they possess . The thorough characterization of halorespiratory key components at the physiological, biochemical and molecular genetic level has revealed both structural and functional similarity of chloroaryl- and chloroalkyl-respiratory chains from different phylogenetically distinct microorganisms . The reductive dehalogenases from halorespiring bacteria were found to comprise a novel class of corrinoid-containing Fe/S-proteins . Sensitive molecular methods for monitoring both presence and fate of halorespiring bacteria have been developed, which will be instrumental for the design and maintenance of optimised in situ bioremediation processes.

Chemosphere, 2001 Feb, 42(4), 425 - 9
Bacterial release of arsenic ions and organoarsenic compounds from soil contaminated by chemical warfare agents; Kohler M et al.; The objective of this paper was to investigate possible participation of microorganisms in the release of soluble arsenical compounds from organoarsenic warfare agents in contaminated soil . A number of bacterial strains were isolated with high resistance against As3+ and As5+ ions which are able to degrade the water insoluble compounds triphenylarsine (TP) and triphenylarsineoxide (TPO) . These strains belong to different genera of bacteria . Release of arsenic ions and soluble organoarsenic compounds from soil by the activity of autochthonic soil bacteria and a mixture of the isolated pure cultures was demonstrated by percolation experiments with undisturbed soil samples (core drills) from the contaminated site . This release increased after addition of nutrients (mineral nitrogen and phosphorus, sodium acetate and ethanol) and is nearly independent of the percolation temperature (5 degrees C and 22 degrees C) . These results show that bacteria play an important role in the release of arsenical compounds from organoarsenic warfare agent contaminated soil . This release is limited by shortage of water and, above all, of nutrients for the microorganisms in the sandy forest soil . These results are important both for the management and security and possibly for bioremediation of military waste sites containing similar contaminations . Furthermore, this is the first report on bacterial degradation of organoarsenic warfare compounds.

Biosci Rep, 2000 Aug, 20(4), 239 - 58
Chemical and biological parameters as tools to evaluate and improve heavy metal phytoremediation; Kamnev AA et al.; In this review, chemical and biological parameters are discussed that strongly influence the speciation of heavy metals, their availability to biological systems and, consequently, the possibilities to use bioremediation as a cleanup tool for heavy metal polluted sites . In order to assess heavy metal availability, a need exists for rapid, cost-effective systems that reliably predict this parameter and, based on this, the feasibility of using biological remediation techniques for site management and restoration . Special attention is paid to phytoremediation as an emerging technology for stabilization and remediation of heavy metal pollution . In order to improve phytoremediation of heavy metal polluted sites, several important points relevant to the process have to be elucidated . These include the speciation and bioavailability of the heavy metals in the soil determined by many chemical and biological parameters, the role of plant-associated soil microorganisms and fungi in phytoremediation, and the plants . Several options are described how plant-associated soil microorganisms can be used to improve heavy metal phytoremediation.

Microb Ecol, 2000 Aug, 40(3), 177 - 188
Analysis of Microbial Communities in a Landfill Leachate Polluted Aquifer using a New Method for Anaerobic Physiological Profiling and 16S rDNA Based Fingerprinting; Roling WF et al.; Databases containing information regarding presence and activity of microbial communities will be very useful for determination of the potential for intrinsic bioremediation in landfill leachate polluted aquifers . Simple analyses such as community-level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA fragments yield large sets of data for inclusion into such databases . In this study we describe the development of a method for anaerobic CLPP, using commercially available Biolog plates . Incubation at the in situ temperature of the aquifer (10 degrees C) for 28 days was optimal for obtaining a specific, reproducible physiological profile . Anaerobic incubation was essential for profiling anaerobic communities . The anaerobic cultivation-dependent CLPP method and cultivation-independent DGGE were applied to groundwater and sediment samples from the aquifer near the Coupepolder landfill in The Netherlands . A combination of computer-assisted CLPP and DGGE analysis of both groundwater and sediment samples yielded the best separating power for characterizing microbial communities in the aquifer . Communities in groundwater were significantly different from those in the corresponding sediment . Microbial communities present in subsamples from sediment cores usually were similar for the various sampling locations . Variation was observed for the heterogeneous sediment beneath the landfill . Both anaerobic CLPP and DGGE analysis clearly separated microbial communities from the polluted aquifer underneath the landfill from those in the less or not polluted aquifer downstream and upstream of the landfill.

FEMS Microbiol Lett, 2000 Nov 15, 192(2), 185 - 90
Utilisation of aliphatic compounds by acidophilic heterotrophic bacteria . The potential for bioremediation of acidic wastewaters contaminated with toxic organic compounds and heavy metals; Gemmell RT et al.; Acidophilic, heterotrophic bacteria isolated from acidic mine effluent metabolised a range of aliphatic compounds . Aliphatic acids, which are normally thought to be toxic to acidophiles, were utilised as substrates for energy and growth by these bacteria . This biodegradative ability, concomitant with their tolerance of heavy metals, has demonstrated the potential for using these organisms for the bioremediation of multiply contaminated acidic wastewaters.

Enzyme Microb Technol, 2000 Nov 15, 27(9), 709 - 713
Hydrocarbon degradation by a soil microbial population with beta-cyclodextrin as surfactant to enhance bioavailability; Bardi L et al.; In general the biodegradation of nonchlorinated aliphatic and aromatic hydrocarbons is influenced by their bioavailability . Hydrocarbons are very poorly soluble in water . They are easily adsorbed to clay or humus fractions in the soil, and pass very slowly to the aqueous phase, where they are metabolised by microorganisms . Surfactants that increase their solubility and improve their bioavailability can thereby accelerate degradation . Cyclodextrins are natural compounds that form soluble complexes with hydrophobic molecules . They are widely used in medicine and harmless to microorganisms and enzymes . This paper describes their in vitro effect on the biodegradative activity of a microbial population isolated from a petroleum-polluted soil, as shown by the decrease of dodecane (C12), tetracosane (C24) anthracene and naphthalene added individually as the sole carbon source to mineral medium liquid cultures . beta-cyclodextrin accelerated the degradation of all four hydrocarbons, particularly naphthalene, and influenced the growth kinetics as shown by a higher biomass yield and better utilization of hydrocarbon as a carbon and energy source . Its low cost, biocompatibility and effective acceleration of degradation make beta-cyclodextrin an attractive option for bioremediation.

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