Bioremediation

Environ Toxicol Chem, 2004 Apr, 23(4), 929 - 37
Methods to assess the amenability of petroleum hydrocarbons to bioremediation; Dobson R et al.; Bioremediation has achieved acceptance as a cost-effective technique for the remediation of soils and groundwater contaminated with petroleum hydrocarbons (PHC) . A range of laboratory techniques to assess the biodegradability and bioavailability of PHCs are presented . Biodegradability and bioavailability are important determinants of the bioremediation performance of PHCs . Novel methods for the assessment of the bioavailability of PHC components are described . The techniques are demonstrated for a hydraulic fluid and a spindle oil from a contaminated site . Biodegradation is measured by oxygen consumption and carbon dioxide production . Bioavailability of the PHCs is estimated based on the PHC-water partitioning of tracer compounds and a novel analysis of gas chromatograms based on Raoult's law . The PHCs tested were only partially biodegradable (< 25% in 78 d) due to the low solubility and likely recalcitrance of some of their components . The combination of techniques outlined is expected to be of use in assessing the likely bioremediation performance of PHCs for which published data are scarce or inadequate.

Environ Pollut, 1998, 99(1), 37 - 43
Soil contamination by crude oil: impact on the mycorrhizosphere and on the revegetation potential of forest trees; Nicolotti G et al.; In vitro and greenhouse biotests were carried out to study the effects of various concentrations of crude oil on the mycorrhizosphere and the ability of ectomycorrhizal fungi to colonise Norway spruce and poplar seedlings grown on contaminated soil . Ectomycorrhizal fungi grown in pure cultures showed a variety of reactions to crude oil, ranging from growth stimulation to total inhibition of growth, depending on the species of fungi . Germination of poplar and spruce seeds was not significantly affected . The growth of spruce seedlings was not affected by crude oil, whereas that of poplar seedlings was significantly reduced at high concentrations . None of the concentrations had any effect on the degree of ectomycorrhizal and endomycorrhizal colonisation of poplar . With spruce, however, the ectomycorrhizal fungi showed species-specific reactions to increasing concentrations, in accordance with the results of the pure culture test . The length of time between soil contamination and seeding affects both seedling growth and the mycorrhizal infection potential of the soil . The results confirm the importance of mycorrhizal fungi in the bioremediation of soils contaminated by crude oil . In Labor- und Gewachshausversuchen wurde die Wirkung von Erdol auf die Mykorrhizaflora und ihr Potential, Feinwurzeln von Fichten und Pappelsamlingen zu besiedeln, durchgefuhrt . In Reinkultur zeigten die 10 untersuchten Ektomykorrhizapilze unterschiedliche Reaktion auf Erdolkontamination, von Stimulation bis zu totaler Hemmung des Wachstums . Ein Einfluss von Erdol auf die Samenkeimung war bei keiner der beiden Baumarten festzustellen . Das Samlingswachstum wurde bei Pappel durch hohe Erdolkonzentrationen signifikant gehemmt, wahrenddem es bei Fichte praktisch unbeeinflusst blieb . Die Besiedlung der Feinwurzeln durch Endo- und Ektomykorrhizapilze wurde bei Pappel durch Erdol nicht beeinflusst, bei Fichte zeigten Ektomykorrhizapilze-in Ubereinstimmung mit den Resultaten der Reinkulturversuche-artspezifische Reaktionen auf Erdolkontamination . Die Wartezeit zwischen der Erdolkontamination des Bodens und der Aussaat beeinflusst sowohl das Samlingswachstum wie das Mykorrhiza-Infektionspotential des Bodens . Die Resultate bestatigen die Bedeutung der Mykorrhizapilzflora im Zusammenhang mit der Wiederbesiedlung von erdolkontaminierten Boden.

Environ Pollut, 2000 Feb, 107(2), 255 - 61
Evaluation of ecological disturbance and intrinsic bioremediation potential of pulp mill-contaminated lake sediment using key enzymes as probes; Wittmann C et al.; A rapid protocol was developed to measure 10 different enzymic activities from a large number of 1-cm-sliced freshly collected lake sediments . Layers heavily polluted by organic halogens (4900 mg Cl kg(-1)) revealed severe depression of phosphatase, sulfatase, leucine-aminopeptidase, chitinase, acetate esterase and butyrate esterase activities as compared to layers above and below the most polluted zone . alpha-Glucosidase, beta-glucosidase, beta-xylosidase and palmitate esterase were less affected . Methane oxidation potential was dramatically depressed in the polluted strata whereas tetrachloromethane dehalogenating activity was observed in the polluted sediment only . The sediment layers formed after the chlorine discharges into the lake had diminished to 1/10, and showed restoration of the activities close to those observed in non-recipient sediment, in spite of the persisting presence of >1000 mg of organic chlorine (kg dry wt)(-1) . We conclude that certain enzymic activities involved in breakdown or oxidation of organic matter in the sediments are useful probes for assessing the degree of ecological damage and its potential for restoration in recipient lakes of industrial discharges.

Environ Pollut, 2000 Feb, 107(2), 245 - 54
Bioremediation of petroleum hydrocarbon-contaminated soil by composting in biopiles; Jorgensen KS et al.; Composting of contaminated soil in biopiles is an ex situ technology, where organic matter such as bark chips are added to contaminated soil as a bulking agent . Composting of lubricating oil-contaminated soil was performed in field scale ( {Formula: see text} m(3)) using bark chips as the bulking agent, and two commercially available mixed microbial inocula as well as the effect of the level of added nutrients (N,P,K) were tested . Composting of diesel oil-contaminated soil was also performed at one level of nutrient addition and with no inoculum . The mineral oil degradation rate was most rapid during the first months, and it followed a typical first order degradation curve . During 5 months, composting of the mineral oil decreased in all piles with lubrication oil from approximately 2400 to 700 mg (kg dry w)(-1), which was about 70% of the mineral oil content . Correspondingly, the mineral oil content in the pile with diesel oil-contaminated soil decreased with 71% from 700 to 200 mg (kg dry w)(-1) . In this type of treatment with addition of a large amount of organic matter, the general microbial activity as measured by soil respiration was enhanced and no particular effect of added inocula was observed.

Environ Pollut, 2000 Feb, 107(2), 233 - 8
Decomposer animals and bioremediation of soils; Haimi J; Although microorganisms are degrading the contaminants in bioremediation processes, soil animals can also have important--while usually an indirect--role in these processes . Soil animals are useful indicators of soil contamination, both before and after the bioremediation . Many toxicity and bioavailability assessment methods utilizing soil animals have been developed for hazard and risk-assessment procedures . Not only the survival of the animals, but also more sensitive parameters like growth, reproduction and community structure have often been taken into account in the assessment . The use of bioassays together with chemical analyses gives the most reliable results for risk analyses . This is because physical, chemical and biological properties of the remediated soil may be changed during the process, and it is possible that transformation rather than mineralization of the contaminants has taken place . In addition, the soil may contain other harmful substances than those searched in chemical analyses . Finally, because the ultimate goal of the bioremediation should be--together with mineralization of the harmful substances--the ecological recovery of the soil, development of diverse decomposer community as a basis of the functioning ecosystem should be ensured . Soil animals, especially the large ones, can also actively take part in the ecological recovery processes through their own activity . The potential risk of transfer of contaminants accumulated in soil animals to the above-ground food webs should be borne in mind.

Environ Pollut, 2000 Feb, 107(2), 217 - 23
Biomarkers for monitoring efficacy of bioremediation by microbial inoculants; Jansson JK et al.; Bioaugmentation of contaminated sites with microbes that are adapted or genetically engineered for degradation of specific toxic compounds is an area that is currently being explored as a clean-up option . Biomarkers have been developed to track the survival and efficacy of specific bacteria that are used as inocula for bioremediation of contaminated soil . Examples of biomarkers include the luc gene, encoding firefly luciferase and the gfp gene, encoding the green fluorescent protein (GFP) . The luc gene was used to tag different bacteria used for bioremediation of gasoline or chlorophenols . The bacteria were monitored on the basis of luciferase activity in cell extracts from soil . The gfp gene was also used to monitor bacteria during degradation of chlorophenol in soil, based on fluorescence of the GFP protein . Other biomarkers can also be used for monitoring of microbial inocula used for bioaugmentation of contaminated sites . The choice of biomarker and monitoring system depends on the particular site, bacterial strain and sensitivity and specificity of detection required.

Environ Pollut, 2000 Feb, 107(2), 179 - 85
Means to improve the effect of in situ bioremediation of contaminated soil: an overview of novel approaches; Romantschuk M et al.; Different aspects of bacterial degradation of organic contaminants in soil, and how to improve the efficiency and reproducibility is discussed in this review . Although bioremediation in principle includes the use of any type of organism in improving the condition of a contaminated site, most commonly bacteria are the degraders and other organisms, such as soil animals or plant roots, play a role in dissemination of bacteria and, indirectly, plasmids between bacteria, and in providing nutrients and co-substrates for the bacteria active in the degradation process . There are a number of different procedures that have been tested more-or-less successfully in attempts to improve reliability, cost efficiency and speed of bioremediation . The methods range from minimal intervention, such as mere monitoring of intrinsic bioremediation, through in situ introduction of nutrients and/or bacterial inocula or improvement of physico-chemical conditions, all the way to excavation followed by on site or ex situ composting in its different varieties . In the past the rule has been that more intervention (leading to higher costs) has been more reliable, but novel ideas are continuously tried out, both as a means to come up with new truly functional applications and also as a line of studies in basic soil microbial ecology . Both approaches generate valuable information needed when predicting outcome of remediation activities, evaluating environmental risks, deciding on cleaning-up approaches, etc . The emphasis of this review is to discuss some of the novel methods for which the value has not been clearly shown, but that in our view merit continued studies and efforts to make them work, separately or in combination.

Environ Pollut, 2000 May, 108(2), 129 - 39
The effects of oil spill and clean-up on dominant US Gulf coast marsh macrophytes: a review; Pezeshki SR et al.; The objective of this review was to synthesize existing information regarding the effects of petroleum hydrocarbons on marsh macrophytes in a manner that will help guide research and improve spill-response efficiency . Petroleum hydrocarbons affect plants chemically and physically . Although plants sometime survive fouling by producing new leaves, even relatively non-toxic oils can stress or kill plants if oil physically prevents plant gas-exchange . Plant sensitivity to fouling varies among species and among populations within a species, age of the plant, and season of spill . Physical disturbance and compaction of vegetation and soil associated with clean-up activities following an oil spill appear to have detrimental effects on the US Gulf coast marshes . Other techniques, including the use of chemicals such as cleaners or bioremediation, may be necessary to address the problem . Clean-up may also be beneficial when timely removal prevents oil from migrating to more sensitive habitats.

Environ Pollut, 1995, 90(1), 127 - 30
Influence of salinity on bioremediation of oil in soil; Rhykerd RL et al.; Spills from oil production and processing result in soils being contaminated with oil and salt . The effect of NaCl on degradation of oil in a sandy-clay loam and a clay loam soil was determined . Soils were treated with 50 g kg(-1) non-detergent motor oil (30 SAE) . Salt treatments included NaCl amendments to adjust the soil solution electrical conductivities to 40, 120, and 200 dS m(-1) . Soils were amended with nutrients and incubated at 25 degrees C . Oil degradation was estimated from the quantities of CO(2) evolved and from gravimetric determinations of remaining oil . Salt concentrations of 200 dS m(-1) in oil amended soils resulted in a decrease in oil mineralized by 44% for a clay loam and 20% for a sandy-clay loam soil . A salt concentration of 40 dS m(-1) reduced oil mineralization by about 10% in both soils . Oil mineralized in the oil amended clay-loam soil was 2-3 times greater than for comparable treatments of the sandy-clay loam soil . Amending the sandy-clay loam soil with 5% by weight of the clay-loam soil enhanced oil mineralization by 40% . Removal of salts from oil and salt contaminated soils before undertaking bioremediation may reduce the time required for bioremediation.

Sci Total Environ, 2004 May 5, 323(1-3), 1 - 19
Crop and irrigation management strategies for saline-sodic soils and waters aimed at environmentally sustainable agriculture; Qadir M et al.; Irrigation has long played a key role in feeding the expanding world population and is expected to play a still greater role in the future . As supplies of good-quality irrigation water are expected to decrease in several regions due to increased municipal-industrial-agricultural competition, available freshwater supplies need to be used more efficiently . In addition, reliance on the use and reuse of saline and/or sodic drainage waters, generated by irrigated agriculture, seems inevitable for irrigation . The same applies to salt-affected soils, which occupy more than 20% of the irrigated lands, and warrant attention for efficient, inexpensive and environmentally acceptable management . Technologically and from a management perspective, a couple of strategies have shown the potential to improve crop production under irrigated agriculture while minimizing the adverse environmental impacts . The first strategy, vegetative bioremediation--a plant-assisted reclamation approach--relies on growing appropriate plant species that can tolerate ambient soil salinity and sodicity levels during reclamation of salt-affected soils . A variety of plant species of agricultural significance have been found to be effective in sustainable reclamation of calcareous and moderately sodic and saline-sodic soils . The second strategy fosters dedicating soils to crop production systems where saline and/or sodic waters predominate and their disposal options are limited . Production systems based on salt-tolerant plant species using drainage waters may be sustainable with the potential of transforming such waters from an environmental burden into an economic asset . Such a strategy would encourage the disposal of drainage waters within the irrigated regions where they are generated rather than exporting these waters to other regions via discharge into main irrigation canals, local streams, or rivers . Being economically and environmentally sustainable, these strategies could be the key to future agricultural and economic growth and social wealth in regions where salt-affected soils exist and/or where saline-sodic drainage waters are generated.

Nat Biotechnol, 2004 May, 22(5), 554 - 9 Epub 2004 Apr 11.
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough; Heidelberg JF et al.; Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions . The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism . The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium . Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system . This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.

J Environ Qual, 2004 Mar-Apr, 33(2), 559 - 64
Fate of colloidal-particulate elemental selenium in aquatic systems; Zhang Y et al.; Bacterial reduction of selenate {Se(VI)} to elemental Se {Se(0)} is considered an effective bioremediation technique to remove selenium (Se) from agricultural drainage water . However, the fate of the newly formed Se(0) in aquatic systems is not known when it flows out of the treatment system . A set of laboratory experiments was conducted to determine the fate of the colloidal-particulate Se(0) in a water column and in a water-sediment system . Results showed that the newly formed colloidal-particulate Se(0) followed two removal pathways in aquatic systems: (i) flocculation-sedimentation to the bottom of the water and (ii) oxidation to selenite {Se(IV)} and Se(VI) . During 58 d of the experiments, 51% of the added Se(0) was precipitated to the bottom of the water and 47% was oxidized to Se(IV) in the water column . In the water-sediment system, Se(IV) in the water accounted for 21 to 25% of the added Se(0) . Adsorption of Se(IV) to the bottom sediment resulted in a relatively low amount of Se(IV) in the water . This study indicates that the newly formed Se(0) may be an available form of Se for uptake by organisms if it flows to aquatic systems from a treatment site . Therefore, an effective bioremediation system for removing Se from drainage water must reduce Se(VI) to Se(0) and remove Se(0) directly from the drainage water.

Environ Sci Technol, 2004 Mar 15, 38(6), 1786 - 93
Assessing the bioavailability of PAHs in field-contaminated sediment using XAD-2 assisted desorption; Lei L et al.; An XAD-2 assisted desorption assay was evaluated to assess its functionality in determining the bioavailability of polycyclic aromatic hydrocarbons (PAHs) in an aged field-contaminated sediment . In the study, various dosages of XAD-2 resin were added to abiotic sediment-water slurry systems to adsorb the PAHs from the aqueous phase thus accelerating the desorbability of these contaminants from the sediment . A parallel experiment on the biodegradation of these PAHs by microorganisms indigenous to the sediment was also conducted . Both the desorbability of the PAHs in the XAD-2 assisted desorption assay and their biodegradability decreased with time and eventually approached constant values . The two procedures showed very similar residual concentrations of PAHs for compounds with less than five benzene rings . This suggests that the XAD-2 assisted desorption assay shows promise in measuring the bioavailability of PAHs in field-contaminated sediments and could be used for predicting the end point of PAH bioremediation.

Appl Environ Microbiol, 2004 Apr, 70(4), 1944 - 55
Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons; Leys NM et al.; Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy . The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes . In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils . PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae.Single-band DGGE profiles were obtained for most Sphingomonas strains tested . Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species . Inoculated strains could be detected at a cell concentration of 10(4) CFU g of soil(-1) . The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity . Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species) . In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.

Environ Microbiol, 2004 May, 6(5), 517 - 27
Perchlorate-reducing microorganisms isolated from contaminated sites; Waller AS et al.; An extensive microcosm survey of perchlorate-contaminated sites was undertaken to assess the ability of indigenous microorganisms to degrade perchlorate . Samples from 12 contaminated sites and from one pristine location were analysed . Perchlorate was degraded to below detection limit in all electron donor-amended microcosms . Perchlorate-reducing microorganisms (PRMs) were numerous at most of these sites . Sixteen distinct PRMs were isolated that were phylogenetically related to either Dechloromonas in the Beta Proteobacteria (9/16 isolates) or to Azospirillum in the Alpha Proteobacteria (7/16 isolates) . The majority of previously isolated PRMs are in the Beta Proteobacteria related to Dechloromonas or Dechlorosoma . This study indicates that PRMs of the genus Azospirillum may be more prevalent at contaminated sites than the current record of isolates suggests . Cell yields, electron donor to perchlorate ratios and maximum specific growth rates were similar among the isolates and similar to the few previously published values . However, the Monod half-saturation constants for perchlorate for the two Azospirillum isolates characterized were lower than those measured for other genera, suggesting that they may be more effective at low concentrations of perchlorate . These results extend the current understanding of PRMs from diverse environments and provide added confidence that microbial perchlorate reduction is ubiquitous, even at highly contaminated sites, and can be harnessed effectively for bioremediation.

Environ Sci Technol, 2004 Mar 1, 38(5), 1582 - 8
Bioremediation process for sediments contaminated by heavy metals: feasibility study on a pilot scale; Seidel H et al.; The core stages of a sediment remediation process--the conditioning of dredged sludge by plants and the solid-bed leaching of heavy metals using microbially produced sulfuric acid--were tested on a pilot scale using a highly polluted river sediment . Conditioning was performed in 50 m3 basins at sludge depths of 1.8 m . During one vegetation period the anoxic sludge turned into a soil-like oxic material and became very permeable to water . Reed canary grass (Phalaris arundinacea) was found to be best suited for conditioning . Bioleaching was carried out in an aerated solid-bed reactor of 2000 L working volume using oxic soil-like sediment supplemented with 2% sulfur . When applying conditioned sediment, the oxidation of easily degradable organic matter by heterotrophic microbes increased the temperature up to 50 degrees C in the early leaching phase, which in turn temporarily inhibited the sulfur-oxidizing bacteria . Nevertheless, most of the metal contaminants were leached within 21 days . Zn, Cd, Mn, Co, and Ni were removed by 61-81%, Cu was reduced by 21%, while Cr and Pb were nearly immobile . A cost-effectiveness assessment of the remediation process indicates it to be a suitable treatment for restoring polluted sediments for beneficial use.

Nat Rev Microbiol, 2003 Oct, 1(1), 35 - 44
Cleaning up with genomics: applying molecular biology to bioremediation; Lovley DR; Bioremediation has the potential to restore contaminated environments inexpensively yet effectively, but a lack of information about the factors controlling the growth and metabolism of microorganisms in polluted environments often limits its implementation . However, rapid advances in the understanding of bioremediation are on the horizon . Researchers now have the ability to culture microorganisms that are important in bioremediation and can evaluate their physiology using a combination of genome-enabled experimental and modelling techniques . In addition, new environmental genomic techniques offer the possibility for similar studies on as-yet-uncultured organisms . Combining models that can predict the activity of microorganisms that are involved in bioremediation with existing geochemical and hydrological models should transform bioremediation from a largely empirical practice into a science.

Environ Toxicol, 2004 Apr, 19(2), 154 - 9
Detoxification of organophosphorus compounds by recombinant carboxylesterase from an insecticide-resistant mosquito and oxime-induced amplification of enzyme activity; Zhang JL et al.; Currently, bioremediation is a promising approach to the degradation of environmental pollutants . Here we describe the application of the recombinant insecticide-resistant mosquito carboxylesterase B1 to detoxify organophosphorous compounds . However, this approach has a major limitation: 1:1 stoichiometry of the enzyme detoxification of those organophosphorous compounds containing no carboxyl ester bonds, such as paraoxon, chlorpyrifos etc . To improve the effectiveness of the enzymatic detoxification of organophosphorous compounds, we used a combination of carboxylesterase B1 with the uncharged oxime diacetylmonoxime . It was demonstrated that the repeated addition of 20 times the molar concentration of paraoxon to carboxylesterase B1 every 2 h in the presence of 4 mM diacetylmonoxime did not result in significant inhibition of the enzyme . The stoichiometry of enzyme detoxification was higher than 45:1 and 20:1 for paraoxon and chlorpyrifos, respectively . The kinetic experiments on reactivation of organophosphorus compound-inhibited carboxylesterase B1 showed that the half-life for paraoxon- and chlorpyrifos-inhibited carboxylesterase reactivation is 0.75 and 0.88 h, respectively . Using the recombinant insecticide-resistant mosquito carboxylesterase with oxime is an effective approach for detoxification of organophosphorous compounds .

J Contam Hydrol, 2004 Apr, 69(3-4), 233 - 61
In situ sequenced bioremediation of mixed contaminants in groundwater; Devlin JF et al.; A mixture of chlorinated solvents (about 0.5-10 mg/l), including tetrachloroethene (PCE) and carbon tetrachloride (CT), together with a petroleum hydrocarbon, toluene (TOL), were introduced into a 24 m long x 2 m wide x 3 m deep isolated section (henceforth called a gate) of the Borden aquifer and subjected to sequential in situ treatment . An identical section of aquifer was similarly contaminated and allowed to self-remediate by natural attenuation, thus serving as a control . The control presents a rare opportunity to critically assess the performance of the treatment systems, and represents the first such study for sequenced in situ remediation . The first treatment step was anaerobic bioremediation . This was accomplished using a modified nutrient injection wall (NIW) to pulse benzoate and a nutrient solution into the aquifer, maximizing mixing by dispersion and minimizing fouling near the injection wells . In the anaerobic bioactive zone that developed, PCE, CT and chloroform (CF), a degradation product of CT, degraded with a half-lives of about 59, 5.9 and 1.7 days, respectively . The second step was aerobic bioremediation, using a biosparge system . TOL and cis-1,2 dichloroethene (cDCE), from PCE degradation, were found to degrade aerobically with half-lives of 17 and 15 days, respectively . Compared to natural attenuation, PCE and TOL removal rates were significantly better in the sequenced treatment gate . However, CT and CF were similarly and completely attenuated in both gates . It is believed that the presence of TOL helped sustain the reducing environment needed for the reduction of these two compounds.

Z Naturforsch {C}, 2004 Jan-Feb, 59(1-2), 140 - 5
Potential for biodegradation of hydrocarbons by microorganisms isolated from Antarctic soils; Vasileva-Tonkova E et al.; Seventeen pure aerobic microbial isolates were obtained from soil samples of three regions of Antarctica: Casey Station, Dewart Island and Terra Nova Bay . Most of them were gram positive coryneform bacteria . Isolates were tested for their ability to grow on mineral salt agar plates supplemented with one of the following model n-alkanes or aromatic hydrocarbons: hexane, heptane, paraffin, benzene, toluene, naphthalene and kerosene . Cell hydrophobicity, the ability to produce anionic glycolipids and extracellular emulsifying activity were also determined and assessed on the basis of growth of soil isolates on hydrocarbons . This study revealed degraders with broader abilities to grow on both types of hydrocarbons, good production of glycolipids and emulsifying activity . On this basis, a mixed culture of strains is proposed, which may find application for bioremediation at temperate temperature of soil environments polluted with different hydrocarbons.

Environ Microbiol, 2004 Apr, 6(4), 388 - 99
Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction; Han JI et al.; To improve the monitoring of methanotrophic activity, a competitive reverse transcription-polymerase chain reaction (RT-PCR) methodology was developed . Homologous internal RNA standards were created for mmoX and pmoA, genes encoding polypeptides of sMMO and pMMO, respectively . Using specific primer sets, expression of sMMO and pMMO could be quantified by means of competitive RT-PCR and capillary electrophoresis with uncoated bare-fused silica columns and UV detection . Using this technique, it was discovered that the amount of mRNA transcript for both mmoX and pmoA correlated well with whole-cell sMMO and pMMO activity respectively . A method for soil RNA extraction was also developed to utilize this RNA quantification technique for the monitoring of methanotrophic activity in situ . In a model soil slurry system with a background concentration of 2.9 micro M copper, it was found that only pmoA was transcribed by cells capable of expressing both forms of MMO . As pMMO and sMMO have very different substrate ranges and kinetics, this methodology may prove useful for optimizing in situ bioremediation by methanotrophs . Provided sufficient sequence information is available to create specific primer sets, these techniques can be applied for monitoring and measuring the activity of other microbial communities in situ.

Environ Sci Pollut Res Int, 2004, 11(1), 22 - 32
Studies in the biodegradation of 5 PAHs (phenanthrene, pyrene, fluoranthene, chrysene und benzo(a)pyrene) in the presence of rooted poplar cuttings; Kuhn A et al.; Cuttings of Populus nigra L . cv . Loenen were cultivated in sand treated with one of the following PAHs: phenanthrene (Phen), fluoranthene (Flt), pyrene (Pyr), chrysene (Chr) and benzo{a}pyrene (BaP) . The PAHs were applied at varying levels of concentration to each test series . After 6 weeks the concentration and the distribution of the PAHs in the substrate of the various sets of tests were compared with the concentration in the substrate of the control . Additionally the substrate and the plant roots were tested for evidence of degradation products of PAHs . The results revealed that the levels of concentration of Phen and Pyr detected in the substrate surrounding the roots was in some cases significantly lower than in the corresponding section of substrate in the unplanted set (= control) . This phenomenon did not occur for Flt and BaP and in the case of Chr only in those substrates, which had been treated with the highest levels of concentration . As the presence of lesser amounts of Phen and Pyr in the plant pots cannot only be attributed to their accumulation and metabolism in the roots, it is fair to assume that the chemical transformation of these three PAHs took place outside the roots . The set of tests treated with Phen revealed the presence of 2- or 3-hydroxy-Phen (main components), a hydroxy-methoxy-Phen, 9,10-Phenanthrenequinone and one unidentified compound in metabolite form . Altogether eleven metabolites of Pyr were identified in the root extracts, which can be divided into three groups: 1-Hydroxy-Pyr and derivatives, dihydroxy-Pyr and derivatives and ring fission products (4-Hydroxy-Pyr and a derivative of the 4-Phen-carbonic acid) . However, the metabolite mass detected for Phen and Pyr represents only an insignificant percentage in comparison with the lesser amounts of PAHs observed in the planted set of tests . This indicates that the three PAHs were reduced to lower molecular compounds, which are methodically impossible to record, and subsequently translocated to other parts of the plant and integrated into the biomass . Although no lesser amount for Flt and BaP was found in the plant pots, 1-Hydroxy-Flt, an unidentified compound of Flt and 1-Methoxy-BaP were detected . These are presumably end products which were enhanced in the roots . It was not possible to identify any transformation products of Chr . It can be assumed that the majority of metabolites were not synthesised in the roots but are a result of microbial degradation in the rhizosphere . The test plants improved the conditions for the biotransformation of Phen and Pyr significantly and accumulated Flt, Pyr, Chr and BaP in their roots . It can therefore be concluded that the use of plants in the bioremediation of contaminated soils is a promising option.

Environ Sci Technol, 2004 Feb 15, 38(4), 1102 - 7
Vinyl chloride and cis-dichloroethene dechlorination kinetics and microorganism growth under substrate limiting conditions; Cupples AM et al.; The reductive dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE) at contaminated sites often results in the accumulation of cis-1,2-dichloroethene (DCE) and vinyl chloride (VC), rather than the nonhazardous end product ethene . This accumulation may be caused by the absence of appropriate microorganisms, insufficient supply of donor substrate, or reaction kinetic limitations . Here, we address the issue of reaction kinetic limitations by investigating the effect of limiting substrate concentrations (electron donor and acceptor) on DCE and VC dechlorination kinetics and microorganism growth by bacterium VS . For this, a model based on Monod kinetics, but also accounting for competition between electron acceptors and the effect of low electron donor and acceptor concentrations (dual-substrate kinetics), was examined . Competitive coefficients for VC (7.8 +/- 1.5 microM) and DCE (3.6 +/- 1.1 microM) were obtained and included in the model . The half velocity coefficient for hydrogen, the electron donor, was experimentally determined (7 +/- 2 nM) through investigating dechlorination over different substrate concentrations . This complete model was then used, along with experimental data, to determine substrate concentrations at which the dechlorinating microorganisms would be in net decay . Notably, the model indicates net decay will result if the total electron acceptor concentration (DCE plus VC) is below 0.7 microM, regardless of electron donor levels . The ability to achieve sustainable bioremediation to acceptable levels can be greatly influenced by this threshold level.

Bioorg Chem, 2004 Apr, 32(2), 92 - 108
Characterization of two polyketide synthase genes in Exophiala lecanii-corni, a melanized fungus with bioremediation potential; Cheng Q et al.; Exophiala lecanii-corni has significant bioremediation potential because it can degrade a wide range of volatile organic compounds . In order to identify sites for the insertion of genes that might enhance this potential, a genetic analysis of E . lecanii-corni was undertaken . Two polyketide synthase genes, ElPKS1 and ElPKS2, have now been discovered by a PCR-based strategy . ElPKS1 was isolated by a marker rescue technique . The nucleotide sequence of ElPKS1 consists of a 6576-bp open reading frame encoding a protein with 2192 amino acids, which was interrupted by a 60-bp intron near the 5' end and a 54-bp intron near the 3' end . Sequence analysis, results from disruption experiments, and physiological tests showed that ElPKS1 encoded a polyketide synthase required for melanin biosynthesis . Since ElPKS1 is non-essential, it is a desirable bioengineering target site for the insertion of native and foreign genes . The successful expression of these genes could enhance the bioremediation capability of the organism . ElPKS2 was cloned by colony hybridization screening of a partial genomic library with an ElPKS2 PCR product . ElPKS2 had a 6465-bp open reading frame that encoded 2155 amino acids and had introns of 56, 67, 54, and 71 bp . Although sequence analysis of the derived protein of ElPKS2 confirmed the polyketide synthase nature of its protein product, the function of that product remains unclear.

Water Res, 2004 Mar, 38(5), 1281 - 8
Bench-scale and field-scale evaluation of catechol 2,3-dioxygenase specific primers for monitoring BTX bioremediation; Mesarch MB et al.; The objective of this work was to test a molecular genetic method for in situ monitoring of aerobic benzene, toluene, and xylene (BTX) biodegrading microorganisms . Catechol 2,3-dioxygenase (C23DO) genes occur in bacteria that biodegrade benzene, toluene, xylenes, phenol, biphenyl, and naphthalene . A competitive quantitative polymerase chain reaction (QC-PCR) technique using a single set of primers specific for an entire subfamily of C23DO genes was recently developed . To determine whether bacteria containing these C23DO genes actually exist in environments contaminated by BTX, aerobic microcosms containing previously uncontaminated soil were amended with different aromatic hydrocarbons and DNA extracts were analyzed by QC-PCR for C23DO genes . Anaerobic microcosms were established to confirm that oxygen was also necessary for the enrichment of C23DO genes . Field testing was done at two sites undergoing monitored natural attenuation . In microcosm experiments naphthalene, m-xylene, and p-xylene strongly enriched for C23DO genes while benzene, toluene, and o-xylene produced only transient, weakly detectable genes . In the field study, C23DO genes were detected in groundwater samples contaminated with either xylenes or naphthalene . The results of this study demonstrated that molecular genetic techniques can provide an accurate and rapid method to detect microorganisms capable of aromatic hydrocarbon biodegradation . Such a technique would be useful for monitoring the effectiveness of aeration technologies and for documenting microbial processes for monitored natural attenuation.

Water Res, 2004 Mar, 38(5), 1139 - 46
Study on characteristics of biocometabolic removal of omethoate by the Aspergillus spp; Chun M et al.; A strain Aspergillus spp . F1 which could effectively metabolized omethoate was screened out in this study . F1 tended to form granula with diameter 4-5mm after 5 days culture in shaker . The pH range from 4.5 to 6.5 was the suitable pH range for growth and metabolism of Aspergillus spp . F1 . The maximum omethoate removal rate was about 3.0mg/(hL), and the removal fraction of omethoate reached 90% after 8 days culture when initial concentrations of omethoate were not more than 2000mg/L in medium . There was no obvious relativity between cell growth and cometabolism of omethoate . Starch was the best carbon source for omethoate removal and the result after 3 days reached 56.6% removal . F1 could use omethoate to metabolize as single nitrogen or phosphate source . The residual fragments in medium after treatment with the Aspergillus spp . F1 were determined by gas chromatography-mass spectrometry . The analysis results showed that only fragment o,o,s,-trimethyl phosphorothioate (TEP) containing phosphorus was available and the fragment containing nitrogen was consumed by F1 thoroughly in culture process . But no accumulations of TEP were observed in the omethoate bioremediation process . F1 could effectively remove omethoate in complex nutritional environment safely.

Biodegradation, 2004 Feb, 15(1), 59 - 65
Bioremediation of BTEX hydrocarbons: effect of soil inoculation with the toluene-growing fungus Cladophialophora sp . strain T1; Prenafeta-Boldu FX et al.; The biodegradation of a mixture of benzene, toluene, ethylbenzene, xylene, (BTEX) and methyl-tert-butyl ether (MTBE) was studied in soil microcosms . Soil inoculation with the toluene-metabolising fungus Cladophialophora sp . strain T1 was evaluated in sterile and non-sterile soil . Induction of biodegradation capacity following BTEX addition was faster in the soil native microflora than in axenic soil cultures of the fungus . Toluene, ethylbenzenes, and the xylenes were metabolized by the fungus but biodegradation of benzene required the activity of the indigenous soil microorganisms . MTBE was not biodegraded under the tested environmental conditions . Biodegradation profiles were also examined under two pH conditions after a long term exposure to BTEX . At neutral conditions the presence of the fungus had little effect on the intrinsic soil biodegradation capacity . At an acidic pH, however, the activity of the indigenous degraders was inhibited and the presence of Cladophialophora sp . increased significantly the biodegradation rates of toluene and ethylbenzene . Comparison of the BTEX biodegradation rates measured in soil batches combining presence and absence of indigenous degraders and the fungal inoculum indicated that no severe antagonism occurred between the indigenous bacteria and Cladophialophora sp . The presence of the fungal inoculum at the end of the experiments was confirmed by PCR-TGGE analysis of small subunits of 18S rDNA.

Biodegradation, 2004 Feb, 15(1), 1 - 8
Effects of fungal bioaugmentation and cyclodextrin amendment on fluorene degradation in soil slurry; Garon D et al.; This study assesses the potential of fungal bioaugmentation and the effect of maltosyl-cyclodextrin amendment, as an approach to accelerate fluorene biodegradation in soil slurries . 47 fungal strains isolated from a contaminated site were tested in the biodegradation of fluorene . Results showed the greater efficiency of "adaptated" fungi isolated from contaminated soil vs . reference strains belonging to the collection of the laboratory . These assays allowed us to select the most efficient strain, Absidia cylindrospora, which was used in a bioaugmentation process . In the presence of Absidia cylindrospora, more than 90% of the fluorene was removed in 288 h while 576 h were necessary in the absence of fungal bioaugmentation . Maltosyl-cyclodextrin, a branched-cyclodextrin was chosen in order to optimize fluorene bioavailability and biodegradation in soil slurries . The results of this study indicate that Absidia cylindrospora and maltosyl-cyclodextrin could be used successfully in bioremediation systems.

Sci Total Environ, 2004 Feb 5, 319(1-3), 27 - 37
Pearl aquaculture-profitable environmental remediation?
Gifford S, Dunstan RH, O'Connor W, Roberts T, Toia R.
Bivalve molluscs are filter feeders, with pearl oysters able to filter water at rates up to 25 lh(-1)g(-1) of dry wt . tissue . Since this process leads to rapid bioaccumulation of recalcitrant pollutants such as heavy metals, organochlorine pesticides and hydrocarbons from impacted sites, it has prompted the widespread use of molluscs as biomonitors to quantify levels of marine pollution . This paper proposes pearl oyster deployment as a novel bioremediation technology for impacted sites to remove toxic contaminants, reduce nutrient loads and lower concentrations of microbial pathogens . Estimates extrapolated from the literature suggest that a modest pearl oyster farm of 100 t oyster material per year could remove 300 kg heavy metals plus 24 kg of organic contaminants via deposition into the tissue and shell . Furthermore, it was estimated that up to 19 kg of nitrogen may be removed from the coastal ecosystem per tonne of pearl oyster harvested . Pearl oysters are also likely to filter substantial amounts of sewage associated microbial pathogens from the water column . Method of cultivation and site selection are the key to minimising negative environmental impacts of bivalve cultivation . Deployment of oysters at sites with high nutrient and contaminant loadings would be advantageous, as these compounds would be removed from the ecosystem whilst generating a value-added product . Future potential may exist for harvesting bio-concentrated elements for commercial production.

J Appl Microbiol, 2004, 96(3), 510 - 20
Bioremediation of creosote-contaminated soil in South Africa by landfarming; Atagana HI; AIMS: To determine the combined effects of biostimulation and bioaugmentation in the landfarming of a mispah form (lithosol; food and Agriculture Organisation (FAO)) soil contaminated with >310000 mg kg-1 creosote with a view to developing a bioremediation technology for soils heavily contaminated with creosote . METHODS AND RESULTS: The excavated soil was mixed with 2500 kg ha-1 dolomitic lime and 2000 kg ha-1 mono-ammonium phosphate (MAP) before spreading over a treatment bed of shale reinforced with clay . Sewage sludge (500 kg) was ploughed into 450 m3 of contaminated soil in the second and sixth months of treatment . A further 1000 kg ha-1 MAP was added to the soil at the end of the fifth month . Moisture was maintained at 70% field capacity . Total creosote was determined by the US Environmental Protection Agency (EPA) method 418.1 and concentrations of selected creosote components were determined by gas chromatography/flame ionisation detection (GC/FID) . Total creosote was reduced by more than 90% by the 10th month of landfarming . The rate of reduction in creosote concentration was highest after the addition of sewage sludge . The three-ring PAHs were more slowly removed than naphthalene and the phenolic compounds . The four- and five-ring PAHs, although persist until the end of treatment, were reduced by 76-87% at the end of the experiment . CONCLUSIONS: A combination of biostimulation and bioaugmentation during landfarming could enhance the bioremediation of soils heavily contaminated with creosote . SIGNIFICANCE AND IMPACT OF THE STUDY: The study provides information on the management of a combination of biostimulation and bioaugmentation during landfarming, and contributes to the knowledge and database necessary for the development of a technology for bioremediating creosote-contaminated land.

Mar Biotechnol (NY), 2002 Dec, 4(6), 559 - 64
Bioremediation of fish cannery wastewater with yeasts isolated from a drainage canal; Urano N et al.; Several yeasts were isolated from a drainage canal in a Japanese fish food processing factory . They were characterized by the decomposition of organic polymers such as proteins and reducing sugars, their growth in the wastewater, the decrease in total organic carbon (TOC), and taxonomy . Three strains of yeast dominated the sample: Debaryomyces occidentalis (P1), Trichosporon ovoides (P19), and a strain that could not be identified (S27) . Strain P19 had the highest TOC-decreasing activity and was immobilized onto chitosan beads . The immobilized yeasts reduced the TOC from 1.2 x 103 to 3.0 x 102 mg of C/L per day in the fish cannery wastewater.

Huan Jing Ke Xue, 2003 Nov, 24(6), 144 - 7
{Experimental research on bioremediation of groundwater contaminated by herbicide atrazine}; Hu H et al.; The experimental research on the static degradation and treatment of groundwater contaminated by herbicide atrazine was conducted by using bacterium AT which was isolated from the sludge outlet of workshop of the pesticide factory . And the result indicated that bacterium AT had the ability of degradation of atrazine with pH ranged from 5.0 to 10.0, and the optimum extent was 6.5-8.0 . The experimental conditions (pH = 7.5, t = 10 degrees C) were similar to that of the aquifer in study area . Then the rate of degradation of atrazine was up to 31.08% for one addition of bacterium AT . And the environmental factors changed simultaneously in the course of experiment such as DO, pH and etc . decreasing with the reducing of concentration of bacterium AT . In addition, a mode of dropping bacteria was designed to simulate the condition of throwing bacteria in field . And the permeability of aquifer decreased 60.54% after treatment and the renewals were 48.96% after washing with clean water for 10 days, which indicated the method of renewal is effectual.

Biotechnol Prog, 2004 Jan-Feb, 20(1), 87 - 95
Toxic effects of chromium(VI) on anaerobic and aerobic growth of Shewanella oneidensis MR-1; Viamajala S et al.; Cr(VI) was added to early- and mid-log-phase Shewanella oneidensis (S . oneidensis) MR-1 cultures to study the physiological state-dependent toxicity of Cr(VI) . Cr(VI) reduction and culture growth were measured during and after Cr(VI) reduction . Inhibition of growth was observed when Cr(VI) was added to cultures of MR-1 growing aerobically or anaerobically with fumarate as the terminal electron acceptor . Under anaerobic conditions, there was immediate cessation of growth upon addition of Cr(VI) in early- and mid-log-phase cultures . However, once Cr(VI) was reduced below detection limits (0.002 mM), the cultures resumed growth with normal cell yield values observed . In contrast to anaerobic MR-1 cultures, addition of Cr(VI) to aerobically growing cultures resulted in a gradual decrease of the growth rate . In addition, under aerobic conditions, lower cell yields were also observed with Cr(VI)-treated cultures when compared to cultures that were not exposed to Cr(VI) . Differences in response to Cr(VI) between aerobically and anaerobically growing cultures indicate that Cr(VI) toxicity in MR-1 is dependent on the physiological growth condition of the culture . Cr(VI) reduction has been previously studied in Shewanella spp., and it has been proposed that Shewanella spp . may be used in Cr(VI) bioremediation systems . Studies of Shewanella spp . provide valuable information on the microbial physiology of dissimilatory metal reducing bacteria; however, our study indicates that S . oneidensis MR-1 is highly susceptible to growth inhibition by Cr(VI) toxicity, even at low concentrations {0.015 mM Cr(VI)}.

J Environ Sci (China), 2003 Nov, 15(6), 859 - 62
Influence of nonionic surfactant on the solubilization and biodegradation of phenanthrene; Yang JG et al.; Phenanthrene was solubilized in two different nonionic surfactants, Tween80 and Triton X-100 . The bioavailability of phenanthrene to the bacteria isolated from the petroleum contaminated soils was studied based on the rotary flasks experiments . The results showed that the concentration of nonionic surfactants above the critical micelle concentration (CMC) can increase the solubility of phenanthrene in water and were innoxious to the phenanthrene-degrading bacteria; phenanthrene solubilized in the micelles of Tween80 was bioavailable and biodegradable . The research demonstrated the potential of surfactant-enhanced bioremediation of soils contaminated by hydrophobic organic compounds (HOCs).

Phytochemistry, 2004 Feb, 65(3), 249 - 59
Horseradish peroxidase: a modern view of a classic enzyme; Veitch NC; Horseradish peroxidase is an important heme-containing enzyme that has been studied for more than a century . In recent years new information has become available on the three-dimensional structure of the enzyme and its catalytic intermediates, mechanisms of catalysis and the function of specific amino acid residues . Site-directed mutagenesis and directed evolution techniques are now used routinely to investigate the structure and function of horseradish peroxidase and offer the opportunity to develop engineered enzymes for practical applications in natural product and fine chemicals synthesis, medical diagnostics and bioremediation . A combination of horseradish peroxidase and indole-3-acetic acid or its derivatives is currently being evaluated as an agent for use in targeted cancer therapies . Physiological roles traditionally associated with the enzyme that include indole-3-acetic acid metabolism, cross-linking of biological polymers and lignification are becoming better understood at the molecular level, but the involvement of specific horseradish peroxidase isoenzymes in these processes is not yet clearly defined . Progress in this area should result from the identification of the entire peroxidase gene family of Arabidopsis thaliana, which has now been completed.

Environ Sci Technol, 2004 Jan 15, 38(2), 632 - 7
Combined bioaugmentation and biostimulation to cleanup soil contaminated with high concentrations of atrazine; Silva E et al.; We developed a joint bioaugmentation and biostimulation approach for the clean up of soil contaminated with high (168.7 and 337.4 microg g(-1)) concentrations of the herbicide atrazine (2-chloro-4-(ethylamino)-6-isopropylamino-s-triazine) . Pseudomonas sp . strain ADP (P . ADP) was used for bioaugmentation (approximately 10(7) cells g(-1) soil), and citrate (concentration range 5.8-40 mg g(-1) soil) and succinate (6.2-30.8 mg g(-1)) were used for biostimulation . The study soil had indigenous potential for atrazine mineralization (54.4 +/- 2% of 168.7 microg g(-1) mineralized after 67 day), but rapid mineralization only took place after a prolonged acclimation phase (approximately 28 days) . Inoculation with P . ADP alone resulted in a limited improvement in mineralization (e.g., 30.6 +/- 1% mineralization of 168.7 microg g(-1) of atrazine in inoculated soil cf . < 0.5% in noninoculated in 7 days) . Quantification of surviving numbers of P . ADP revealed a 10-fold decline from initial levels . However, bioaugmentation together with citrate or succinate biostimulation markedly increased P . ADP cell survival and atrazine mineralization (e.g., addition of 11.6 mg g(-1) of citrate increased mineralization of 337.4 microg g(-1) of atrazine from < 2 to 79.9 +/- 1% in 13 days) . A critical parameter in determining the extent of atrazine mineralization by P . ADP was C(s):N(atz) (soluble carbon to atrazine nitrogen ratio): C(s):N(atz) > 40 was required for maximal atrazine mineralization . We suggest our observations may be used as a framework for rational bioremediation of field soils contaminated with atrazine.

Environ Sci Technol, 2004 Jan 15, 38(2), 617 - 31
Combined application of stable carbon isotope analysis and specific metabolites determination for assessing in situ degradation of aromatic hydrocarbons in a tar oil-contaminated aquifer; Griebler C et al.; To evaluate the intrinsic bioremediation potential in an anoxic tar oil-contaminated aquifer at a former gasworks site, groundwater samples were qualitatively and quantitatively analyzed by compound-specific isotope analysis (CSIA) and signature metabolites analysis (SMA) . 13C/12C fractionation data revealed conclusive evidence for in situ biodegradation of benzene, toluene, o-xylene, m/p-xylene, naphthalene, and 1-methylnaphthalene . In laboratory growth studies, 13C/12C isotope enrichment factors for anaerobic degradation of naphthalene (epsilon = -1.1 +/- 0.4) and 2-methylnaphthalene (epsilon = -0.9 +/- 0.1) were determined with the sulfate-reducing enrichment culture N47, which was isolated from the investigated test site . On the basis of these and other laboratory-derived enrichment factors from the literature, in situ biodegradation could be quantified for toluene, o-xylene, m/p-xylene, and naphthalene . Stable carbon isotope fractionation in the field was also observed for ethylbenzene, 2-methylnaphthalene, and benzothiophene but without providing conclusive results . Further evidence for the in situ turnover of individual BTEX compounds was provided by the presence of acetophenone, o-toluic acid, and p-toluic acid, three intermediates in the anaerobic degradation of ethylbenzene, o-xylene, and p-xylene, respectively . A number of groundwater samples also contained naphthyl-2-methylsuccinic acid, a metabolite that is highly specific for the anaerobic degradation of 2-methylnaphthalene . Additional metabolites that provided evidence on the anaerobic in situ degradation of naphthalenes were 1-naphthoic acid, 2-naphthoic acid, 1,2,3,4-tetrahydronaphthoic acid, and 5,6,7,8-tetrahydronaphthoic acid . 2-Carboxybenzothiophene, 5-carboxybenzothiophene, a putative further carboxybenzothiophene isomer, and the reduced derivative dihydrocarboxybenzothiophene indicated the anaerobic conversion of the heterocyclic aromatic hydrocarbon benzothiophene . The combined application of CSIA and SMA, as two reliable and independent tools to collect direct evidence on intrinsic bioremediation, leads to a substantially improved evaluation of natural attenuation in situ.

Int J Phytoremediation, 2003, 5(4), 281 - 92
Technical note: fate and transport of jet fuel (JP-8) in soils with selected plants; Karthikeyan R et al.; Remediation of soil and groundwater contaminated by leaking fuel storage tanks may be assisted by plants, although plant effects on abiotic and biotic removal processes remain unclear . The objectives of this study were to investigate abiotic and biotic removal of JP-8, a kerosene-based jet fuel, in soils with plants, and to determine the effects of plant-induced water movement . Loss of JP-8 in a dry-soil, control column was 25% after 5 months, primarily due to volatilization and gas-phase diffusion . By comparison, managed treatments with simulated surface spills averaged 86% mass reduction at 5 months, indicating an important contribution of biodegradation . Overall JP-8 mass reduction was similar in surface and subsurface-irrigated systems, indicating water content, not mode of water application, influences bioremediation in near-surface systems . The JP-8 concentration reductions in soil columns contaminated above a simulated watertable were 36% after 3 months and 50% after 12 months for vegetated columns compared to 26% and 34% in unplanted columns . Downward movement of JP-8 in unplanted columns was double that in planted columns . Near the groundwater table, JP-8 persists longer than near the soil surface . Plants promote upward movement of water and help draw spilled JP-8 to aerobic near-surface soil.

Int J Phytoremediation, 2003, 5(3), 225 - 34
Degradation of crude oil in the rhizosphere of Sorghum bicolor; Banks MK et al.; Dissipation of petroleum contaminants in the rhizosphere is likely the result of enhanced microbial degradation . Plant roots may encourage rhizosphere microbial activity through exudation of nutrients and by providing channels for increased water flow and gas diffusion . Phytoremediation of crude oil in soil was examined in this study using carefully selected plant species monitored over specific plant growth stages . Four sorghum (Sorghum bicolor L.) genotypes with differing root characteristics and levels of exudation were established in a sandy loam soil contaminated with 2700 mg crude oil/kg soil . Soils were sampled at three stages of plant growth: five leaf, flowering, and maturity . All vegetated treatments were associated with higher remediation efficiency, resulting in significantly lower total petroleum hydrocarbon concentrations than unvegetated controls . A relationship between root exudation and bioremediation efficiency was not apparent for these genotypes, although the presence of all sorghum genotypes resulted in significant removal of crude oil from the impacted soil.

Environ Int, 2004 Apr, 30(2), 261 - 78
Metal bioremediation through growing cells; Malik A; Heavy-metal pollution represents an important environmental problem due to the toxic effects of metals, and their accumulation throughout the food chain leads to serious ecological and health problems . Metal remediation through common physico-chemical techniques is expensive and unsuitable in case of voluminous effluents containing complexing organic matter and low metal contamination . Biotechnological approaches that are designed to cover such niches have, therefore, received great deal of attention in the recent years . Biosorption studies involving low-cost and often dead/pretreated biomass have dominated the literature and, subsequently, extensive reviews focusing on equilibrium and kinetics of metal biosorption have also come up . However, the low binding capacity of biomass for certain recalcitrant metals such as Ni and failure to effectively remove metals from real industrial effluents due to presence of organic or inorganic ligands limit this approach . At times, when pure biosorptive metal removal is not feasible, application of a judicious consortium of growing metal-resistant cells can ensure better removal through a combination of bioprecipitation, biosorption and continuous metabolic uptake of metals after physical adsorption . Such approach may lead to simultaneous removal of toxic metals, organic loads and other inorganic impurities, as well as allow optimization through development of resistant species . However, sensitivity of living cells to extremes of pH or high metal concentration and need to furnish metabolic energy are some of the major constraints of employing growing cells for bioremediation . The efforts to meet such challenges via isolation of metal-resistant bacterial/fungal strains and exploitation of organic wastes as carbon substrates have began . Recent studies show that the strains (bacteria, yeast and fungi) isolated from contaminated sites possess excellent capability of metal scavenging . Some bacterial strains possess high tolerance to various metals and may be potential candidates for their simultaneous removal from wastes . Evidently, the stage has already been set for the application of metal-resistant growing microbial cells for metal harvesting . This review focuses on the applicability of growing bacterial/fungal/algal cells for metal removal and the efforts directed towards cell/process development to make this option technically/economically viable for the comprehensive treatment of metal-rich effluents.

J Microbiol Methods, 2004 Feb, 56(2), 181 - 91
Soil washing improves the recovery of total community DNA from polluted and high organic content sediments; Fortin N et al.; Treatment of soil with surfactants and chelating agents is used in bioremediation studies to desorb and solubilize contaminants to increase their bioavalability to microorganisms . In the same way that pollutants are made more bioavailable to microorganisms, the procedure can be used to remove potential interfering materials from soil prior to cell lysis and extraction of DNA from indigenous microorganisms . The effect of soil washing was evaluated by extracting DNA from sediments of an intertidal freshwater wetland contaminated with hydrocarbons and from highly contaminated marine sediments from Sydney Harbour, Nova Scotia, Canada . Sediment samples had total organic carbon (TOC) contents that varied between 0.2% and 13% . The chemical lysis technique was also examined by comparison of an ammonium acetate precipitation of proteins and humic acids with a hexadecyltrimethylammonium bromide (CTAB) incubation and phenol:chloroform extraction . In this study, the incorporation of soil washing steps facilitated the desorption of contaminants from sediment surfaces and improved the recovery of DNA of amplifiable quality from both freshwater and marine sediments . CTAB contributed only slightly to the recovery of DNA of higher quality in the most contaminated sample from Sydney Harbour and was concomitant with a decrease in DNA yield in both sediment types . The incorporation of a soil washing step prior to the extraction of DNA from polluted environments may be important to solubilize and remove contaminants when high-quality DNA is required for subsequent analyses.

Environ Sci Technol, 2004 Jan 1, 38(1), 148 - 55
Sorption of phenanthrene to environmental black carbon in sediment with and without organic matter and native sorbates; Cornelissen G et al.; Strong sorption to soot- and charcoal-like material (collectively termed black carbon or BC) in soils and sediments is possibly the reason for recent observations of elevated geosorbent-water distribution ratios, slow desorption, limited uptake, and restricted bioremediation . We evaluated the role of environmental BC in the sorption of phenanthrene (PHE) to a polluted lake sediment from a Rhine River sedimentation area . Sorption isotherms were determined over a wide concentration range (0.0005-6 microg/ L) for the original sediment (with organic matter or OM, native sorbates, and BC), sediment from which we had stripped > 90% of the native sorbates (only OM and BC), and sediment combusted at 375 degrees C (only BC) . The sorption isotherms of the original and stripped sediments were almost linear (Freundlich coefficient or n(F) > 0.9), whereas the isotherm of the BC remaining after the sediment combustion was highly nonlinear (n(F) = 0.54) . At low concentrations (ng/L range), PHE sorption to BC in the combusted sediment was found to exceed the total PHE sorption in the original and stripped sediments . This implies that it may not be possible to use a BC-water sorption coefficient measured in combusted sediment to estimate total sorption to the original sediment . This "intrinsic" BC-water sorption coefficient after combustion was calculated to be 9 times larger than the "environmental" one in the untreated sediment . Competition between the added PHE and the native PAHs and/or OM may explain this difference . It appears that, at low aqueous PHE concentrations (ng/L and below), BC is the most important geosorbent constituent with respect to sorption . At higher concentrations (microg/L), BC sorption sites become saturated and BC sorption is overwhelmed by sorption to the other OM constituents . Because sorption is a central process affecting contaminant behavior and ecotoxicity, understanding this process can strongly contribute to risk assessment and fate modeling.

Environ Pollut, 2004, 128(3), 429 - 35
Priming effects on PAH degradation and ecotoxicity during a phytoremediation experiment; Joner EJ et al.; An experiment was conducted to distinguish priming effects from the effects of phytoremediation of a creosote-polluted soil . The concentration of 13 polycyclic aromatic hydrocarbons (PAHs), and their combined soil toxicity (using four bioassays), was determined on recently excavated, homogenized soil and on such soil subjected to a time-course phytoremediation experiment with lucerne . The results showed a high priming effect, with minor positive and synergistic effects of planting and fertilization on PAH degradation rates . At the end of the experiment, PAH degradation reached 86% of the initial 519 mg PAHs kg(-1) . Two of the four toxicity tests (bioluminescence inhibition and ostracod growth inhibition) corroborated the chemical data for residual PAHs, and indicated a significant reduction in soil toxicity . We conclude that priming effects can easily surpass treatment effects, and that an unintentional pre-incubation that ignores these effects can jeopardize the full quantitative assessment of in situ bioremediation of contaminated soil.

Biotechnol Lett, 2003 Nov, 25(22), 1925 - 32
Aerobic biodegradation of trichloroethylene using a consortium of five bacterial strains; Meza L et al.; Degradation with an aerobic consortium was used to evaluate the bioremediation trichloroethylene (TCE) as a model substrate . After one week, 228-1186 mg TCE l(-1) was degraded at rates of 20-50 microg TCE l(-1) h(-1) . The introduction of 10 mg toluene l(-1) enhanced the degradation rates for TCE when greater than 600 mg l(-1) . Using isolated enzymes, a TCE degradation intermediate(s) appears inhibitory to the oxygenase enzymes thereby diminishing the overall degradation.

Mol Plant Microbe Interact, 2004 Jan, 17(1), 6 - 15
Rhizoremediation: a beneficial plant-microbe interaction; Kuiper I et al.; Worldwide, contamination of soil and ground water is a severe problem . The negative effects of pollutants on the environment and on human health are diverse and depend on the nature of the pollution . The search for alternative methods for excavation and incineration to clean polluted sites resulted in the application of bioremediation techniques . In this review, we describe some generally accepted bioremediation tools and subsequently focus on the combination of two approaches, phytoremediation and bioaugmentation, resulting in rhizoremediation . During rhizoremediation, exudates derived from the plant can help to stimulate the survival and action of bacteria, which subsequently results in a more efficient degradation of pollutants . The root system of plants can help to spread bacteria through soil and help to penetrate otherwise impermeable soil layers . The inoculation of pollutant-degrading bacteria on plant seed can be an important additive to improve the efficiency of phytoremediation or bioaugmentation.

Environ Toxicol Chem, 2003 Dec, 22(12), 2853 - 60
Assessment of bioavailability limitations during slurry biodegradation of petroleum hydrocarbons in aged soils; Huesemann MH et al.; In an effort to determine whether bioavailability limitations are responsible for the slow or incomplete hydrocarbon biodegradation in aged soils, both the rate of desorption (rdes) and biodegradation (rbio) was measured for n-alkanes and polynuclear aromatic hydrocarbons (PAHs) at different times during the slurry biotreatment of six different soils . While all n-alkanes were biodegraded to various degrees depending on their respective carbon number and the soil organic matter content, none of them were desorbed to a significant extent, indicating that these saturated hydrocarbons do not need to be transferred from the soil particles into the aqueous phase in order to be metabolized by microorganisms . Most two- and three-ring PAHs biodegraded as fast as they were desorbed (rbio = rdes); that is, desorption rates controlled biodegradation rates . By contrast, the biodegradation kinetics of four-, five-, and six-ring PAHs was limited by microbial factors during the initial phase (rbio < rdes) while becoming mass-transfer rate limited during the final phase of bioremediation treatment (rbio = rdes) . Whenever PAH biodegradation stalled or did not occur at all (rbio = 0), it was never due to bioavailability limitations (rdes >> 0) but was more likely caused by microbial factors . such as the absence of specific PAH degraders or cometabolic substrates . Consequently, PAHs that are found to be microbially recalcitrant in aged soils may not be so because of limited bioavailability and thus could pose a greater risk to the environment than previously thought.

Adv Appl Microbiol, 2003, 53, 61 - 84
Anaerobic dehalogenation of organohalide contaminants in the marine environment; Haggblom MM et al.; Microbially mediated dehalogenation processes contribute to the global cycling of both biogenic and anthropogenic halogenated organic compounds . Detailed information on biodegradation mechanisms for a variety of organohalides and on the microorganisms mediating these processes has greatly increased our understanding of the cycling and fate of these unique and widespread compounds in our environment . The marine environment appears to be a particularly rich source of dehalogenating microorganisms . It is well established by laboratory and field studies that anaerobic dehalogenation of sediment contaminants, such as PCBs, pesticides, and dioxins, occurs intrinsically and can be enhanced via various methods . Specific dehalogenating bacterial populations can be enriched on various organohalides . Biodehalogenation processes are likely to be significantly affected by the prevailing terminal electron-accepting condition, and thus, biotransformation of organohalide contaminants in marine and estuarine environments will vary as a function of the redox conditions within the sediment profile . Fundamental knowledge of the activities and interactions of dehalogenating microorganisms is providing a strong basis for development of new bioremediation technologies for removal of harmful halogenated compounds from our environment.

J Agric Food Chem, 2003 Dec 31, 51(27), 8015 - 9
Biodegradation kinetics of endosulfan by Fusarium ventricosum and a Pandoraea species; Siddique T et al.; Endosulfan, classified as an organochlorine pesticide, is rated by the U.S . EPA as a Category 1 pesticide with extremely high acute toxicity . This study describes the biodegradation kinetics of endosulfan and the metabolic pathway utilized by Fusarium ventricosum and a Pandoraea sp . Complete disappearance of both alpha- and beta-endosulfan was observed during 12 days of incubation with F . ventricosum in flasks containing 100 mg L(-)(1) of endosulfan . The rate constants (k) for biodegradation of alpha- and beta-endosulfan by F . ventricosum using zero-order kinetics were 14.22 and 6.60 mg L(-)(1) day(-)(1), respectively . The Pandoraea sp . degraded about 95 and 100% of alpha- and beta-endosulfan, respectively, in 18 days of incubation in flasks spiked with 100 mg L(-)(1) of endosulfan . The rate constants (k) for biodegradation of alpha- and beta-endosulfan by the Pandoraea sp . were 8.19 and 3.78 mg L(-)(1) day(-)(1), respectively . Both fungal and bacterial strains formed less toxic endosulfan diol and endosulfan ether as metabolites during metabolism of endosulfan . The results of this study suggest that these novel strains may be used for the bioremediation of endosulfan-contaminated sites.

Microb Ecol, 2004 May, 47(4), 407 - 15
Biostimulation of natural microbial assemblages in oil-amended vegetated and desert sub-Antarctic soils; Delille D et al.; A field study was initiated in December 2000 in two selected soils of The Grande Terre (Kerguelen Archipelago) with the objective of determining the long-term effects of fertilizer addition on the biodegradation rate and the toxicity of oil residues under severe sub-Antarctic conditions . Two soils were selected . The first site supports an abundant vegetal cover; the second one was desert soil, devoid of plant material . These two soils were located in the vicinity of the permanent station of Port-aux-Francais (69 degrees 42'E; 49 degrees 19'S) . A series of five experimental plots (0.75 x 0.75 m) were settled firmly into each of the studied soils . Each plot received 500 mL of diesel or Arabian light crude oil, and some of them were treated with a bioremediation agent: slow-release fertilizer Inipol EAP-22 (Elf Atochem) . All the plots were sampled on a regular basis over a 1 year period . Heterotrophic and hydrocarbon-degrading microorganisms increased by two orders of magnitude during the first month of the experimentation in all treated enclosures, but differences appeared between the different plots . The microbial response was improved by bioremediation treatments . However, fertilizer addition had a greater impact on the desert soil when compared to the vegetated one . All chemical indices show a reduction of alkanes and light aromatics . Toxicity results show a high variability between treatments and environmental conditions . As a conclusion, it is clear that the microbial response was rapid and efficient in spite of the severe weather conditions, and the rate of degradation was improved by bioremediation treatments . However, after 1 year of treatment, the signal of a relatively high toxicity of oiled residues remained present in the two studied soils.

Water Res, 2004 Jan, 38(2), 267 - 76
Biosorption of phenol and chlorophenols by acclimated residential biomass under bioremediation conditions in a sandy aquifer; Antizar-Ladislao B et al.; Phenol and chlorophenols are common environmental contaminants . The fate and transport of these chemicals must be sufficiently understood to predict detrimental environmental impacts and to develop technically and economically appropriate remedial action to minimise environmental degradation . In order to gain a better understanding of the many mechanisms influencing the fate of phenol and chlorophenols in a sandy aquifer, we conducted biosorption experiments with biomass collected from a simulated aquifer polluted by consecutive accidental spills of phenol, 2-monochlorophenol, 2,4,6-trichlorophenol and pentachlorophenol under continuous bioremediation conditions following a closed-loop configuration during 180 days . A comparative study of the biosorption capacity of phenol and chlorophenols characterised by different physicochemical properties, at different pHs in the range of 6.0+/-0.1 to 9.0+/-0.1 showed the following: (i) the biosorption of phenol and chlorophenols on resident biomass was rapid (equilibrium reached in less than 2h); (ii) the experimental data followed the Freundlich isotherm; (iii) changes in pH from 6.0+/-0.1 to 9.0+/-0.1 resulted in a decrease in the equilibrium biosorption capacity (qeq); (iv) both Freundlich parameters (KF, n) should be used together as predictive parameters in mathematical models to simulate the fate of phenol and chlorophenols in the aquifer; (v) qeq of phenol and chlorophenols investigated in this study were satisfactorily correlated to their hydrophobicity (Kow) with a correlation factor 0.98 . In addition, available data from other reported studies fell in the same correlation curve . The results of the present study should be introduced in mathematical models developed to predict the effect of biomass fate and transport of contaminants in aquifers during bioremediation conditions.

Science, 2003 Dec 12, 302(5652), 1967 - 9
Genome of Geobacter sulfurreducens: metal reduction in subsurface environments; Methe BA et al.; The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior . These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments . As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.

Environ Technol, 2003 Oct, 24(10), 1291 - 302
The effect of amount of crude oil on extent of its biodegradation in open water- and sandy beach-laboratory simulations; Lepo JE et al.; We examined the biodegradation of varying amounts of artificially weathered Alaskan North Slope crude oil in laboratory microcosm test systems that use natural seawater and simulate spills in open water and on sandy beaches . The model bioremediation treatment consisted of periodic applications of marine bacteria, selected to degrade n-alkanes and a range of aromatic compounds, suspended in a salts solution that supplied inorganic nitrogen and phosphorous . Beach microcosms dosed with low and high oiling lost an average of 22.5% and 11.3% oil weight, respectively . Open-water microcosms dosed with high and low oiling lost 19.1% and 2.9% oil weight, respectively . Thus, the lower doses of oil were more efficiently degraded . The model bioremediation treatment also affected a greater number of selected analytical endpoints in the lower-oil-dose than higher-dose experiments and the former showed more substantial degradation of recalcitrant components . Above a certain threshold oil concentration, bioremediation did not effectively remove oil . Below this threshold the distinction between active bioremediation treatment and intrinsic biodegradation of the controls was less prominent; i.e., fewer of the oil components were statistically depleted by remediation treatment relative to controls . Furthermore, the oil-dose range over which bioremediation was realized in these systems occurred at very low oiling levels . Thus, under the environmental conditions simulated in these microcosms, the effectiveness of bioremediation peaked over a rather narrow low-dose oiling range.

Environ Technol, 2003 Oct, 24(10), 1211 - 9
Effects of oil and bioremediation on mussel (Mytilus edulis L.) growth in mudflats; Le Floch S et al.; Mussels (Mytilus edulis L.) were exposed to crude oil during a field experiment to evaluate two bioremediation strategies (nutrient addition and nutrient addition with tilling) . The mussels were placed in 4 mesocosms: Control, Oil, Oil + Nutrients, and Oil + Nutrients + Tilled . Tilling appeared to be clearly detrimental to mussel growth . Additionally, this field experiment demonstrated that at temperatures below 5 degrees C, growth was reduced to rates undetectable by the laser diffraction method . The data on mussel shell length show that this technique does offer very sensitive and useful comparative measurements of physiological function . Measurement of shell growth has the advantage over other techniques in that it is non-invasive and non-destructive and thus may be used continuously without disturbing critical physiological and biochemical functions; however, bivalve physiology is strongly linked to environmental conditions, so it is important to include such measures (i.e . seawater temperature and turbidity) in the design of the biomonitoring program . Elevated polycyclic aromatic hydrocarbon (PAH) levels reflected bioaccumulation in mussels from all the oiled mesocosms . This correlated with reduction in growth rate . Maximum reduction in growth was observed in mussels from the tilled mesocosm which contained the lowest phenanthrene and dibenzothiophene concentrations . The tilling caused an increase in suspended solids which inhibited filter feeding activity, and resulted in suppressed growth and slower intake of PAH-laden sediment.

Chemosphere, 2004 Mar, 54(10), 1481 - 93
Extended bioremediation of PAH/PCP contaminated soils from the POPILE wood treatment facility; Hansen LD et al.; A study was conducted using two pilot-scale land-treatment units (LTUs) to evaluate the efficacy of different cultivation and maintenance schedules during bioremediation of contaminated soil from a wood treatment facility using landfarming technology . The soil contained high concentrations of polycyclic aromatic hydrocarbons (PAHs, approximately 13000 ppm) as well as of pentachlorophenol (PCP, approximately 1500 ppm) . An initial 6-month intensive-treatment phase was followed by 24 months of less-intensive treatment . During the first phase, traditional landfarming practice of regular cultivation was compared with a gas-phase composition based cultivation strategy, and both the landfarming units were intensively monitored and maintained with respect to moisture control and delivery of nutrients . The two strategies resulted in similar contaminant concentration profiles with time during this phase, although different microbial populations developed in the two-landfarming units . The second (less-intensive) treatment phase involved no moisture control and nutrient delivery beyond the initial adjustments, and compared natural attenuation (no cultivation) with quarterly cultivation of soil . Both the strategies showed similar behavior again . GC/MS analysis of the soil samples showed PAH removal including four-ring homologues . Leachability tests at zero time and after 6 and 22 months of operation showed significant reductions in leaching of PCP and low molecular weight PAHs . Extended treatment resulted in some leaching of high molecular weight PAHs . Significant biological activity was demonstrated, even at the high contaminant concentrations . Phospholipid ester-linked fatty acid (PLFA) analysis showed an increase in biomass and a divergence in community composition in soils depending on the treatment conducted.

Biotechnol Prog, 2003 Nov-Dec, 19(6), 1812 - 5
Detection of benzene, toluene, ethyl benzene, and xylenes (BTEX) using toluene dioxygenase-peroxidase coupling reactions; Xu Z et al.; We have developed a simple, whole-cell bioassay for the detection of bioavailable benzene, toluene, ethyl benzene, and xylenes (BTEX) and similar compounds . A genetically engineered E . coli strain expressing toluene dioxygenase (TDO) and toluene dihydrodiol dehydrogenase (TodD) was constructed, enabling the conversion of BTEX into their respective catechols, which were quickly converted into colored products by a horseradish peroxidase (HRP)-coupled reaction . The intensity of the color formation was correlated to concentrations of the BTEX compounds . Under the optimized conditions, a detection limit (defined as three times the standard deviation of the response obtained from the blank) of 10, 10, 20, and 50 microM was observed for benzene, toluene, ethyl benzene, and xylene, respectively . The bioassay was selective toward BTEX-related compounds with no interference observed with commonly used pesticides, herbicides, and organic solvent . The bioassay was very stable with little change in response over a 10-week period . The excellent stability suggests that the reported bioassay may be suitable for field monitoring of BTEX to identify and track contaminated water and follow the bioremediation progress.

Bioresour Technol, 2004 Mar, 92(1), 7 - 13
Activity and elution profile of laccase during biological decolorization and dephenolization of olive mill wastewater; Dias AA et al.; The performance and enzymatic strategy exhibited by basidiomycete Euc-1, a laccase producing strain, was investigated during the biodegradation of olive mill wastewater (OMW) . This strain yielded better decolorization of solidified OMW than Phanerochaete chrysosporium and removed 90% of phenols (initial concentration=800 mg l(-1)), 73% of color (initial A465=4.4), and 45% of chemical oxygen demand in batch cultures containing OMW . Since partial phenol removal occurred before the detection of enzymatic activity, no plausible correlation could be established between them . In contrast, decolorization occurred only after the detection of laccase activity and coincided with its production over time . Two laccase fractions (Lac1 and Lac2) were separated by chromatography . OMW strongly induced Lac2 that was almost absent in defined liquid medium . Furthermore, Lac2 was the main laccase fraction in the presence of OMW . This study pointed out that basidiomycete Euc-1 and its ligninolytic system could be a useful tool for the bioremediation of wastewater generated in the process of olive oil extraction.

Anal Chem, 2003 Sep 1, 75(17), 4432 - 40
Integration of electrokinetic-based multidimensional separation/concentration platform with electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry for proteome analysis of Shewanella oneidensis; Mohan D et al.; This work focuses on the development of a multidimensional electrokinetic-based separation/concentration platform coupled with electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) for achieving the high resolution and ultrasensitive analysis of complex protein/peptide mixtures . A microdialysis junction is employed as the interface for on-line combination of capillary isoelectric focusing (CIEF) with transient capillary isotachophoresis/zone electrophoresis (CITP/CZE) in an integrated platform . Besides the excellent resolving power afforded by both CIEF and CZE separations, the electrokinetic focusing/stacking effects of CIEF and CITP greatly enhance the dynamic range and detection sensitivity of MS for protein identification . The constructed multidimensional separation/concentration platform is demonstrated for the analysis of Shewanella oneidensis proteome, which has considerable implications toward the bioremediation of environmental pollutants . The electrokinetic-based platform offers the overall peak capacity comparable to those obtained using multidimensional chromatography systems, but with a much shorter run time and no need for column regeneration . Most importantly, a total of 1174 unique proteins, corresponding to 26.5% proteome coverage, are identified from the cytosolic fraction of S . oneidensis, while requiring <500 ng of proteolytic digest loaded in the CIEF capillary . The ultrasensitive capabilities of electrokinetic-based proteome approach are attributed to the concentration effect in CIEF, the electrokinetic stacking of CITP, the nanoscale peak volume in CZE, the "accurate mass tag" strategy for protein/peptide identification, and the high-sensitivity, high-resolution, and high-mass measurement accuracy of FTICR-MS.

Environ Sci Technol, 2003 Nov 1, 37(21), 5057 - 61
Chemical and biological regeneration of HDTMA-modified montmorillonite after sorption with phenol; Yang L et al.; Hexadecyltrimethylammonium (HDTMA)-modified montmorillonite (HMM) has recently been recognized as a potential sorbentto remove organic contaminants from environmental systems . Potential applications of this material highly depend on the efficiency of regenerating contaminant-sorbing HMM . In this study, we investigated a chemical (NaOH solution) and a biological (yeast Pityrosporum sp.) method to regenerate phenol-sorbing HMM . Our results showed that the sorption coefficient of phenol to HMM is not a linear function of the ratio of the substitution of HDTMA in HMM . Chemical regeneration of HMMs (0-0.7 times of its cation exchange capacity (CEC)) proved the existence of a phenol residual amount of about 3 mg x g(-1) in the HMMs tested when aqueous pH is maintained above 11 . In addition, the obvious deductions in the sorption capacity of the chemically regenerated HMMs were observed after four cycles of sorption-regeneration . However, the sorption capacities of intermediate substituted HMMs (0.3-0.7 CEC) can be completely restored by bioregeneration with yeast for extended cycles of reuse . The results imply that the bioregeneration method with yeast could be a promising technique for in-situ bioremediation of phenol-contaminated groundwater in the subsurface or for treatment of phenol containing wastewater.

Environ Sci Technol, 2003 Nov 1, 37(21), 5040 - 9
Field evaluation of the solvent extraction residual biotreatment technology; Mravik SC et al.; The Solvent Extraction Residual Biotreatment (SERB) technology was evaluated at a former dry cleaner site in Jacksonville, FL, where an area of tetrachloroethylene (PCE) contamination was identified . The SERB technology is a treatmenttrain approach for complete site restoration, which combines an active in situ dense nonaqueous-phase liquid (DNAPL) removal technology, cosolvent extraction, with a passive enhanced in situ bioremediation technology, reductive dechlorination . During the in situ cosolvent extraction test, approximately 34 kL of 95% ethanol/5% water (v:v) was flushed through the contaminated zone, which removed approximately 60% of the estimated PCE mass . Approximately 2.72 kL of ethanol was left in the subsurface, which provided electron donorfor enhancement of biological processes in the source zone and downgradient areas . Quarterly groundwater monitoring for over 3 yr showed decreasing concentrations of PCE in the source zone from initial values of 4-350 microM to less than 150 microM during the last sampling event . Initially there was little to no daughter product formation in the source zone, but after 3 yr, measured concentrations were 242 microM for cis-dichloroethylene (cis-DCE), 13 microM for vinyl chloride, and 0.43 microM for ethene . In conjunction with the production of dissolved methane and hydrogen and the removal of sulfate, these measurements indicate that in situ biotransformations were enhanced in areas exposed to the residual ethanol . First-order rate constants calculated from concentration data for individual wells ranged from -0.63 to -2.14 yr(-1) for PCE removal and from 0.88 to 2.39 yr(-1) for cis-DCE formation . First-order rate constants based on the change in total mass estimated from contour plots of the groundwater concentration data were 0.75 yr(-1) for cis-DCE, -0.50 yr(-1) for PCE, and -0.33 yr(-1) for ethanol . Although these attenuation rate constants include additional processes, such as sorption, dispersion, and advection, they provide an indication of the overall system dynamics . Evaluation of the groundwater data from the former dry cleaner site showed that cosolvent flushing systems can be designed and utilized to aid in the enhancement of biodegradation processes at DNAPL sites.

Environ Res, 2003 Nov, 93(3), 316 - 27
HCH distribution and microbial parameters after liming of a heavily contaminated soil in Rio de Janeiro; Osterreicher-Cunha P et al.; The closing down of a lindane factory near Rio de Janeiro, over 45 years ago, left an area heavily contaminated with hexachlorocyclohexane (HCH) . Remediation by soil liming was applied by government authorities in 1995 . This study aims to evaluate the HCH distribution and impact on soil microbiota due to contamination and liming . Microcosm experiments with uncontaminated soil mixed with HCH and lime indicated that lime-promoted dechlorination of HCH molecules led to leaching and volatilization of metabolites . The treatment applied transformed but did not solve the problem as most of the HCH remains in the soil . Reduced microbial respiratory activity was measured in contaminated field samples . Higher respiration rates in uncontaminated soil were reduced by HCH and lime addition; the sole addition of HCH caused a temporary increase in soil respiration, and stimulation occurred with oxygen and/or nutrient addition . A heterotrophic bacterial population around 10(9)CFU/g was found in polluted field soil, some well-known degraders having been isolated . Native soil microbiota showed resistance to high amounts of HCH and alkaline pH . The results allow considering bioremediation rather than chemical treatments to clean up the area.

J Microbiol Methods, 2003 Dec, 55(3), 865 - 74
Activity assessment of microorganisms eluted from sediments using 5-cyano-2,3-ditolyl tetrazolium chloride: a quantitative comparison of flow cytometry to epifluorescent microscopy; Gruden CL et al.; Enhanced natural recovery may be successfully implemented at contaminated sediment sites, which are often characterized by large volumes of sediments with low to moderate levels of contamination to cost-effectively reduce human and ecological risks . In order to evaluate the potential for microbial contribution to remediation strategies, physiological assessment of indigenous microorganisms is essential . We report here a method for rapid and accurate assessment of metabolically (5-cyano-2,3-ditolyl tetrazolium chloride {CTC}) active microorganisms eluted from sediment, based on flow cytometry (FCM) . Microorganisms eluted from sediment and suspended in estuarine medium were stained with CTC and counterstained with the DNA stain Picogreen (PG) . Optimal stain concentrations and incubation times were employed . FCM quantification of the dual-stained microorganisms was not statistically different (paired t test; alpha=0.05; df=10) from enumeration (total or active numbers) by an established method (fluorescent microscopy) over two orders of magnitude (approximately 10(4)-10(6)/ml) . This research suggests that FCM, which allows the collection and analysis of multiple parameters (light scatter and fluorescence emission), is a good candidate for microbial characterization in complex environmental matrices, such as sediments, across a broad range of activity levels (approximately 2% to 84% of total) . Potential applications for this FCM-based method include the rapid assessment of changes in sediment microbial activity in response to enhanced bioremediation strategies.

Water Res, 2003 Dec, 37(20), 4885 - 94
Enhanced PCE dechlorination by biobarrier systems under different redox conditions; 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 evaluate the (1) feasibility of enhancing PCE biodegradation using cane molasses and sludge cakes as the primary substrates under methanogenic and iron reducing conditions, and (2) potential of installation a sludge cake/cane molasses biobarrier to clean up PCE-contaminated aquifers . The biodegradability of sludge cake (from secondary wastewater treatment system) and cane molasses was tested using bioavailability experiments . Results show that biodegradable materials were released from sludge cake/cane molasses and utilized by microbial consortia . Based on the chemical oxygen demand (COD) tests, approximately 28 and 248 mg of biodegradable COD can be released from 1g of sludge cake and 1g of cane molasses under anaerobic conditions, which have the potential to convert 70 and 620 mg of PCE to ethylene (ETH), respectively . Reductive dechlorination was evaluated using microcosms containing primary substrates (sludge cake/cane molasses) and inocula (aquifer sediments) . Results indicate that sludge cake and cane molasses can serve as the diffusion sources of primary substrates, and enhance the reductive dechlorination of PCE under methanogenic processes . However, results from this study were not sufficient enough to show that reductive dechlorination of PCE would occur under iron-reducing conditions . This indicates that more studies need to be performed to further evaluate the role of iron reduction on the PCE dechlorination . Results reveal that it is feasible and applicable to install a sludge cake or cane molasses biobarrier to clean up PCE contaminated aquifers . From an engineering point of view, the sludge cake/cane molasses biobarrier has the potential to become an environmentally and economically acceptable technology for PCE bioremediation.

Acta Microbiol Pol, 2003, 52(2), 173 - 82
Relationship between soil microbial diversity and bioremediation process at an oil refinery; Plaza G et al.; Microbial diversity in hydrocarbon-contaminated soil was characterized during a bioremediation project at an oil refinery . The project consisted of isolation and cultivation of microbes on laboratory media and the subsequent characterization of pure isolates . In a lagoon at the Czechowice Oil Refinery, Poland, a biopile with actively and passively aerated sections was constructed and has been operated since 1997 . The bioremediation process has been continuously monitored by physical, chemical, and microbiological methods . One hundred and forty nine bacterial and fungal strains were isolated from site soils by standard procedures . Analysis of cultivable microorganisms revealed a diverse microbial population within the cultured isolates . Among isolated strains, Pseudomonas and Chryseomonas genera predominated in the bacterial population while Candida, Fusarium, and Trichophyton dominated the fungal population . This paper describes the application of traditional microbiological methods (plating and microscopic methods) to evaluate cultivable microbial diversity in bioremediated soil.

Bioresour Technol, 2004 Jan, 91(2), 123 - 33
Microbiological changes during bioremediation of explosives-contaminated soils in laboratory and pilot-scale bioslurry reactors; Fuller ME et al.; Changes in the microbial community during bioremediation of explosives-contaminated soil in a molasses-fed bioslurry process were examined . Upon addition of molasses to laboratory-scale reactors, total culturable heterotrophs increased rapidly by three to four orders of magnitude . However, heat-shocked heterotrophs and the percentage of gram-positive bacterial isolates did not increase until the soluble concentrations of 2,4,6-trinitrotoluene (TNT) and 2,4,6-trinitrobenzene (TNB) began to decrease . The number of identified phospholipid fatty acids (PLFA) and the total PLFA concentration also exhibited an immediate increase in response to molasses addition, while the concentration of branched PLFA, indicative of the gram-positive population, remained low until soluble TNT and TNB concentrations had significantly decreased . This same general relationship between explosives degradation and gram-positive-specific PLFA was observed during an experiment with a large field-scale bioslurry lagoon reactor . These results indicate that the gram-positive organisms, which have been shown to be severely impacted by even low concentrations of TNT and TNB {Current Microbiol . 35 (1997) 77; Environ . Toxicol . Chem . 17 (1998) 2185}, are able to increase in concentrations after explosives compounds are reduced to non-inhibitory levels, and should therefore be able to reestablish themselves in remediated soils.

Trends Biotechnol, 2003 Nov, 21(11), 504 - 11
Cyanobacterial postgenomic research and systems biology; Burja AM et al.; The genomic era brought with it the capacity to unlock complex interactions in organisms and biological systems . Currently, by exploiting genomic and associated protein information through in silico analyses, postgenomic research is developing rapidly . This field, which encompasses functional genomics, structural genomics, transcriptomics, pharmacogenomics, proteomics and metabolomics, allows for a systems-wide approach to biological studies . To date, bacterial postgenomic research has focused mainly on a few representative pathogenic species, leaving the vast majority of the microbial community relatively overlooked . Amongst the under-represented microorganisms are the cyanobacteria, which are important for their beneficial natural product production, bioremediation and energy applications . Here, we highlight the current status of cyanobacterial postgenomic research and assess the potential for future metabolic engineering and "cell factory" or "microbial cell" development.

Environ Sci Technol, 2003 Oct 1, 37(19), 4410 - 6
Vinyl bromide as a surrogate for determining vinyl chloride reductive dechlorination potential; Gu AZ et al.; Site evaluation for bioremediation of chlorinated ethenes may need treatability studies to assess the reductive dechlorination potential of vinyl chloride (VC) . Dehalogenation of vinyl bromide (VB) was investigated as a surrogate measurement for the dechlorination potential of VC . VB dehalogenation rates and kinetics were studied and compared with those of VC by a methanogenic reductive dechlorinating enrichment culture that was dominated by Dehalococcoides species and by microcosms from two chloroethene-contaminated sites . The enrichment culture dehalogenated VB to ethene at higher rates than VC at similar concentrations . VB was dehalogenated with a higher enzyme affinity than was VC, as indicated by their half-velocity constants, 240 +/- 150 and 21 +/- 8 microM, for VC and VB, respectively . Cross-inhibition study exhibited some evidence for competitive inhibition between VC and VB, suggesting that their degradation might be catalyzed by the same enzyme in the culture . Laboratory microcosm studies using subsurface soil and groundwater from two contaminated sites demonstrated that the production of the reductive dehalogenation product (ethene) could be detected faster with VB as a substrate than with VC . As a result, a substantially shorter (up to 5-10 times) incubation time would be required to detect the same level of reductive dehalogenation activity using VB as a surrogate for VC in treatability assessments.

Biodegradation, 2003 Oct, 14(5), 321 - 9
Naphthalene and anthracene mineralization linked to oxygen, nitrate, Fe(III) and sulphate reduction in a mixed microbial population; Ramsay JA et al.; A microbial consortium from a mixture of garden soil and an enrichment of a coal-tar contaminated sediment mineralized naphthalene and anthracene when oxygen, nitrate, Fe(III) (soluble and insoluble) or sulphate were provided as terminal electron acceptors (TEAs) . Rates of polyaromatic hydrocarbon disappearance and mineralization were similar in the presence of oxygen and nitrate, and slower with the other TEAs . A maximum mineralization of 37.5% naphthalene and 8.5% anthracene occurred in 30 and 160 days respectively when oxygen was provided as the TEA . On the other hand, only 9.5% naphthalene and 3.2% anthracene were mineralized in 42 and 160 days respectively with FeOOH . Mineralization occurred only when a TEA was provided and ceased when the naphthalene concentration decreased to non-detectable levels (less than 0.008 micromoles/L), as measured by fluorescence spectroscopy . CH4 was not detected in the headspace of any microcosm . These results showed that mineralization of polyaromatic hydrocarbons such as naphthalene and anthracene can be linked to wide range of TEAs demonstrating that intrinsic polyaromatic hydrocarbon bioremediation is possible if any of these TEAs were available.

Environ Manage, 2003 Jun, 31(6), 741 - 7
Bioremediation of soil degraded by sewage sludge: effects on soil properties and erosion losses; Ros M et al.; Soils in the Mediterranean area are very prone to erosion due to the loss of organic matter and the consequent lack of protective vegetation . In this experiment a Mediterranean degraded soil with a 15% slope was amended at a rate of 250 t ha(-1) wet weight with sewage sludge and with a mixture of sewage sludge and barley straw (70% carbon from sewage sludge and 30% from the straw) in order to study their influence on soil structure recovery and hence the soils's resistance to erosion processes . Both types of organic amendment led to an improvement in several soil properties (physical, biological, and microbiological) as a result of the spontaneous growth plant covering that became evident three months after amendment . This vegetation remained throughout the two years of the experiment and prevented the water erosion processes that normally precede soil degradation . Amendment by sewage sludge alone reduced soil loss by 80% compared with the control soil, while the mixture that included both sewage sludge and barley straw reduced losses by 84%, both reducing runoff by 57% . The amended soils showed increases in the percentage of stable aggregates, the levels of the total and water-soluble C fractions, microbial biomass C, basal respiration, and the activity of the different enzymes involved in the biogeochemical cycles of C, N, and P . The results confirm the usefulness of sewage sludge as an organic amendment for recovering damaged soils.

Adv Microb Physiol, 2003, 47, 131 - 86
The biodiversity of microbial cytochromes P450; Kelly SL et al.; The cytochrome P450 (CYP) superfamily of genes and proteins are well known for their involvement in pharmacology and toxicology, but also increasingly for their importance and diversity in microbes . The extent of diversity has only recently become apparent with the emergence of data from whole genome sequencing projects and the coming years will reveal even more information on the diversity in microbial eukaryotes . This review seeks to describe the historical development of these studies and to highlight the importance of the genes and proteins . CYPs are deeply involved in the development of strategies for deterrence and attraction as well as detoxification . As such, there is intense interest in pathways of secondary metabolism that include CYPs in oxidative tailoring of antibiotics, sometimes influencing potency as bioactive compounds . Further to this is interest in CYPs in metabolism of xenobiotics for use as carbon sources for microbial growth and as biotransformation agents or in bioremediation . CYPs are also current and potential drug targets; compounds inhibiting CYP are antifungal and anti-protozoan agents, and potentially similar compounds may be useful against some bacterial diseases such as tuberculosis . Of note is the diversity of CYP requirements within an organism, ranging from Escherichia coli that has no CYPs as in many bacteria, to Mycobacterium smegmatis that has 40 representing 1% of coding genes . The basidiomycete fungus Phanerochaete chrysosporium surprised all when it was found to contain a hundred or more CYPs . The functional genomic investigation of these orphan CYPs is a major challenge for the future.

Biotechnol Adv, 2002 Nov, 20(3-4), 215 - 28
Fulfilling the promise of biotechnology; Colwell RR; Genetic engineering has produced pharmaceuticals, disease-resistant plants, cloned animals and research and industrial products . While the comparably mature field of medical biotechnology now reveals its true potential, marine biotechnology is still in the realm of the future . As we explore the earth for new sources of natural chemicals, we now search the waters . Myriad organisms, most unknown to us, live there . Many produce compounds that can be commercialized, or the organisms themselves may be commercialized, through genetic engineering methods . For decades, scientists studied the ocean depths searching for unique molecules and organisms . But not until the early 1980s was there a synthesis uniting marine natural products, ecology, aquaculture and bioremediation research under the heading of marine biotechnology . As harvesting enough products from marine sources to produce sufficient amounts, even for study, is nearly impossible, we need to use genomics techniques to identify biologically active compounds . As we damage our oceanic ecosystems through pollution, overfishing and destructive fishing methods, opportunities to learn more about marine organisms and their commercial potential may be limited . Although governments and intergovernmental agencies are committed to funding and expanding oceanic research, more funding is needed to discover and study the ocean's vast, unplumbed resources.

Biotechnol Adv, 1994, 12(4), 653 - 62
The use of macrophytes in bioremediation; Wood B et al.; The development of reedbed technology for bioremediation is reviewed . The future development, potential and implementation of these systems are considered in detail together with the cost effectiveness and ease of maintenance.

Biotechnol Adv, 2000 Mar, 18(1), 23 - 34
Exploitation of plants for the removal of organics in environmental remediation; Macek T et al.; This review concentrates on the description of various phytoremediation technologies, paying special attention to removal of organics and the application of in vitro systems for basic research in the role of plants for the remediation of contaminated sites or flows, and in the improvement of their effectiveness . Various aspects of xenobiotic metabolism in plant cells, the role of enzymes involved, and the cooperation with rhizospheric microorganisms accelerating remediation of organics are shown . Application of this approach as well as the possibility of introduction of foreign genes into plant genome that can enhance the rate of the bioremediation are discussed.

Environ Sci Pollut Res Int, 2003, 10(5), 277 - 80
Effect of expandable clays and cometabolism on PAH biodegradability; Hwang S et al.; Pyrene and phenanthrene degradation was examined in both single and binary slurry systems for three different natural soils . It was found that the amount of total expandable clays (smectite and vermiculite) was in a good agreement with the achieved rate and extent of biodegradation . For instance, the intrinsic phenanthrene biodegradation rate was 626 microg/L/day for the soil with the largest expandable clay and 3203 microg/L/day for the soil with the least . Similarly, the smallest total pyrene biodegradation (65%) was found for the soil rich in expandable clays, compared to an 82% pyrene reduction in the soil that had the lowest amount . Mass transfer limitation after compound sorption to the clays was more pronounced for the more hydrophobic pyrene . In the presence of phenanthrene, total pyrene biodegradation increased by 2 to 7% due to cometabolism, while the total phenanthrene biodegradation was only enhanced by 0.5 to 5% in the binary system . This research demonstrated that expandable clays might govern the substrate availability to microorganisms and microbial accessibility to substrates . Therefore, the contribution of organic matter and expandable clays to sorption, desorption and biodegradation should be taken equally into account in order to better understand complex bioremediation issues.

Folia Microbiol (Praha), 2003, 48(4), 525 - 8
Decolorization and bioremediation of molasses wastewater by white-rot fungi in a semi-solid-state condition; Kahraman S et al.; Molasses wastewater (vinasse; the by-product of distillation of fermented sugar) was decolorized and its chemical oxygen demand (COD) was reduced in static cultivation using the fungi Coriolus versicolor, Funalia trogii, Phanerochaete chrysosporium and Pleurotus pulmonarius ('Pleurotus sajorcaju') . The effect of cotton stalk on decolorizing and COD removing capability of four fungi was determined . In the entire concentration range tested (10-30%), wastewater was effectively decolorized by C . versicolor and F . trogii . Cotton stalk addition stimulated the decolorization activity of all fungi . The utilization of cotton stalk represents several advantages due to its function as an attachment place and as a source of nutrients; its use also reduces process costs.

Appl Environ Microbiol, 2003 Oct, 69(10), 6337 - 9
Petroleum pollution bioremediation using water-insoluble uric acid as the nitrogen source; Koren O et al.; The biodegradation of hydrocarbon pollutants in open systems is limited by the availability of a utilizable nitrogen source . This limitation can be overcome by using uric acid . Enrichment cultures grown on crude oil-uric acid media yielded mixed and pure cultures that degraded petroleum . In a simulated open system, uric acid bound to crude oil and was available for bacterial growth and petroleum biodegradation.

Appl Environ Microbiol, 2003 Oct, 69(10), 6133 - 42
Characterization of multiple-substrate utilization by anthracene-degrading Mycobacterium frederiksbergense LB501T; Wick LY et al.; Stable carbon isotope analysis of biomass and analyses of phospholipid fatty acids (PLFA), glycolipid fatty acids (GLFA), and mycolic acids were used to characterize mixed-substrate utilization by Mycobacterium frederiksbergense LB501T under various substrate regimens . The distinct (13)C contents of anthracene and glucose as representatives of typical hydrophobic pollutants and naturally occurring organic compounds, respectively, were monitored during formation into biomass and used to quantify the relative contributions of the two carbon sources to biomass formation . Moreover, the influence of mixed-substrate utilization on PLFA, GLFA, and mycolic acid profiles and cell surface hydrophobicity was investigated . Results revealed that M . frederiksbergense LB501T degrades anthracene and forms biomass from it even in the presence of more readily available dissolved glucose . The relative ratios of straight-chain saturated PLFA to the corresponding unsaturated PLFA and the total fraction of saturated cyclopropyl-branched PLFA of M . frederiksbergense LB501T depended on the carbon source and the various rates of addition of mixed substrates, whereas no such trend was observed with GLFA . Higher proportions of anthracene in the carbon source mixture led to higher cell surface hydrophobicities and more-hydrophobic mycolic acids, which in turn appeared to be valuable indicators for substrate utilization by M . frederiksbergense LB501T . The capability of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria to utilize readily available substrates besides the poorly available PAHs favors the buildup of PAH-degrading biomass . Feeding of supplementary carbon substrates may therefore promote bioremediation, provided that it sustains the pollutant-degrading population rather than other members of the microbial community.

Appl Environ Microbiol, 2003 Oct, 69(10), 5884 - 91
Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer; Anderson RT et al.; The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo . Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells . U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 micro M in some of the monitoring wells . Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone . Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction . As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed . Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community . This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater . These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2003, 38(10), 2447 - 52
Capacity of the bioremediation technology for clean-up of soil and groundwater contaminated with petroleum hydrocarbons; Masak J et al.; A column reactor was designed and used to simulate conditions affecting the bioremediations of petroleum hydrocarbons . The work illustratively describes the aerobic (model) clean-up of soil samples enabling to predict the efficiency of a technology installed in parallel on contaminated former airport . The data showing the performance of thus precharacterized technology are presented.

Appl Biochem Biotechnol, 2003 Aug, 110(2), 75 - 90
1H-NMR study of Na alginates extracted from Sargassum spp . in relation to metal biosorption; Davis TA et al.; The use of a number of species of marine brown algae in the implementation of bioremediation strategies for toxic heavy metals is being considered and evaluated . The biosorption capacity of these algae for heavy metals resides mainly in a group of linear polysaccharides known as alginates that occur as a gel in the algal thallus . The potential for selective metal binding by the biomass of two species of Sargassum was evaluated by 1H-NMR (nuclear magnetic resonance) following a high temperature, alkaline extraction and purification of their alginate polysaccharide . The alkaline extraction protocol applied to Sargassum fluitans and Sargassum siliquosum yielded alginate samples of low viscosity, suitable for direct acquisition of well-resolved spectra . Estimates of both the ratio of beta-D-mannopyranuronosyl (M) and alpha-L-gulopyranuronosyl (G) residues along the polymer chain and the frequencies of occurrence of diad uronic acid residue pairs were obtained . Guluronic acid (G) was the major component in all extracts and the GG diads accounted for more than 49% of the polymer diads . Whereas the performance of Sargassum spp . in the metal biosorption process is a function of both its alginate content and composition, the occurrence of "G-blocks" in both purified alginates and in the raw brown seaweed is critical because it results in a well-established selectivity for divalent ions, potentially increasing the commercial effectiveness of targeted biosorption as a means of remediation.

Water Res, 2003 Jul, 37(13), 3189 - 93
Adsorption of vitamin B12 to alumina, kaolinite, sand and sandy soil; Hashsham SA et al.; Vitamin B12 is an important component of media used to stimulate the growth of many anaerobic microbes that dechlorinate aliphatic compounds . Its delivery to the subsurface is therefore a concern for enhanced in situ bioremediation and bioaugmentation . In situ circulation of vitamin B12 and a chemical reductant has also been field tested for treatment of chlorinated methanes, ethanes, and ethenes . The objective of this study was to determine the extent of B12 (added as cyanocobalamin) adsorption to aquifer solids . Batch studies indicated a minor amount of adsorption to kaolinite clay (Freundlich Kf = 1.5 (microgram/g) (mL/microgram)1/n and 1/n = 0.39) and sand (Kf = 0.70 (microgram/g) (mL/microgram)1/n and 1/n = 0.84), and no detectable adsorption to alumina . Column studies using a 3H2O tracer and vitamin B12 in distilled water (10 microM) resulted in a B12 retardation factor (R) of approximately 2 for both sand (0.14% organic carbon) and a sandy soil (2.5% organic carbon) . Using groundwater containing organic carbon (2.8 mg/L) in place of distilled water did not significantly change R . The relatively low value for R indicates vitamin B12 can be distributed throughout a contaminated aquifer without experiencing significant losses to adsorption.

Environ Toxicol, 2003 Oct, 18(5), 279 - 83
Cyst-based toxicity tests . XVIII . Application of ostracodtoxkit microbiotest in a bioremediation project of oil-contaminated sediments: sensitivity comparison with Hyalella azteca solid-phase assay; Chial BZ et al.; To further validate the scope of use of the 6-day sediment contact microbiotest conducted with the ostracod Heterocypris incongruens, we compared the sensitivity of this small-scale culture/maintenance-free assay with the 14-day solid-phase Hyalella azteca test . The present study was undertaken within the framework of a Canadian bioremediation project on oil-contaminated freshwater sediments along an intertidal shoreline of the Saint-Lawrence River near the town of Sainte-Croix, Quebec, Canada . Sediment subsamples, collected during three sampling periods over 21 weeks from five plots (each with four replicates) contaminated with different treatments, were analyzed for their toxic effects on the two test species . Sediment samples taken immediately after the plots were spread with oil were very toxic to both crustaceans (mortality between 80% and 100%), but the mortality of the amphipods was substantially lower than that of the ostracods for samples collected after 6 weeks . Fifteen weeks after the onset of the controlled oil spill experiment, the sediments of all plots were still quite toxic to Heterocypris but not to Hyalella . Statistical analysis of the mortality figures was performed by Blaise et at . (2003) and revealed a statistically significant correlation (R = 0.584 at the P = 0.001 level) between data pairs . Analysis of the precision of the two assays showed a substantially higher uniformity (lower variation coefficients between the four replicas) of the ostracod results over that of the amphipod assay . This study corroborated the findings of two previous investigations conducted in Canada and in Belgium with the same test species . All three investigations concur in pointing out the potential of the new ostracod microbiotest as a reliable and sensitive ecotoxicological test for routine and low-cost monitoring of contaminated sediments .

Anal Bioanal Chem, 2003 Nov, 377(6), 1071 - 8 Epub 2003 Sep 11.
Flow-injection spectrophotometric determination of cyanate in bioremediation processes by use of immobilised inducible cyanase; Luque-Almagro VM et al.; A new flow injection (FI) method for photometric monitoring of cyanate in bioremediation processes using immobilised native cyanase is described . The method is based on the catalytic reaction between cyanate and bicarbonate to produce ammonia and carbon dioxide in the presence of an inducible native cyanase, immobilised in a reactor packed with glass beads . Two degrees of purification of the biocatalyst were used-heated cell-free extract and purified extract of cyanase from Pseudomonas pseudoalcaligenes CECT 5344 . The ammonia produced by the enzymatic reaction is finally monitored photometrically at 700 nm using a modification of the conventional Berthelot method . The method furnishes different calibration curves depending on the degree of purification of the cyanase, with linear ranges between 1.23 and 616.50 micromol L(-1) ( r(2)=0.9979, n=7) and between 1.07 and 308.25 micro mol L(-1) ( r(2)= 0.9992, n=7) for the heated cell-free extract and the purified cyanase extract, respectively . No statistically significant differences between the samples were found in the precision study evaluated at two cyanate concentration levels using one-way analysis of variance . A sampling frequency of 15 h(-1) was achieved . The method was used to monitor cyanate consumption in a cyanate bioremediation tank inoculated with Pseudomonas pseudoalcaligenes CECT 5344 strain . The correlation between cyanate degradation and ammonia production was tested using a conventional method . Finally, the method was applied to different samples collected from the bioremediation tank using the standard addition method; recoveries between 85.9 and 97.4% were obtained.

Int J Antimicrob Agents, 2003 Sep, 22(3), 211 - 6
Solvent tolerance in bacteria: role of efflux pumps and cross-resistance with antibiotics; Fernandes P et al.; Microorganisms have mechanisms that enable them to tolerate lethal concentrations of toxic compounds . This feature has been exploited in a wide range of bioprocesses that range from bioremediation applications to production of fine chemicals in two-phase reaction media . The ability to modify the physical properties of cellular membranes has long been put forward as a protection mechanism that enables microorganisms to tolerate solvents . More recently, efflux pumps have been shown to extrude deleterious compounds, such as antibiotics, drugs and solvents . An understanding of the mechanism of solvent tolerance and its relationship to cross-resistance of pathogenic organisms to antibiotics has major impact on the type and use of disinfectants and disinfecting procedures . The presence of solvents in the growth environment may lead to the emergence of solvent resistant strains and, therefore, overuse may propagate resistant microbial variants . In this paper, mechanisms that lead to solvent tolerance of microbes and accompanying specific antibiotic resistance are reviewed.

Ying Yong Sheng Tai Xue Bao, 2003 Jun, 14(6), 963 - 8
{Effect of Suining Tributary ecoremediation to all size-fractionated chlorophyll-a contents}; Liu D et al.; Through analysis of the size-fractionated chlorophyll-a contents in the remedied part, control part and non-remedied part in Suining Tributary, this paper discussed the effect of bioremediation to all size-fractionated chlorophyll-a contents . The averaged Chlorophy-a content of nano-plus pico-phytoplankton made up 85.232%, 92.402%, 95.205% of the total, respectively for the remedied, control and non-remedied part . Among these, the nano fraction alone made up 78.460%, 87.943%, 87.211%, respectively . Nano-phytoplankton contributed most to the total biomass of Chl a . Its average contribution was 84.538% to the whole tributary, whereas net-phytoplankton contribued only 9.054% . Nano- and pico-phytoplankton was most sensitive to the test eco-remedy . The remedy reduced the relative biomass of net-phytoplankton, and increased the relative biomass of Pico-enhance . The relative biomass of nano- and ultra-phytoplankton fraction was little effected.

EMBO Rep, 2003 Oct, 4(10), 994 - 9 Epub 2003 Sep 05.
The organization of the microbial biodegradation network from a systems-biology perspective; Pazos F et al.; Microbial biodegradation of environmental pollutants is a field of growing importance because of its potential use in bioremediation and biocatalysis . We have studied the characteristics of the global biodegradation network that is brought about by all the known chemical reactions that are implicated in this process, regardless of their microbial hosts . This combination produces an efficient and integrated suprametabolism, with properties similar to those that define metabolic networks in single organisms . The characteristics of this network support an evolutionary scenario in which the reactions evolved outwards from the central metabolism . The properties of the global biodegradation network have implications for predicting the fate of current and future environmental pollutants.

Environ Sci Technol, 2003 Sep 1, 37(17), 3859 - 63
Chlorine isotope fractionation during microbial reduction of perchlorate; Sturchio NC et al.; Perchlorate contamination of surface water and groundwater is an emerging public health problem that has adversely affected the drinking water supplies of millions of people in the western United States . Microbial reduction has shown promise as a cost-effective means for in situ bioremediation of perchlorate-contaminated water . Measurements of stable isotope ratios of light elements (H, C, N, O, S, Cl) can often be used to distinguish biodegradation of organic and inorganic molecules from abiotic loss mechanisms such as adsorption, dispersion, or volatilization because of the relatively large kinetic isotope effects accompanying biodegradation . We quantified chlorine isotope fractionation during perchlorate biodegradation by a common perchlorate-reducing bacterium, Dechlorosoma suillum, initially isolated from a perchlorate-contaminated groundwater source in southern California . The values of the chlorine isotopic fractionation factor alpha derived from two microcosm experiments were alpha = 0.9834 +/- 0.0001 (R2 = 0.9999) and alpha = 0.9871 +/- 0.0008 (R2 = 0.9832) . These alpha values indicate that the rate of the 35ClO4 reduction is approximately 1.3-1.7% faster than that of the 37ClO4 reduction . This relatively large kinetic isotope effect indicates that chlorine isotope analysis provides a sensitive technique by which to document in situ bioremediation of perchlorate in groundwater.

Environ Pollut, 2003, 126(3), 287 - 91
Bio-diversity: an effective safety net against environmental pollution; Swaminathan MS; Biodiversity is the feedstock for the biotechnology industry . Hence, the conservation, enhancement and sustainable and equitable use of biodiversity should be accorded high priority in all national environment protection programmes . Lichens serve as useful indicators of environmental health . Similarly, several blue green algae help to sequester salt from water . There is need for the more widespread use of such biomonitoring and bioremediation agents . Bioprospecting research designed to identify novel metabolites must be rooted in the principle of equity in sharing benefits with the holders of traditional knowledge . There is need for greater vigil against alien invasive species, since with growing world trade in food grains and other agricultural commodities, there is an increasing possibility of introducing new pests, weeds and harmful micro-organisms . Finally, biological scientists should place emphasis on their ethical responsibility for the consequences of their research, since otherwise bioterrorism could become a major threat to human security.

Environ Sci Technol, 2003 Aug 15, 37(16), 3574 - 80
Preferential surfactant utilization by a PAH-degrading strain: effects on micellar solubilization phenomena; Kim HS et al.; Biodegradable nonionic Tween series surfactants were employed to assess the effects of synthetic surfactants on the bioavailability of a target polycyclic aromatic hydrocarbon (PAH), phenanthrene, in soil/sediment-free micellar solutions . Dosages of surfactants in excess of their respective critical micelle concentrations (CMCs) dramatically enhanced solubilization of phenanthrene, but the micellar-solubilized phenanthrene was neither directly nor readily bioavailable to the PAH-degrading strain, Sphingomonas paucimobilis EPA 505, used in these bioavailability experiments . The microorganism preferred instead to utilize hydrophobic fractions of the Tween surfactants as a carbon source, resulting in an imbalance of amphiphilic moieties in surfactant molecules and associated destabilization of micelles . This effect was assessed by measurements of surface tension, CMCs, weight-based PAH solubilization ratios, and by characterizations of the surfactants via HPLC separation and emulsification behavior . The observations and analyses lead to a conclusion that preferential biological destabilization of surfactant micelles effects an associated release of phenanthrene to the aqueous phase . The phenanthrene so released then apparently reverts to a crystallized form that appears to be bioavailable only through normal re-dissolution to the aqueous phase . This is, to our knowledge, the first attempt to characterize and quantify changes in the properties and solubilization behaviors of surfactant micelles resulting from their partial and preferential biodegradation . The associated re-deposition of previously micellar-solubilized PAHs observed and the loss of solubilization capacity of recovered surfactants have significant implications for applications of surfactant-enhanced bioremediation of contaminated soils and sediments.

J Bacteriol, 2003 Sep, 185(18), 5536 - 45
Epoxyalkane: coenzyme M transferase in the ethene and vinyl chloride biodegradation pathways of mycobacterium strain JS60; Coleman NV et al.; Mycobacterium strains that grow on ethene and vinyl chloride (VC) are widely distributed in the environment and are potentially useful for biocatalysis and bioremediation . The catabolic pathway of alkene assimilation in mycobacteria is not well characterized . It is clear that the initial step is a monooxygenase-mediated epoxidation that produces epoxyethane from ethene and chlorooxirane from VC, but the enzymes involved in subsequent transformation of the epoxides have not been identified . We investigated epoxyethane metabolism in Mycobacterium strain JS60 and discovered a coenzyme M (CoM)-dependent enzyme activity in extracts from VC- and ethene-grown cells . PCR amplifications using primers targeted at epoxyalkane:CoM transferase (EaCoMT) genes yielded part of the JS60 EaCoMT gene, which was used to clone an 8.4-kb genomic DNA fragment . The complete EaCoMT gene (etnE) was recovered, along with genes (etnABCD) encoding a four-component monooxygenase and two genes possibly involved in acyl-CoA ester metabolism . Reverse transcription-PCR indicated that the etnE and etnA genes were cotranscribed and inducible by ethene and VC . Heterologous expression of the etnE gene in Mycobacterium smegmatis mc(2)155 using the pMV261 vector gave a recombinant strain capable of transforming epoxyethane, epoxypropane, and chlorooxirane . A metabolite identified by mass spectrometry as 2-hydroxyethyl-CoM was produced from epoxyethane . The results indicate that the EaCoMT and monooxygenase enzymes encoded by a single operon (etnEABCD) catalyze the initial reactions in both the VC and ethene assimilation pathways . CoM-mediated reactions appear to be more widespread in bacteria than was previously believed.

Biodegradation, 2003 Aug, 14(4), 297 - 307
Optimization of soil physical and chemical conditions for the bioremediation of creosote-contaminated soil; Atagana HI et al.; Mispah type soil (FAO : Lithosol) contaminated with > 250 000 mg kg(-1) creosote was collected from the yard of a creosote treatment plant . The soil's carbon, nitrogen and phosphorus contents were determined . Due to creosote contamination, the carbon content of the soil was found to be 130,000 mg C kg(-1) . This concentration was found to greatly affect the nitrogen content (0.08%) . The phosphorus content was less affected (4.5%) . It was estimated that a nutrient amendment to bring the soil to a C : N 10 : 1 would be adequate to stimulate microbial growth and creosote degradation . The soil was amended with a range of C : N ratios below and above the estimated ratio . In one of the treatments, the phosphorus content was amended . Sterile and natural controls were also set up . The soil was incubated at 30 +/- 2 degrees C on a rotary shaker at 150 rpm in the dark for six weeks . Water content was maintained at 70% field capacity . The lowest nitrogen supplementation (C : N = 25 : 1) was more effective in enhancing microbial growth (3.12E + 05) and creosote removal (68.7%) from the soil . Additional phosphorus was not very effective in enhancing the growth of microorganisms and removal of creosote . The highest nitrogen supplementation (C : N = 5 : 1) did not enhance microbial growth and creosote removal . Phenolics and lower molecular mass polycyclic aromatic hydrocarbons (PAHs) were observed to be more susceptible to microbial degradation than higher molecular mass compounds . Nutrient concentration, moisture content and pH were thus observed to play very significant roles in the utilization of creosote in soil . These results are being used for the development of a bioremediation technology for the remediation of creosote contaminated soils in a treatment plant in South Africa.

Water Res, 2003 Oct, 37(17), 4143 - 50
Influence of biosurfactants produced by Candida antarctica on surface properties of microorganism and biodegradation of n-alkanes; Hua Z et al.; The objective of this study was to investigate the influence of the biosurfactant BS-UC on surface properties of microbial cells and biodegradation of petroleum hydrocarbons . The biosurfactant BS-UC was produced by Candida antarctica from n-undecane as the substrate . It was found that the addition of BS-UC influenced positively the emulsification and the biodegradation of a variety of n-alkanes substrates . Besides, BS-UC also changed the hydrophobicity and zeta potential of the cell surface, and thus made the microbial cell attach to the hydrophobic substrate easily . The cell transport experiment also indicated that the addition of BS-UC changed both zeta potential of the cell and that of the porous media, and improved the retention of the cells in the media . So it will make BS-UC a promising choice for use in bioremediation of petroleum contamination.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2003 Sep, 38(9), 1877 - 87
Amplification of marine methanotrophic enrichment DNA with 16S rDNA PCR primers for type II alpha proteobacteria methanotrophs; Rockne KJ et al.; Type II alpha proteobacteria methanotrophs are capable of a wide range of cometabolic transformations of chlorinated solvents and polycyclic aromatic hydrocarbons (PAHs), and this activity has been exploited in many terrestrial bioremediation systems . However, at present, all known obligately marine methanotrophic isolates are Type I gamma proteobacteria which do not have this activity to the extent of Type II methanotrophs . In previous work in our laboratory, determining the presence of Type II alpha proteobacteria methanotrophs in marine enrichment cultures that co-metabolized PAHs required a more sensitive assay . 16S rDNA PCR primers were designed based on oligonucleotide probes for serine pathway methanotrophs and serine pathway methylotrophs with an approximate amplification fragment size of 870 base pairs . Comparison of the primers using double primer BLAST searches in established nucleotide databases showed potential amplification with all Methylocystis and Methylosinus spp., as well as potential amplification with Methylocella palustrus . DNA from Methylosinus trichosporium OB3b, a Type II methanotroph, amplified with the primers with a fragment size of approximately 850 base pairs, whereas DNA extracted from Methylomonas methanica, a Type I methanotroph, did not . The primers were used to amplify DNA extracted from two marine methanotrophic enrichment cultures: a low nitrogen/low copper enrichment to select for Type II methanotrophs and a high nitrogen/high copper enrichment to select for Type I methanotrophs . Although DNA from both cultures amplified with the PCR primers, amplification was stronger in cultures that were specifically enriched for Type II methanotrophs, suggesting the presence of higher numbers of Type II methanotrophs . These results provide further evidence for the existence of Type II marine methanotrophs, suggesting the possibility of exploiting cometabolic activity in marine systems.

Mar Pollut Bull, 2003 Sep, 46(9), 1164 - 73
Bacteria and organic matter dynamics during a bioremediation treatment of organic-rich harbour sediments; Fabiano M et al.; We studied the dynamics of bacteria and organic matter in the Ancient Port of Genoa (Italy) during a bioremediation treatment of sediment (during summer-autumn 1998) in an area characterised by continuous sewage discharge . A strong increase in total benthic bacterial density (TBN) was recorded at the end of the study, from 14 x 10(8) to 58-172 x 10(8) cell g(-1) in different parts of the treated area . The TBN increase was linked to organic matter depletion, from more than 40 to less than 20 mg x g(-1) . In order to highlight the main ecological mechanisms involved in bioremediation, a laboratory experiment based on both water and sediment from the basin studied was carried out . We observed an increase in TBN during the first 20 days and a decrease in sediment organic matter (up to about 20%) . Increases of organic matter (about 2-fold) and TBN (from 21 to 33 x 10(9) cell l(-1)) occurred in the overlying water, suggesting a strong association between the sediments and water column processes . Hydrolytic activities, which double in the sediment and increase up to a 300-fold in the water, are consistent with the decrease in sediment organic matter and with the water fraction dynamics.

J Environ Qual, 2003 Jul-Aug, 32(4), 1234 - 43
Effect of nutrient amendments on indigenous hydrocarbon biodegradation in oil-contaminated beach sediments; Xu R et al.; Nutrient amendment to oil-contaminated beach sediments is a critical factor for the enhancement of indigenous microbial activity and biodegradation of petroleum hydrocarbons in the intertidal marine environment . In this study, we investigated the stimulatory effect of the slow-release fertilizers Osmocote (Os; Scotts, Marysville, OH) and Inipol EAP-22 (Ip; ATOFINA Chemicals, Philadelphia, PA) combined with inorganic nutrients on the bioremediation of oil-spiked beach sediments using an open irrigation system with artificial seawater over a 45-d period . Osmocote is comprised of a semipermeable membrane surrounding water-soluble inorganic N, P, and K . Inipol, which contains organic N and P, has been used for oil cleanup on beach substrate . Nutrient concentrations and microbial activity in sediments were monitored by analyzing sediment leachates and metabolic dehydrogenase activity of the microbial biomass, respectively . Loss of aliphatics (n-C12 to n-C33, pristane, and phytane) was significantly greater (total loss between 95 and 97%) in oil-spiked sediments treated with Os alone or in combination with other nutrient amendments, compared with an unamended oil-spiked control (26% loss) or sediments treated with the other nutrient amendments (28-65% loss) . A combination of Os and soluble nutrients (SN) was favorable for the rapid metabolic stimulation of the indigenous microbial biomass, the sustained release of nutrients, and the enhanced biodegradation of petroleum hydrocarbons in leached, oil-contaminated sediments.

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2003 Aug, 38(8), 1557 - 68
A landfarming application technique used as environmental remediation for coal oil pollution; Giasi CI et al.; Since the massive exploitation of the Val d'Agri (Basilicata-Italy) oilfield has started, a lot of environmental pollution accidents have occurred in the same region . This research takes as starting point the heavy accident occurred in the year 2000, when 15,150 kg of coal oil were spilt all over the Agri river bed and the surrounding fields . In that particular case, the environmental reclamation was achieved by the removal of the polluted soil and its dump-storage . This research work suggests an environmental restoration which is an alternative solution to what has been practiced before, and it is achieved by the so called bioremediation methods, particularly the "landfarming on site" technique.

Biomol Eng, 2003 Jul, 20(4-6), 459 - 66
Commercial development of microalgal biotechnology: from the test tube to the marketplace; Olaizola M; While humans have taken limited advantage of natural populations of microalgae for centuries (Nostoc in Asia and Spirulina in Africa and North America for sustenance), it is only recently that we have come to realize the potential of microalgal biotechnology . Microalgal biotechnology has the potential to produce a vast array of products including foodstuffs, industrial chemicals, compounds with therapeutic applications and bioremediation solutions from a virtually untapped source . From an industrial (i.e . commercial) perspective, the goal of microalgal biotechnology is to make money by developing marketable products . For such a business to succeed the following steps must be taken: identify a desirable metabolite and a microalga that produces and accumulates the desired metabolite, establish a large-scale production process for the desired metabolite, and market the desired metabolite . So far, the commercial achievements of microalgal biotechnology have been modest . Microalgae that produce dozens of desirable metabolites have been identified . Aided by high throughput screening technology even more leads will become available . However, the successes in large-scale production and product marketing have been few . We will discuss those achievements and difficulties from the industrial point of view by considering examples from industry, specially our own experience at Mera Pharmaceuticals.

Biomol Eng, 2003 Jul, 20(4-6), 429 - 39
Realizing the promises of marine biotechnology; Luiten EE et al.; High-quality research in the field of marine biotechnology is one of the key-factors for successful innovation in exploiting the vast diversity of marine life . However, fascinating scientific research with promising results and claims on promising potential applications (e.g . for pharmaceuticals, nutritional supplements, (feed-)products for aquaculture and bioremediation solutions) is not the only factor to realise the commercial applications of marine biotechnology . What else is needed to exploit the promising potential of marine biotechnology and to create new industrial possibilities? In the study project 'Ocean Farming-Sustainable exploitation of marine organisms', we explore the possibilities of marine organisms to fulfill needs, such as safe and healthy food, industrial (raw) materials and renewable energy in a sustainable way . One of the three design groups is envisioning the future of strong land-based 'marine' market chains . Marine biotechnology is one of the foci of attention in this design group . This article provides a model of future-oriented thinking in which a variety of experts actively participate.

Biomol Eng, 2003 Jul, 20(4-6), 363 - 8
The marine sponge Chondrilla nucula Schmidt, 1862 as an elective candidate for bioremediation in integrated aquaculture; Milanese M et al.; The use of sponges for marine bioremediation in a farming scenario has been investigated focusing on Chondrilla nucula . We report experiments examining clearance and retention rates of the bacterium Escherichia coli . Despite low values expressed for clearance tests, C . nucula exhibited a marked ability to retain high quantities of bacteria . One square meter patch of this sponge can filter up to 14 l/h of sea water retaining up to 7 x 10(10) bacterial cells/h . This suggests that C . nucula is a suitable species for marine environmental bioremediation.

Chemosphere, 2003 Oct, 53(3), 269 - 75
Assessing the microbial activity of soil samples, its nutrient limitation and toxic effects of contaminants using a simple respiration test; Hollender J et al.; Eight soil samples from five wells of a former gas plant site differing in the contamination with BTEX and PAHs as well as the nutrient content were investigated by soil respiration measurements . The basal, glucose as well as NH4+ and PO4(3-) induced cumulative oxygen consumption and carbon dioxide production in 72 and 120 h were determined and additionally the maximal turnover rates and the limitation quotients were calculated . Without additional carbon source only one of five investigated samples was clearly nutrient limited . After glucose supplementation four of seven investigated samples showed nutrient limitation that was in accordance with the available ammonium and phosphorous content . BTEX and PAHs did not exhibit an inhibiting effect on the respiration rate . In contrast, BTEX containing samples exhibited the highest oxygen consumption indicating biodegradation of the contaminants . The results show that oxygen consumption and carbon dioxide production as well as the kinetic of these processes are all informative parameters characterizing the whole microbial respiration potential and their nutrient limitation in soil samples . Therefore this fast respirometric method can be used for the decision if further detailed studies of the bioremediation are useful and if nutrient supplementation is recommended to enhance natural attenuation.

Genet Mol Res, 2003 Mar 31, 2(1), 92 - 101
Operon mer: bacterial resistance to mercury and potential for bioremediation of contaminated environments; Nascimento AM et al.; Mercury is present in the environment as a result of natural processes and from anthropogenic sources . The amount of mercury mobilized and released into the biosphere has increased since the beginning of the industrial age . Generally, mercury accumulates upwards through aquatic food chains, so that organisms at higher trophic levels have higher mercury concentrations . Some bacteria are able to resist heavy metal contamination through chemical transformation by reduction, oxidation, methylation and demethylation . One of the best understood biological systems for detoxifying organometallic or inorganic compounds involves the mer operon . The mer determinants, RTPCDAB, in these bacteria are often located in plasmids or transposons and can also be found in chromosomes . There are two classes of mercury resistance: narrow-spectrum specifies resistance to inorganic mercury, while broad-spectrum includes resistance to organomercurials, encoded by the gene merB . The regulatory gene merR is transcribed from a promoter that is divergently oriented from the promoter for the other mer genes . MerR regulates the expression of the structural genes of the operon in both a positive and a negative fashion . Resistance is due to Hg2+ being taken up into the cell and delivered to the NADPH-dependent flavoenzyme mercuric reductase, which catalyzes the two-electron reduction of Hg2+ to volatile, low-toxicity Hg0 . The potential for bioremediation applications of the microbial mer operon has been long recognized; consequently, Escherichia coli and other wild and genetically engineered organisms for the bioremediation of Hg2+-contaminated environments have been assayed by several laboratories.

Environ Technol, 2003 Jul, 24(7), 831 - 43
Oxygen dynamics in petroleum hydrocarbon contaminated salt marsh soils: III . A rate model; Shin WS et al.; A model describing oxygen dynamics due to crude oil biodegradation under flooded conditions in saltwater wetlands was developed . The model is composed of three non-linear ordinary differential equations (ODEs) that simulate oxygen uptake, cell growth, and oil degradation simultaneously . The model equations were solved by using a stiff version of ODE solver, ODEPACK, which employs a multistep method and allows the change of step sizes and order of methods (ie., Gear's method) . The results of model simulation were compared with experimental data obtained from a fully aerated microcosm study . The results of model simulation indicate that dissolved oxygen concentration in the overlying water rapidly depleted below 3 mg l(-1) unless the reaeration coefficient was higher than 2.0 day(-1) . Active aerobic biodegradation of crude oil did not occur under flooded conditions because (i) dissolved oxygen is rapidly depleted, (ii) reaeration is not sufficient enough to replenish dissolved oxygen and (iii) the oil dissolution rate constant decreases over time . The model may lead to better understanding of oxygen demand for a long bioremediation period . The results of this study may be applicable for the establishment of an engineered bioremediation strategy.

Acta Microbiol Pol, 2003, 52(1), 5 - 13
Overuse of high stability antibiotics and its consequences in public and environmental health; Zdziarski P et al.; In this paper the ecological aspects of widespread antibiotic consumption are described . Many practitioners, veterinarians, breeders, farmers and analysts work on the assumption that a antibiotics undergo spontaneous degradation . It is well documented that the indiscriminate use of antibiotics has led to the water contamination, selection and dissemination of antibiotic-resistant organisms, alteration of fragile ecology of the microbial ecosystems . The damages caused by the overuse of antibiotics include hospital, waterborne and foodborne infections by resistant bacteria, enteropathy (irritable bowel syndrome, antibiotic-associated diarrhea etc.), drug hypersensitivity, biosphere alteration, human and animal growth promotion, destruction of fragile interspecific competition in microbial ecosystems etc . The consequences of heavy antibiotic use for public and environmental health are difficult to assess: utilization of antibiotics from the environment and reduction of irrational use is the highest priority issue . This purpose may be accomplished by bioremediation, use of probenecid for antibiotic dosage reduction and by adoption of hospital infections methodology for control resistance in natural ecosystems.

Huan Jing Ke Xue, 2003 May, 24(3), 74 - 8
{Two phases bioremediation of oil contaminated soil from Liaohe oil field}; Li P et al.; A treatment engineering of prepared bed was set up for the bioremediation of oil contaminated soil with oil in this study, soils contaminated with different type of oils were treated using composting process in the prepared bed and the treatment period was divided into 2 phases with total time of 210 days . When the concentration of total petroleum hydrocarbons (TPH), 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, petroleum removal rates can reach 38.37%-56.74% by 53 days operation . In the second phase, total petroleum removal rates reached 66.59%-80.96% by the 156 days operation in the next year . The results showed that most hydrocarbon pollutants that are easier to be degraded were removed in the first phase, the remedying efficiency obviously dropped in the second phase.

Biochem Biophys Res Commun, 2003 Aug 29, 308(3), 511 - 7
Generation of 2,3,7,8-TCDD-metabolizing enzyme by modifying rat CYP1A1 through site-directed mutagenesis; Shinkyo R et al.; Polychlorinated dibenzo-p-dioxins (PCDDs) are known as g environmental contaminants on account of the extreme toxicity . Among these compounds, 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TetraCDD) is regarded as the most toxic one . The extremely high toxicity of 2,3,7,8-TetraCDD is based on its high affinity for Ah receptor and nearly undetectable metabolism in mammalian body . Based on our previous studies, we assumed that enlarging the space of substrate-binding pocket of rat CYP1A1 might generate the catalytic activity toward 2,3,7,8-TetraCDD . Large-sized amino acid residues located at putative substrate-binding sites of rat CYP1A1 were substituted for alanine by site-directed mutagenesis . Among eight mutants examined, the mutant in the putative F-G loop, F240A, showed metabolic activity toward 2,3,7,8-TetraCDD . HPLC and GC-MS analyses strongly suggested that the metabolite was 8-hydroxy-2,3,7-TriCDD . Ah receptor assay revealed that the affinity of 8-hydroxy-2,3,7-TriCDD for Ah receptor was less than 0.01% of 2,3,7,8-TetraCDD, indicating that the F240A-dependent metabolism resulted in remarkable detoxification of 2,3,7,8-TetraCDD . The novel 2,3,7,8-TetraCDD-metabolizing enzyme could be applicable to bioremediation of contaminated soils with dioxin, elimination of dioxin from foods, and clinical treatment for people who accidentally take dioxin into their systems.

Microbiol Res, 2003, 158(2), 99 - 106
Biodegradation of methyl tertiary butyl ether (MTBE) by a bacterial enrichment consortia and its monoculture isolates; Okeke BC et al.; Methyl tertiary butyl ether (MTBE), an important gasoline additive, is a recalcitrant compound posing serious environmental health problems . In this study, MTBE-degrading bacteria were enriched from five environmental samples . Enrichments from Stewart Lake sediments and an MTBE contaminated soil displayed the highest rate of MTBE removal; 29.6 and 27.8% respectively, in 28 days . A total of 12 bacterial monocultures isolated from enrichment cultures were screened for MTBE degradation in liquid cultures . In a nutrient-limited medium containing MTBE as the sole source of carbon and energy, the highest rate of MTBE elimination was achieved with IsoSL1, which degraded 30.6 and 50.2% in 14 and 28 days, respectively . In a nutrient-rich medium containing ethanol and yeast extract, the bacterium (Iso2A) substantially removed MTBE (20.3 and 28.1% removal in 14 and 28 days, respectively) . Based upon analysis of the 16s rRNA gene sequence and data base comparison, IsoSL1 and Iso2A were identified as a Streptomyces sp . and Sphingomonas sp., respectively . The Streptomyces sp . is a new genera of bacteria degrading MTBE and could be useful for MTBE bioremediation.

Can J Microbiol, 2003 May, 49(5), 362 - 6
High TNT-transforming activity by a mixed culture acclimated and maintained on crude-oil-containing media; Popesku JT et al.; A mixed microbial culture originating from a petroleum-contaminated site and maintained on crude oil exhibited high 2,4,6-trinitrotoluene (TNT) transformation activity . Cultivation of the mixed culture in glucose-containing medium for 29 h resulted in almost complete transformation of 100 ppm TNT . TNT transformation was observed with both growing and resting cells . With subculturing, it was found that TNT could support growth of the mixed culture when supplied as sole carbon source, sole nitrogen source, or sole carbon and nitrogen source . The finding that a mixed microbial culture maintained on crude oil exhibited high TNT transformation activity without prior subculture on TNT-containing media is novel and may have potential practical applications in the bioremediation of munitions-contaminated soil and wastewater.

Bioresour Technol, 2003 Nov, 90(2), 159 - 68
Enhanced bioremediation of n-alkane in petroleum sludge using bacterial consortium amended with rhamnolipid and micronutrients; Rahman KS et al.; The purpose of the present study was to investigate possible methods to enhance the rate of biodegradation of oil sludge from crude oil tank bottom, thus reducing the time usually required for bioremediation . Enhancement of biodegradation was achieved through bioaugmentation and biostimulation . About 10% and 20% sludge contaminated sterile and non-sterile soil samples were treated with bacterial consortium (BC), rhamnolipid biosurfactant (RL) and nitrogen, phosphorus and potassium (NPK) solution . Maximum n-alkane degradation occurred in the 10% sludge contaminated soil samples . The effects of treatment carried out with the non-sterile soil samples were more pronounced than in the sterile soils . Maximum degradation was achieved after the 56th day of treatment . n-Alkanes in the range of nC8-nC11 were degraded completely followed by nC12-nC21, nC22-nC31 and nC32-nC40 with percentage degradations of 100%, 83-98%, 80-85% and 57-73% respectively . Statistical analysis using analysis of variance and Duncan's multiple range test revealed that the level of amendments, incubation time and combination of amendments significantly influenced bacterial growth, protein concentration and surface tension at a 1% probability level . All tested additives BC, NPK and RL had significant positive effects on the bioremediation of n-alkane in petroleum sludge.

Chemosphere, 2003 Sep, 52(9), 1539 - 46
Use of spent mushroom compost to bioremediate PAH-contaminated samples; Lau KL et al.; Spent mushroom compost (SMC) is a bulky waste byproduct of mushroom industry and produced abundantly . The SMC of Pleurotus pulmonarius immobilized laccase (0.88 mmoles min(-1) g(-1)) and manganese peroxidase (0.58 mmoles min(-1) g(-1)) of which the optimal temperatures were 45 and 75 degrees C, respectively . In laboratory test, complete degradative removal of individual naphthalene, phenanthrene, benzo{a}pyrene and benzo{g,h,i}perylene (200 mg PAH kg(-1) sandy-loam soil) by 5% SMC was obtained in two days under continuous shaking at 80 degrees C . The SMC-treated PAH samples had significantly reduced or removed their toxicities as revealed by the Microtox bioassay . These results were confirmed by gas chromatography-mass spectrometry analysis on the breakdown products . A phthalic derivative which is reported as a degradative product of PAHs by ozonation or ligninolysis was also detected in the SMC-treated samples . The results demonstrate the potential in employing SMC in ex situ bioremediation.

Chemosphere, 2003 Sep, 52(9), 1523 - 9
Reduction of chromate (CrO4(2-)) by an enrichment consortium and an isolate of marine sulfate-reducing bacteria; Cheung KH et al.; An enrichment consortium and an isolate (isolate TKW) of sulfate-reducing bacteria (SRB) have been obtained from metal-contaminated marine sediments of Tokwawan, Hong Kong SAR . These bacteria are capable of reducing highly toxic and soluble hexavalent chromium (Cr6+) enzymatically into less toxic and insoluble trivalent chromium (Cr3+) under anaerobic conditions . The enrichment consortium almost completely (98.5%) reduced 0.6 mM Cr6+ in 168 h and the rate of reduction was 0.5 g (Cr6+) g(protein)(-1)h(-1) . In comparison, with Cr6+ as the sole electron acceptor (as a surrogate for SO4(2-)), isolate TKW reduced 94.5% of the initially added Cr6+ (0.36 mM) in 288 h, with the rate of 0.26 g (Cr6+) g(protein)(-1)h(-1) . Adsorption by these bacteria was not the major mechanism contributing to the transformation or removal of Cr6+ . The biomass and Cr3+ in the cultures increased simultaneously with the reduction of Cr6+ . These indigenous SRB might have potential application in bioremediation of metal contaminated sediments.

J Liposome Res, 2003 May, 13(2), 173 - 86
Liposomes enhance bioremediation of oil-contaminated soil; Barenholz A et al.; Liposomes (composed of soy phosphatides) in the form of small unilamellar vesicles (SUV), when added to soil contaminated by crude oil, accelerate bioremediation . After three weeks incubation at 30 degrees C, using soil experimentally contaminated (with 10,000 ppm crude oil), level of bioremediation increased from 40% without SUV to 75% with SUV (0.1 wt% phospholipids per dry weight soil) . Similarly, for accidentally contaminated soil (with approximately 17,000 ppm crude oil), addition of 0.1 wt% SUV to the soil increased the bioremediation level from 55 to 80% . The enhancing effect of liposomes is explained by two interrelated phenomena: a large increase both in total bacteria number and in diversity of bacterial species in the soil . Comparison after four weeks revealed 21 bacterial species in the presence of liposomes (many being oil-degrading bacterial species) and only nine species in the absence of liposomes . Both effects may be related to the physical effects of liposome phospholipids, which modify the crude oil by wetting it, thereby making it more accessible to the microorganisms . In addition, liposome phospholipids serve as phosphate and nitrogen sources for the bacteria.

Curr Opin Biotechnol, 2003 Jun, 14(3), 289 - 95
Molecular and physiological approaches to understanding the ecology of pollutant degradation; Watanabe K et al.; Pollutant biodegradation in the environment occurs in the context of various interactions among microorganisms . To understand this ecological process, identification of functionally important populations is considered to be the primary step, which can be followed by isolation and laboratory pure-culture studies of the important organisms . Laboratory studies can then proceed to the analysis of in situ activity and interactions with other organisms . Such studies will shape a deeper understanding of the ecology of pollutant degradation and facilitate the development of new bioremediation strategies.

Environ Sci Pollut Res Int, 2003, 10(3), 173 - 6
Oxidation of polycyclic aromatic hydrocarbons by fungal isolates from an oil contaminated refinery soil; Zheng Z et al.; BACKGROUND AND OBJECTIVE: Indigenous soil microorganisms are used for the biodegradation of petroleum hydrocarbons in oily waste residues from the petroleum refining industry . The objective of this investigation was to determine the potential of indigenous strains of fungi in soil contaminated with petroleum hydrocarbons to biodegrade polycyclic aromatic hydrocarbons (PAH) . MATERIALS AND METHODS: Twenty one fungal strains were isolated from a soil used for land-farming of oily waste residues from the petrochemical refining industry in Singapore and identified to genus level using laboratory culture and morphological techniques . Isolates were incubated in the presence of 30 mg/L of phenanthrene over a period of 28 days at 30 degrees C . The most effective strain was further evaluated to determine its ability to oxidise a wider range of PAH compounds of various molecular weight i.e acenaphthene, fluorene, fluoranthene, chrysene, benzo(a)pyrene and dibenz(ah)anthracene RESULTS AND DISCUSSION: After 28 days of incubation, 18 of the 21 fungal cultures were capable of oxidising over 50% of the phenanthrene present in culture medium, relative to abiotic controls . Fungal isolate, Penicillium sp . 06, was able to oxidise 89% of the phenanthrene present . This isolate could also oxidise more than 75% of the acenaphthene, fluorene and fluoranthene after 30 days of incubation . However, the oxidation of high molecular weight PAH i.e . chrysene, benzo(a)pyrene and dibenz(ah)anthracene by the Penicillium sp . 06 isolate was limited, where the extent of oxidation was inversely proportional to PAH molecular weight . CONCLUSIONS: Fungal isolate, Penicillium sp . 06, was effective at oxidising a range of PAH in petroleum contaminated soils, but higher molecular weight PAH were more recalcitrant . RECOMMENDATIONS AND OUTLOOK: There is potential for the re-application of this fungal strain to soil for bioremediation purposes.

Mar Pollut Bull, 2003 Jul, 46(7), 887 - 99
Intrinsic bioremediation of a petroleum-impacted wetland; Mills MA et al.; Following the 1994 San Jacinto River flood and oil spill in southeast Texas, a petroleum-contaminated wetland was reserved for a long-term research program to evaluate bioremediation as a viable spill response tool . The first phase of this program, presented in this paper, evaluated the intrinsic biodegradation of petroleum in the contaminated wetland . Sediment samples from six test plots were collected 11 times over an 11-month period to assess the temporal and spatial petroleum concentrations . Petroleum concentrations were evaluated using gas chromatography-mass spectrometer analyses of specific target compounds normalized to the conservative biological marker, C(30)17alpha,21beta(H)-hopane . The analyses of specific target compounds were able to characterize that significant petroleum biodegradation had occurred at the site over the one-year period . Total resolved saturate and total resolved aromatic hydrocarbon data indicated the petroleum was degraded more than 95% . In addition, first-order biodegradation rate constants were calculated for the hopane-normalized target compounds and supported expected biodegradation patterns . The rapid degradation rates of the petroleum hydrocarbons are attributed to conditions favorable to biodegradation . Elevated nutrient levels from the flood deposition and the unconsolidated nature of the freshly deposited sediment possibly provided a nutrient rich, oxic environment . Additionally, it is suggested that an active and capable microbial community was present due to prior exposure to petroleum . These factors provided an environment conducive for the rapid bioremediation of the petroleum in the contaminated wetland.

Curr Opin Microbiol, 2003 Jun, 6(3), 244 - 50
Wax ester production by bacteria; Ishige T et al.; The enzymological and genetic aspects of microbial metabolism of hydrocarbons have been extensively revealed . Such molecular information is useful for understanding the bioremediation of oil spill environments and production of hydrocarbon-specific fine chemicals.

Pharmacogenomics, 2003 Jul, 4(4), 387 - 95
P450 structures and oxidative metabolism of xenobiotics; Lewis DF; This review focuses on the structural models for cytochrome P450, which are improving our knowledge and understanding of the P450 catalytic cycle, and the way in which substrates bind to the enzyme leading to catalytic conversion and subsequent formation of mono-oxygenated metabolites . Various stages in the P450 reaction cycle have now been investigated using X-ray crystallography and electronic structure calculations, whereas homology modeling of mammalian P450s is currently revealing important aspects of pharmaceutical and other xenobiotic metabolism mediated by P450 involvement . These features are explored in the current review on P450-based catalysis, which emphasizes the importance of structural modeling to our understanding of this enzyme's function . In addition, the results of various quantitative structure-activity relationships (QSAR) analyses on series of chemicals, which are metabolized via P450 enzymes, are presented such that the importance of electronic and other structural factors in explaining variations in rates of metabolism can be appreciated . As an important example of biocatalysis, the P450 system has a major future as an enzyme for use in many biotechnological applications, including biodegradation and bioremediation.

Environ Sci Technol, 2003 Jun 1, 37(11), 2525 - 33
Inoculation of a DNAPL source zone to initiate reductive dechlorination of PCE; Adamson DT et al.; The ability to inoculate a PCE-NAPL source zone with no prior dechlorinating activity was examined using a near field-scale simulated aquifer . A known mass of PCE was added to establish a source zone, and the groundwater was depleted of oxygen using acetate and lactate prior to culture addition . An active and stable dechlorinating culture was used as an inoculum, and dechlorination activity was observed within 2 weeks following culture transfer . PCE reduction to TCE and cis-DCE was observed initially, and the formation of these compounds was accelerated by the addition of a long-term source of hydrogen (Hydrogen Releasing Compound) . cis-DCE was the predominant chlorinated ethene present in the effluent after 225 days of operation, and production of VC and ethene lagged the formation of TCE and cis-OCE . However, dechlorination extent continued to improve over time, and VC eventually became a major product, suggesting that reinoculation was unnecessary . The detection of Dehalococcoides species in the source culture and in the simulated aquifer postinoculation indicated that the metabolic capability to dechlorinate beyond cis-DCE (t = 86 days and t = 245 days) was present . Elevated levels of TCE and cis-DCE were present in the source zone, but neither VC nor ethene were detected in the vicinity of NAPL . The results of this research indicated that adding dechlorinating cultures may be useful in the application of source zone bioremediation but that dechlorination beyond cis-DCE may be limited to regions downgradient of the source zone.

Appl Microbiol Biotechnol, 2003 Oct, 62(5-6), 601 - 7 Epub 2003 Jun 26.
Monitoring of white-rot fungus during bioremediation of polychlorinated dioxin-contaminated fly ash; Suhara H et al.; Bioremediation is a low-cost treatment alternative for the cleanup of polychlorinated-dioxin-contaminated soils and fly ash when pollution spread is wide-ranging . An interesting fungus, Ceriporia sp . MZ-340, with a high ability to degrade dioxin, was isolated from white rotten wood of a broadleaf tree from Kyushu Island in Japan . We have attempted to use the fungus for bioremediation of polychlorinated-dioxin-contaminated soil on site . However, we have to consider that this trial has the potential problem of introducing a biohazard to a natural ecosystem if this organism is naturalized . We have therefore developed a monitoring system for the introduced fungus as a part of the examination and evaluation of bioremediation in our laboratory . We have also developed a PCR-based assay to reliably detect the fungus at the bioremediation site . DNA isolated from the site was amplified by PCR using a specific primer derived from internal transcribed spacer region (ITS: ITS1, 5.8S rDNA and ITS2) sequences of Ceriporia sp . MZ-340 . We successfully monitored Ceriporia sp . MZ-340 down to 100 fg/ micro l DNA and down to 2 mg/g mycelium . We also successfully monitored the fungus specifically at the bioremediation site . The polychlorinated dibenzo- p-dioxin and polychlorinated dibenzofuran content was observed to decrease in response to treatment with the fungus . The species-specific PCR technique developed in the present work is useful in evaluating the possibility of on-site bioremediation using the fungus Ceriporia sp . MZ-340.

Environ Pollut, 2003, 125(3), 361 - 8
Bioremediation of diesel oil-contaminated soil by composting with biowaste; Van Gestel K et al.; Soil spiked with diesel oil was mixed with biowaste (vegetable, fruit and garden waste) at a 1:10 ratio (fresh weight) and composted in a monitored composting bin system for 12 weeks . Pure biowaste was composted in parallel . In order to discern the temperature effect from the additional biowaste effect on diesel degradation, one recipient with contaminated soil was hold at room temperature, while another was kept at the actual composting temperature . Measurements of composting parameters together with enumerations and identifications of microorganisms demonstrate that the addition of the contaminated soil had a minor impact on the composting process . The first-order rate constant of diesel degradation in the biowaste mixture was four times higher than in the soil at room temperature, and 1.2 times higher than in the soil at composting temperature.

J Contam Hydrol, 2003 Jul, 64(3-4), 283 - 307
Simulating bioremediation of uranium-contaminated aquifers; uncertainty assessment of model parameters; Wang S et al.; Bioremediation of trace metals and radionuclides in groundwater may require the manipulation of redox conditions via the injection of a carbon source . For example, after nitrate has been reduced, soluble U(VI) can be reduced simultaneously with other electron acceptors such as Fe(III) or sulfate to U(IV), which may precipitate as a solid (uraninite).To simulate the numerous biogeochemical processes that will occur during the bioremediation of trace-metal-contaminated aquifers, a time-dependent one-dimensional reactive transport model has been developed . The model consists of a set of coupled mass balance equations, accounting for advection, hydrodynamic dispersion, and a kinetic formulation of the biological or chemical transformations affecting an organic substrate, electron acceptors, corresponding reduced species, and trace metal contaminants of interest, uranium in this study . This set of equations is solved numerically, using a finite difference approximation . The redox conditions of the domain are characterized by estimating the pE, based on the concentration of the dominant terminal electron acceptor and its corresponding reduced species . This pE and the concentrations of relevant species are then used by a modified version of MINTEQA2, which calculates the speciation/sorption and precipitation/dissolution of the species of interest under equilibrium conditions . Kinetics of precipitation/dissolution processes are described as being proportional to the difference between the actual and calculated equilibrium concentration . A global uncertainty assessment, determined by Random Sampling High Dimensional Model Representation (RS-HDMR), was performed to attain a phenomenological understanding of the origins of output variability and to suggest input parameter refinements as well as to provide guidance for field experiments to improve the quality of the model predictions . By decomposing the model output variance into its different input contributions, RS-HDMR can identify the model inputs with the most influence on various model outputs, as well as their behavior pattern on the model output . Simulations are performed to illustrate the effect of biostimulation on the fate of uranium in a saturated aquifer, and to identify the key processes that need to be characterized with the highest accuracy prior to designing a uranium bioremediation scheme.

ScientificWorldJournal, 2002 Feb 12, 2, 407 - 20
Bioremediation of heavy metals and organic toxicants by composting; Barker AV et al.; Hazardous organic and metallic residues or by-products can enter into plants, soils, and sediments from processes associated with domestic, municipal, agricultural, industrial, and military activities . Handling, ingestion, application to land or other distributions of the contaminated materials into the environment might render harm to humans, livestock, wildlife, crops, or native plants . Considerable remediation of the hazardous wastes or contaminated plants, soils, and sediments can be accomplished by composting . High microbial diversity and activity during composting, due to the abundance of substrates in feedstocks, promotes degradation of xenobiotic organic compounds, such as pesticides, polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs) . For composting of contaminated soils, noncontaminated organic matter should be cocomposted with the soils . Metallic pollutants are not degraded during composting but may be converted into organic combinations that have less bioavailability than mineral combinations of the metals . Degradation of organic contaminants in soils is facilitated by addition of composted or raw organic matter, thereby increasing the substrate levels for cometabolism of the contaminants . Similar to the composting of soils in vessels or piles, the on-site addition of organic matter to soils (sheet composting) accelerates degradation of organic pollutants and binds metallic pollutants . Recalcitrant materials, such as organochlorines, may not undergo degradation in composts or in soils, and the effects of forming organic complexes with metallic pollutants may be nonpermanent or short lived . The general conclusion is, however, that composting degrades or binds pollutants to innocuous levels or into innocuous compounds in the finished product.

Appl Environ Microbiol, 2003 Jun, 69(6), 3672 - 5
Microorganisms associated with uranium bioremediation in a high-salinity subsurface sediment; Nevin KP et al.; Although stimulation of dissimilatory metal reduction to promote the reductive precipitation of uranium has been shown to successfully remove uranium from some aquifer sediments, the organisms in the family Geobacteraceae that have been found to be associated with metal reduction in previous studies are not known to grow at the high salinities found in some uranium-contaminated groundwaters . Studies with a highly saline uranium-contaminated aquifer sediment demonstrated that the addition of acetate could stimulate the removal of U(VI) from the groundwater . This removal was associated with an enrichment in microorganisms most closely related to Pseudomonas and Desulfosporosinus species.

Mar Pollut Bull, 2003, 47(1-6), 85 - 90
Effects of spilled oil on microbial communities in a tidal flat; Katayama Y et al.; Effects of spilled oil on microbial communities in tidal flats were examined by use of a simulator for a tidal flat ecosystem . The simulator is composed of a wave generator, a tide control device, and a tidal flat . Sediment for the tidal flat was obtained at a natural tidal flat in Hiroshima Bay, Japan . After stabilizing the benthic organisms, fuel oil C was added to the surface of the flat at 1 lm(-2) . Although the total number of micro-organisms remained at 1.5-3.5 x 10(9) cells g(-1) dry sediment irrespective of the addition of oil, bacterial communities which were analyzed based on the 16S rDNA showed clear changes after the addition of fuel oil C and after a subsequent recovery period . Bacterial colonies were randomly isolated from the oil-supplemented sediment during the experiments, and the isolates were examined for susceptibility to hydrocarbons in order to screen the oil-susceptible bacteria . The proportion of oil-susceptible bacteria in the isolates decreased with the addition of the oil . Oil-susceptible bacteria showed an inability to assimilate petroleum compounds as well as an inhibition of growth . The possibility of using oil-susceptible bacteria as an indicator of bioremediation in tidal flats was discussed.

Mar Pollut Bull, 2003, 47(1-6), 74 - 7
Crude oil bioremediation field experiment in the Sea of Japan; Maki H et al.; Experimental bioremediation of crude oil was conducted for approximately 3 months in the intertidal zone of the Sea of Japan, Hyogo Prefecture . Artificial mixtures of weathered Arabian light crude oil and sand taken from the experimental site were wrapped in polyester net envelopes . The envelopes were placed in drum-shaped acrylic vessels with perforated sides to facilitate seawater exchange . The vessels were laid in the intertidal area . Slow release nitrogen and phosphorus synthetic fertilizer granules were added to the oil-sand mixtures in three different amounts . Some oil-sand mixtures were unfertilized controls . The oil-sand mixtures were periodically sampled and changes in the composition of the residual oils were monitored . Oil samples were subjected to gas chromatography coupled with mass spectrometry for analysis of some representative semi-volatile aliphatic and aromatic compounds . All values for each analyte were normalized against that of hopane to evaluate the extent of oil biodegradation . Significant increases in the concentrations of both nitrogen and phosphorus were found in the fertilized sections in accordance with the amounts of added fertilizers . Although significant natural attenuation of oil was observed in the unfertilized sections, fertilization stimulated the degradation rate of the oil in the early stage of the experimental term . The extent of the oil biodegradation increased as the amount of added fertilizer increased . However, the final degradation efficiencies for each oil component in the fertilized sections were not significantly different from those in the unfertilized sections, and the degradation of each oil component had almost ceased after 6 weeks . We conclude that excessive amounts of macronutrients are required to accelerate oil biodegradation and that fertilization is only effective in the early stages.

Environ Toxicol Chem, 2003 Jun, 22(6), 1238 - 43
Incomplete degradation of polycyclic aromatic hydrocarbons in soil inoculated with wood-rotting fungi and their effect on the indigenous soil bacteria; Andersson BE et al.; Soil artificially contaminated with fluorene, phenanthrene, pyrene, and benz{a}anthracene was inoculated with the wood-rotting fungi Plrurotus ostreatus and Antrodia vaillantii . During 12 weeks of incubation, polycyclic aromatic hydrocarbon (PAH) degradation and the formation of persistent degradation products were monitored by chemical analysis . In addition, the effect on the indigenous soil bacteria was studied by plate count techniques and by measuring the concentration of bacteria-specific phospholipid fatty acids (PLFAs) . In both soils inoculated with fungi, the PAH degradation was enhanced compared to the control soil without fungi . The white-rot fungus P . ostreatus accelerated the degradation rate radically the first weeks, while the effect of the brown-rot fungus was more pronounced at later stages during the 12-week study . In a soil with no amendments, the final degradation result was similar to that in the soil with added fungi, although the degradation pattern for the individual PAHs was different . Furthermore, the degradation by P . ostreatus was accompanied by an accumulation of PAH metabolites, that is, 9-fluorenone, benz{a}anthracene-7,12-dione, and two compounds identified as 4-hydroxy-9-fluorenone and 4-oxapyrene-5-one, that was not seen in the other soils . The inoculation with the white-rot fungus also had a large negative effect on the indigenous soil bacteria . This could be an important drawback of using the white-rot fungus P . ostreatus in soil bioremediation since a sequential fungal-bacterial degradation probably is needed for a complete degradation of PAHs in soil . In the soil inoculated with A . vaillantii, on the other hand, no metabolites accumulated, and no negative effects were observed on the indigenous microorganisms.

Biosens Bioelectron, 2003 Aug 1, 18(8), 1077 - 83
Monitoring freshwater sediments; Alcock S et al.; The objectives of the SENSPOL Expert Meeting on 'Monitoring Freshwater Sediments' held in Antwerp, Belgium, 12-13 September, 2001, were firstly to identify and define problems and secondly to develop a realistic strategy to solve these problems . Both of the stakeholder groups (governmental authorities and the dredging industry) present at the workshop participated in detailed discussions to elucidate the role of sensors in the field of sediments and sediment/water interfaces . The 19 invited experts were agreed that in situ monitoring systems are needed to monitor freshwater sediments . New recognised tools for sediment monitoring would help industry to meet the governmental sediment quality criteria and to handle the data concerning historic river contamination and geological background data . The need to monitor by effect-related studies together with chemical monitoring was stressed . The main focus for development of new sensor tools should be for on site determination of certain priority pollutants where there would be advantage over existing methods or where no suitable method exists, and to monitor biological effects (alarm systems and effect-related on site tests) . Sensing technologies would also be useful to monitor bioavailability in sediments in situ to provide information for risk assessment . In addition, they could be of use to monitor bioremediation in situ . A useful role was forseen in dredging sediments, for in situ sediment screening and to guide treatment of dredged material . The new sensing tools presented, included determination of metal concentrations in sediments using the diffuse gradients in thin films (DGT) technique (Lancaster University, UK), an analytical protocol for determination of metal speciation in sediments (Universitat Autonoma de Barcelona, Spain), microbiotests for determination of sediment toxicity (University of Ghent, Belgium), a portable whole cell sensors device for heavy metal bioavailability (VITO, Belgium) and a microfabricated sensor array system for Pb concentration profile measurement in the microM range at the liquid-solid interface (University of Geneva, Switzerland).

Chemosphere, 2003 Aug, 52(6), 975 - 87
Effects of temperature on mineralisation of petroleum in contaminated Antarctic terrestrial sediments; Ferguson SH et al.; Although petroleum contamination has been identified at many Antarctic research stations, and is recognized as posing a significant threat to the Antarctic environment, full-scale in situ remediation has not yet been used in Antarctica . This is partly because it has been assumed that temperatures are too low for effective biodegradation . To test this, the effects of temperature on the hydrocarbon mineralisation rate in Antarctic terrestrial sediments were quantified . 14C-labelled octadecane was added to nutrient amended microcosms that were incubated over a range of temperatures between -2 and 42 degrees C . We found a positive correlation between temperature and mineralisation rate, with the fastest rates occurring in samples incubated at the highest temperatures . At temperatures below or near the freezing point of water there was a virtual absence of mineralisation . High temperatures (37 and 42 degrees C) and the temperatures just above the freezing point of water (4 degrees C) showed an initial mineralisation lag period, then a sharp increase in the mineralisation rate before a protracted plateau phase . Mineralisation at temperatures between 10 and 28 degrees C had no initial lag phase . The high rate of mineralisation at 37 and 42 degrees C was surprising, as most continental Antarctic microorganisms described thus far have an optimal temperature for growth of between 20 and 30 degrees C and a maximal growth temperature <37 degrees C . The main implications for bioremediation in Antarctica from this study are that a high-temperature treatment would yield the most rapid biodegradation of the contaminant . However, in situ biodegradation using nutrients and other amendments is still possible at soil temperatures that occur naturally in summer at the Antarctic site we studies (Casey Station 66 degrees 17(') S, 110 degrees 32(') E), although treatment times could be excessively long.

Biochem Soc Trans, 2003 Jun, 31(Pt 3), 558 - 62
Engineering substrate recognition in catalysis by cytochrome P450cam; Bell SG et al.; We have a continuing interest in applying the current knowledge of cytochrome P450cam substrate recognition to engineer the enzyme for the biotransformation of unnatural substrates with the long-term aim of applications in the synthesis of fine chemicals and bioremediation of environmental contaminants . Comparisons of the structure of target substrates with that of camphor, the natural substrate, led to the design of active-site mutants with greatly enhanced activity for the oxidation of chlorinated benzenes and selectivity of (+)-alpha-pinene oxidation . The crystal structures of the F87W/Y96F/V247L mutant with 1,3,5-trichlorobenzene or (+)-alpha-pinene bound have revealed the enzyme-substrate contacts and provided insights into the activity and selectivity patterns . The structures have also provided a novel basis for further engineering of P450cam for increased activity in the oxidation of the highly inert pentachlorobenzene and hexachlorobenzene, and increased selectivity of (+)-alpha-pinene oxidation.

Water Res, 2003 Jul, 37(12), 2905 - 18
Evaluation of polyethylene hollow-fiber membranes for hydrogen delivery to support reductive dechlorination in a soil column; Ma X et al.; Engineered systems are often needed to supply an electron donor, such as hydrogen (H(2)), to the subsurface to stimulate the biological dehalogenation of perchloroethene (PCE) to ethene . A column study was performed to evaluate the ability of gas permeable hollow-fiber membranes to supply H(2) directly to PCE-contaminated groundwater to facilitate bioremediation . Two glass columns were packed with soil obtained from a trichloroethene-contaminated site at Cape Canaveral, Florida, and were fed a minimal medium spiked with PCE (7 microM) for 391 days . The columns were operated in parallel, with one column receiving H(2) via polyethylene hollow-fiber membranes (lumen H(2) pressure of approximately 1atm) and a control column receiving no H(2) . PCE was initially dechlorinated at a similar rate and to a similar extent in both columns, likely due to the presence of soil organic matter that was able to support dechlorination . After 265 days of operation, dechlorination performance declined in the control column and the benefits of membrane-supplied H(2) became evident . Although the membrane-supplied H(2) effectively stimulated PCE dechlorination at the end of the experiment (days 359-391), the system was inefficient in that only 5% of the supplied H(2) was used for dechlorination . Most of the remainder was used to support methanogenesis (94%) . Despite the dominance of methanogens, nearly complete dechlorination of PCE to ethene was observed in the H(2)-fed column . In addition to the inefficient use of H(2), operational problems included excessive foulant accumulation on the outside of the membrane fibers and water condensation inside the fibers . Use of alternative membrane materials and changes to the operating approach (e.g . pulsing or supplying H(2) at low partial pressures) may help to overcome these problems so that this technology can provide effective and stable remediation of aquifers contaminated with chlorinated ethenes.

Appl Microbiol Biotechnol, 2003 Jun, 61(5-6), 405 - 12 Epub 2003 Feb 26.
Phytoremediation: an overview of metallic ion decontamination from soil; Singh OV et al.; In recent years, phytoremediation has emerged as a promising ecoremediation technology, particularly for soil and water cleanup of large volumes of contaminated sites . The exploitation of plants to remediate soils contaminated with trace elements could provide a cheap and sustainable technology for bioremediation . Many modern tools and analytical devices have provided insight into the selection and optimization of the remediation process by plant species . This review describes certain factors for the phytoremediation of metal ion decontamination and various aspects of plant metabolism during metallic decontamination . Metal-hyperaccumulating plants, desirable for heavily polluted environments, can be developed by the introduction of novel traits into high biomass plants in a transgenic approach, which is a promising strategy for the development of effective phytoremediation technology . The genetic manipulation of a phytoremediator plant needs a number of optimization processes, including mobilization of trace elements/metal ions, their uptake into the root, stem and other viable parts of the plant and their detoxification and allocation within the plant . This upcoming science is expanding as technology continues to offer new, low-cost remediation options.

J Basic Microbiol, 2003, 43(3), 167 - 74
Microflora involved in textile dye waste removal; Abd El-Rahim WM et al.; Textile dyes are heavily used in factories for coloring different cloth materials . This work was designed to identify microorganisms capable of removing textile dyes, either by biodegradation or by biosorption . We expected to isolate microorganisms adapted to high dye concentrations from sites near textile industry complex . An experiment was conducted to study the efficiency of the isolates in removing textile dyes . The tested dyes were used as carbon and nitrogen sources for isolation of soil and/or water microorganisms capable of removing textile dyes wastes from factories effluent . The results indicated the low efficiency of both bacteria and actinomycetes in clean-up the effluent from the waste dyes in 10-21 days . On the other hand six fungal isolates were obtained by plating factory effluent on Martin's medium and media containing dyes as the sole source of carbon and nitrogen for growth . These isolates fell in two genera, Aspergillus and Trichoderma . Results of these studies revealed the potential capacity of these fungi to decolorize the tested dyes in comparatively short time (2-24 hours) indicating strong efficiency of dye bioremediation by the fungal isolates . Since the process involved is mostly fast interaction between the fungal mycelium and the dye in the media, the possible mechanism could be based on a biosorption of such chemicals on the intact fungal biomass, rather than direct biodegradation of the compounds.

Mycopathologia, 2002, 156(3), 151 - 6
Optimization of an extracellular protease of Chrysosporium keratinophilum and its potential in bioremediation of keratinic wastes; Singh CJ; Chrysosporium keratinophilum IMI 338142 isolated from a waste site containing organopollutants was studied for its ability to produce extracellular proteases on glucose-gelatin medium . Fungus was observed to be a potent producer of such enzymes . Enzyme secretion was best at 15 days of incubation period at pH 8 and temperature 40 degrees C . Asparagine was repressive to protease expression . No relationship existed between the enzyme yield and increase in biomass . Exogenous sugars suppressed enzyme production in the descending order as follows: glucose > arabinose > maltose > mannose > fructose . The enzyme released showed the ability to decompose two keratin substrates tested . Buffalo skin was the most actively degraded substrate when exogenous glucose was absent . Presence of glucose suppressed both enzyme production and degradation of keratin . However, the rate of keratin degradation was independent of enzyme production.

Ecotoxicol Environ Saf, 2003 Jun, 55(2), 199 - 203
Effects of certain heavy metals on the growth, dye decolorization, and enzyme activity of Lentinula edodes; Hatvani N et al.; Various physiological parameters of Lentinula edodes (Shiitake) in the presence of nine heavy metal salts were investigated . The mycelial growth was highly sensitive to cadmium and mercury, but less sensitive to zinc, copper, and lead . This resistance can be particularly dangerous to humans in the case of edible fungi such as Shiitake because of the possible heavy metal accumulation during growth and fruiting body production . All of the tested heavy metals inhibited decolorization of the dye Poly R-478 and the production of manganese peroxidase to a greater extent than they inhibited growth . Interestingly, with the exception of iron, the addition of all heavy metal salts investigated led to the increase of laccase production . Apart from cadmium and iron, none of the heavy metals inhibited the in vitro enzyme activities in concentrations up to 3mM . The results of this study indicated the applicability of L . edodes in biosorption technologies used in the removal of toxic metals from contaminated effluents and in bioremediation technologies designed to treat complex wastes contaminated with heavy metals in addition to other xenobiotics.

Environ Manage . 2003 May 13; {Epub ahead of print}
Bioremediation of Soil Degraded by Sewage Sludge: Effects on Soil Properties and Erosion Losses; Ros M et al.; Soils in the Mediterranean area are very prone to erosion due to the loss of organic matter and the consequent lack of protective vegetation . In this experiment a Mediterranean degraded soil with a 15% slope was amended at a rate of 250 t ha(-1) wet weight with sewage sludge and with a mixture of sewage sludge and barley straw (70% carbon from sewage sludge and 30% from the straw) in order to study their influence on soil structure recovery and hence the soils's resistance to erosion processes . Both types of organic amendment led to an improvement in several soil properties (physical, biological, and microbiological) as a result of the spontaneous growth plant covering that became evident three months after amendment . This vegetation remained throughout the two years of the experiment and prevented the water erosion processes that normally precede soil degradation . Amendment by sewage sludge alone reduced soil loss by 80% compared with the control soil, while the mixture that included both sewage sludge and barley straw reduced losses by 84%, both reducing runoff by 57% . The amended soils showed increases in the percentage of stable aggregates, the levels of the total and water-soluble C fractions, microbial biomass C, basal respiration, and the activity of the different enzymes involved in the biogeochemical cycles of C, N, and P . The results confirm the usefulness of sewage sludge as an organic amendment for recovering damaged soils.

Arch Microbiol, 2003 Jul, 180(1), 1 - 10 Epub 2003 May 09.
Mercury pretreatment selects an enhanced cadmium-accumulating phenotype in Euglena gracilis; Aviles C et al.; Pre-treatment of heterotrophic cultures of Euglena gracilis with 1.5 microM HgCl(2) for at least 60 generations resulted in a cell population that showed both increased resistance to Cd(2+) and ability to accumulate it, when compared to non-Hg(2+)-pretreated Euglena . These Hg(2+)-enhanced capacities were evident in cells cultured in the dark in a medium with lactate, but not in cells cultured with glutamate plus malate . After culturing with 0.1 mM CdCl(2) through three consecutive transfers, the mercury-pretreated cells still grew and maintained high levels of glutathione-related metabolites, while the non-Hg(2+)-pretreated cells died . Cultures of Hg(2+)-pretreated cells, after transfer to media with or without cadmium, did not alter either their enhanced Cd(2+) accumulation or their increased production of glutathione-related metabolites . These observations suggested that the Hg(2+)-pretreated population underwent a permanent change that improved its Cd(2+) resistance . Several factors that contributed to the improved capacities included: (a) higher cellular malate, cysteine and glutathione levels induced by Hg(2+) before and after Cd(2+) exposure; and (b) increased storage of Cd(2+) in mitochondria along with increased intramitochondrial citrate, cysteine, and glutathione levels . These characteristics suggested that this Cd(2+) hyper-accumulating strain of E . gracilis might be a suitable candidate for Cd(2+)-bioremediation of polluted water systems.

Chemosphere, 2003 Jul, 52(4), 663 - 71
Biodegradation capability of Absidia fusca Linnemann towards environmental pollutants; Guiraud P et al.; The purpose of this work was to study the bioremediation capability of Absidia fusca Linnemann (Zygomycete) towards different classes of xenobiotics (lignin-derived compounds, chloroaromatic compounds, polycyclic aromatic hydrocarbons) the presence of which in contaminated soils, water and sediments poses a significant risk to the environment and human health . Two strains from different origins were compared . One was from an official collection and grown in non-inducing conditions, while the other was isolated during the course of the survey of fungal flora in a polluted soil from Annaba (Algeria) . All data were analyzed and results validated via a statistical treatment . We showed the effect of the factors studied (origin of the strain, xenobiotic) but also the interactions between these factors . The strain of A . fusca isolated from a polluted soil was able to efficiently degrade most of the xenobiotics tested, particularly: pentachlorophenol, phenol, catechol, guaiacol and ferulic acid . This property also existed in the other strain but at a very low level.

J Mol Microbiol Biotechnol, 2003, 5(2), 67 - 77
Applications of the Saccharomyces cerevisiae Flp-FRT system in bacterial genetics; Schweizer HP; The Flp-FRT site-specific recombination system from Saccharomyces cerevisiae is a powerful and efficient tool for high-throughput genetic analysis of bacteria in the postgenomic era . This review highlights the features of the Flp-FRT system, describes current bacterial genetic methods incorporating this technology and, finally, suggests potential future uses of this system . In combination with improved allele replacement methods, recyclable FRT mutagenesis cassettes, whose antibiotic resistance markers can be excised from the chromosome in vivo, are useful for the rapid construction of multiple, unmarked mutations in the same chromosome, and thus aid in the generation of live vaccine strains or food-safe bacteria . The high-specificity of the Flp-FRT system makes it also applicable for manipulation of whole genomes, including in vivo cloning of large genomic segments . Integration-proficient vectors, from which antibiotic resistance markers and replication functions can be evicted after integration of the desired sequences into the chromosome, are useful for the construction of strains destined for environmental release, e.g . strains used as biosensors or for bioremediation . Although the Flp-FRT system is extremely efficient and easy to use, its true potential in bacterial genetics has not yet been fully exploited . On the contrary, in many instances this technology is probably greatly underutilized, especially in gram-positive bacteria .

Environ Monit Assess, 2003 May, 84(1-2), 45 - 60
Bioremediation of metal contamination; Mulligan CN et al.; A study was initiated to evaluate the use of the fungus Aspergillus niger for bioleaching and then to determine the effect of process steps, the tailings concentration and type of substrate . An oxidized mining tailing containing mainly copper (7240 mg kg(-1) tailings) was studied . A sucrose and mineral salts medium was initially used to produce citric and gluconic acids by A . niger at various concentrations of tailings ( 1, 5, 7, 10 and 15% w/v) . Maximal removal of up to 60% of the copper was obtained for the 5% tailings when the organic acid supernatant was added to the tailings . In a single step process, A . niger was then grown in the presence of mining tailings at various concentrations . Maximum copper solubilization (63%) occurred with 10% mining tailings using sucrose as the substrate . Other substrates were then evaluated including molasses, corn cobs and brewery waste (10% mining tailings) . Sucrose gave the best results for copper removal, followed by molasses, corn cobs and brewery waste . Other experiments using ultrasound as a pretreatment showed that 80% removal of the copper could be obtained for a 5% tailings concentration . In conclusion, leaching of copper from mining tailings is technically feasible using A . niger but further research will be required to increase the economic feasibility of the process.

Appl Environ Microbiol, 2003 May, 69(5), 2879 - 83
Specific detection of Dehalococcoides species by fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes; Yang Y et al.; Dehalococcoides ethenogenes is the only known cultivated organism capable of complete dehalogenation of tetrachloroethene (PCE) to ethene . The prevalence of Dehalococcoides species in the environment and their association with complete dehalogenation of chloroethenes suggest that they play an important role in natural attenuation of chloroethenes and are promising candidates for engineered bioremediation of these contaminants . Both natural attenuation and bioremediation require reliable and sensitive methods to monitor the presence, distribution, and fate of the organisms of interest . Here we report the development of 16S rRNA-targeted oligonucleotide probes for Dehalococcoides species . The two designed probes together encompass 28 sequences of 16S rRNA genes retrieved from the public database . Except D . ethenogenes and CBDB1, all the others are environmental clones obtained from sites contaminated with chlorinated ethenes . They are all closely related and form a unique cluster of Dehalococcoides species . In situ hybridization of probe Dhe1259t with D . ethenogenes strain 195 and two enrichment cultures demonstrated the applicability of the probe to monitoring the abundance of active Dehalococcoides species in these enrichment samples.

Curr Opin Biotechnol, 2003 Apr, 14(2), 151 - 62
Plant cytochromes P450: tools for pharmacology, plant protection and phytoremediation; Morant M et al.; Cytochromes P450 catalyse extremely diverse and often complex regiospecific and/or stereospecific reactions in the biosynthesis or catabolism of plant bioactive molecules . Engineered P450 expression is needed for low-cost production of antineoplastic drugs such as taxol or indole alkaloids and offers the possibility to increase the content of nutraceuticals such as phytoestrogens and antioxidants in plants . Natural products may serve important functions in plant defence and metabolic engineering of P450s is a prime target to improve plant defence against insects and pathogens . Herbicides, pollutants and other xenobiotics are metabolised by some plant P450 enzymes . These P450s are tools to modify herbicide tolerance, as selectable markers and for bioremediation.

Environ Sci Pollut Res Int, 2003, 10(2), 108 - 12
Bioremediation of crude oil polluted soil by the white rot fungus, Pleurotus tuberregium (Fr.) Sing; Isikhuemhen OS et al.; Bioremediation has become an attractive alternative to physicochemical methods of remediation of polluted sites . White rot fungi (WRF) are increasingly being investigated and used in bioremediation, because of their ability to degrade an extremely diverse range of very persistent or toxic environmental pollutants . The white rot fungus, Pleurotus tuberregium, was examined for its ability to ameliorate crude oil polluted soil . This was inferred from the ability of the polluted soil to support seed germination and seedling growth in Vigna unguiculata, at 0, 7 and 14 days post treatment . Results obtained from the present study showed that bioremediation of soil contaminated with crude oil was possible, especially when the fungus had been allowed to establish and fully colonize the substrate mixed with the soil . There were significant improvements in % germination, plant height and root elongation values of test plants, when seeds were planted 14 days post soil treatment . At 1 to 5% crude oil pollution, % germination values were comparable with the values in control plants in the 14 days treatment, and significantly higher than values obtained in the day 0 treatment . Also, at the highest level of crude oil pollution (15%), there was about 25% improvement in % germination value over the 0 day treatment . This trend of improvement in values was also observed for plant height, root elongation and biomass accumulation as well as decreased total hydrocarbon content.

Trends Biotechnol, 2003 May, 21(5), 187 - 90
'Super bugs' for bioremediation; Furukawa K; Chlorinated organic compounds are among the most significant pollutants in the world . Sequential use of anaerobic halorespiring bacteria, which are the key players in biological dehalogenation processes, and aerobic bacteria whose oxygenases are modified by directed evolution could lead to efficient and total degradation of highly chlorinated organic pollutants . Recently three interesting papers on halorespiration and polychlorinated biphenyl biodegradation were published.

Can J Microbiol, 2003 Feb, 49(2), 151 - 6
Metal resistance among aerobic chemoheterotrophic bacteria from the deep terrestrial subsurface; Benyehuda G et al.; The metal resistance of 350 subsurface bacterial strains from two U.S . Department of Energy facilities, the Savannah River Site (SRS), South Carolina, and the Hanford site, Washington, was determined to assess the effect of metal toxicity on microorganisms in the deep terrestrial subsurface . Resistance was measured by growth inhibition around discs containing optimized amounts of Hg(II), Pb(II), and Cr(VI) . A broad range of resistance levels was observed, with some strains of Arthrobacter spp . demonstrating exceptional tolerance . A higher level of resistance to Hg(II) and Pb(II) (P < 0.05) and a higher occurrence of multiple resistances suggested that metals more effectively influenced microbial evolution in subsurface sediments of the SRS than in those of the Hanford site . Common resistance to heavy metals suggests that toxic metals are unlikely to inhibit bioremediation in deep subsurface environments that are contaminated with mixed wastes.

J Contam Hydrol, 2003 Apr-May, 62-63, 553 - 75
Microbial impacts to the near-field environment geochemistry: a model for estimating microbial communities in repository drifts at Yucca Mountain; Jolley DM et al.; Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada . The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock . The simulations, which spanned 1 million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING) . MING uses environmental thresholds for limiting microbial growth to temperatures below 120 degrees C and above relative humidities of 90% in repository drifts . Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley et al . {FEMS Microbiol . Rev . 20 (1997) 545} by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift to perform two separate mass balance calculations as a function of time . The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C(160)(H(280)O(80))N(30)P(2)S . The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature and pH at that time . This optimization maximizes those reactions that produce >15 kJ/mol (limit on useable energy) using an iterative linear optimization technique . The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy . These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time . MING can also be adapted to investigate other problems of interest as the model can be used in saturated and unsaturated environments and in laboratory situations to establish microbial growth limitations . Other projected uses include investigations of contaminated locations where monitored natural attenuation or engineered bioremediation could be employed.

Mar Pollut Bull, 2003 Apr, 46(4), 430 - 43
Response of estuarine meio- and macrofauna to in situ bioremediation of oil-contaminated sediment; Schratzberger M et al.; Numerous studies have demonstrated the efficacy of bioremediation for enhancing oil removal but the ecological effect on shoreline biota is unclear . Therefore, a field experiment was designed at an intertidal sandflat in SW England to assess the effects of nutrient addition to oiled sediments on meio- and macrofauna for a period of up to 45 weeks . Natural assemblages were exposed to different types of experimental treatments (no oil, oil alone, oil treated with slow-release fertiliser or liquid fertiliser) . Bioremediation stimulated the microbial population and increased oil biodegradation . This, however, did not result in faster recolonisation rates of fertilised versus non-fertilised oiled sediments . Mild effects of oil and bioremediation treatments on benthic fauna were observed, including short-term shifts in dominance patterns . Decreased abundance of dominant species in the oiled compared to unoiled sediments resulted in significantly higher evenness of benthic assemblages within the first 11 weeks of the experiment.

J Microbiol Methods, 2003 Jun, 53(3), 343 - 53
A procedure for quantitation of total oxidized uranium for bioremediation studies; Elias DA et al.; A procedure was developed for the quantitation of complexed U(VI) during studies on U(VI) bioremediation . These studies typically involve conversion of soluble or complexed U(VI) (oxidized) to U(IV) (the reduced form which is much less soluble) . Since U(VI) freely exchanges between material adsorbed to the solid phase and the dissolved phase, uranium bioremediation experiments require a mass balance of U in both its soluble and adsorbed forms as well as in the reduced sediment bound phase . We set out to optimize a procedure for extraction and quantitation of sediment bound U(VI) . Various extractant volumes to sediment ratios were tested and it was found that between 1:1 to 8:1 ratios (v/w) there was a steady increase in U(VI) recovered, but no change with further increases in v/w ratio.Various strengths of NaHCO(3), Na-EDTA, and Na-citrate were used to evaluate complexed U(VI) recovery, while the efficiency of a single versus repeated extraction steps was compared with synthesized uranyl-phosphate and uranyl-hydroxide . Total recovery with 1 M NaHCO(3) was 95.7% and 97.9% from uranyl-phosphate and uranyl-hydroxide, respectively, compared to 80.7% and 89.9% using 450 mM NaHCO(3) . Performing the procedure once yielded an efficiency of 81.1% and 92.3% for uranyl-phosphate and uranyl-hydroxide, respectively, as compared to three times . All other extractants yielded 7.9-82.0% in both experiments.Biologically reduced U(IV) was treated either alone or mixed with uncontaminated sediment slurries to ensure that the procedure was not interfering with subsequent U(IV) quantitation . While U(VI) was recovered, it represented 0.07% of the total uranium alone or 7.8% when mixed with sediments . Total uranium recovered did not change.The procedure was then used to monitor changes in complexed U(VI) levels during uranium-reduction in pure culture and sediments . There was no appreciable complexed U(VI) concentration in pure culture . In sediments however, once soluble U(VI) levels and reduction rates decreased, complexed U(VI) levels began to decrease while U(IV) levels continued to increase . This indicated that once soluble U(VI) was nearly exhausted, sorbed U(VI) became bioavailable and was reduced microbiologically.Typically, uranium is quantified in two steps, soluble U(VI) and U(IV) . However, the present study shows that after successive washings with water to remove soluble U(VI), a significant pool of oxidized uranium remains which may be mistakenly quantified as U(IV) . This procedure can be used to quantified this pool, does not interfere with U(IV) quantitation, and has an overall efficiency of 95.8%.

Chemosphere, 2003 Feb, 50(6), 847 - 53
Interactions between arbuscular mycorrhizae and heavy metals under sand culture experiment; Liao JP et al.; A sand culture experiment was established to determine interactions between arbuscular mycorrhizae and heavy metals . Mycorrhizal infection rates, spore densities, maize root and shoot weights, and heavy metal contents in maize were as indexes of responses of arbuscular mycorrhizal fungi (Acaulospora laevis, Glomus caledonium and Glomus manihotis) to heavy metals (Cu and Cd) . The mycorrhizal infection rates of G . caledonium were the highest among these three mycorrhizal fungi, but the sporulating ability of G . caledonium was the poorest in the heavy metal treatments . The shoot and root weights of non-mycorrhizal plants were usually greater than those of mycorrhizal plants when the Cu concentrations in solutions are less than 3 mg l(-1) or Cd concentrations less than 1 mg l(-1) . When Cd concentrations were 0.5 and 1 mg(-1), the root and shoot weights of plants inoculated with A . laevis were significantly (p < 0.05) lower than those of other treatments . Copper concentrations in shoots of mycorrhizal plants were higher than those of non-mycorrhizal ones at all Cu concentrations in solution, especially at low Cu concentrations . As to A . laevis, Cu concentrations in roots and shoots of the host were higher than those of non-mycorrhizal plants in these treatments . Thus A . laevis was sensitive to Cu and Cd, especially Cd, and G . caledonium was more tolerant to these two heavy metals . It is suggested that G . caledonium might be a promising mycorrhizal fungus for bioremediation of heavy metal contaminated soil.

Lett Appl Microbiol, 2003, 36(5), 272 - 6
Isolation and characterization of an atrazine-degrading bacterium from industrial wastewater in China; Cai B et al.; AIMS: To isolate and characterize atrazine-degrading bacteria in order to identify suitable candidates for potential use in bioremediation of atrazine contamination . METHODS AND RESULTS: A high efficiency atrazine-degrading bacterium, strain AD1, which was capable of utilizing atrazine as a sole nitrogen source for growth, was isolated from industrial wastewater . 16S rDNA sequencing identified AD1 as an Arthrobacter sp . The atrazine chlorohydrolase gene (atzA) isolated from strain AD1 differed from that found in the Pseudomonas sp . ADP by only one nucleotide . However, it was found located on the bacterial chromosome rather than on plasmids as previously reported for other bacteria . CONCLUSIONS: Atrazine chlorohydrolase gene, atzA, either encoded by chromosome or plasmid, is highly conserved . SIGNIFICANCE AND IMPACT OF THE STUDY: Comparison analysis of atrazine degradation gene structure and arrangement in this and other bacteria provides insight into our understanding of the ecology and evolution of atrazine-degrading bacteria.

Environ Toxicol Chem, 2003 Apr, 22(4), 692 - 8
Bioaugmentation of tar-contaminated soils under field conditions using Pleurotus ostreatus refuse from commercial mushroom production; Hestbjerg H et al.; The influence of the white rot fungus Pleurotus ostreatus on the degradation of selected poly- and heterocyclic aromatic hydrocarbons (referred to as polycyclic aromatic hydrocarbons {PAHs}) in soil was investigated under field conditions representing the Northern temperate zone . Pleurotus ostreatus was added to two contaminated soils in the form of homogenized refuse from the commercial production of fungus . The soils were collected from a former shipyard (the B&W soil) and underneath a former coal tar storage at an old asphalt factory in Denmark (the Ringe soil) . Treatments (control, soil mixed with autoclaved sawdust medium, and soil mixed with P . ostreatus refuse) were set up in triplicate in concrete cylinders (height, 50 cm; diameter, 60 cm) . The activity of P . ostreatus was measured as laccase activity and phenanthrene (PHE)- and pyrene (PYR)-degrading bacteria were enumerated . Twenty-one different PAHs were quantified . After nine weeks the concentrations of the 3-, 4-, 5-, and 6-ring PAHs in the Ringe soil were reduced by 78, 41, and 4%, respectively . These reductions corresponded with high initial laccase activity, a decrease in pH caused by the fungus, and an increase in the number of PHE- and PYR-degrading bacteria . No significant PAH degradation was observed in the B&W soil . Reasons for the difference in performance of P . ostreatus in the two soils are discussed in terms of soil histories and bioavailability . The use of P . ostreatus refuse holds promising potential for bioremediation purposes.

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