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 site