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 (lan