Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology

Inhibition of microbial trichloroethylene dechlorination [corrected] by Fe (III) reduction depends on Fe mineralogy: a batch study using the bioaugmentation culture KB-1

Microbial reductive dechlorination of trichloroethylene (TCE) in groundwater can be stimulated by adding of electron donors. However, side reactions such as Fe (III) reduction competes with this reaction. This study was set-up to relate the inhibition of microbial TCE dechlorination to the quantity and quality (mineralogy) of Fe (III) in the substrate and to calibrate a substrate extraction procedure for testing bioavailable Fe (III) in sediments. Batch experiments were set-up with identical inoculum (KB-1 culture) and liquid medium composition, and adding either 1) variable amounts of ferrihydrite or 2) 14 different Fe (III) minerals coated onto or mixed in with quartz sand (at constant total Fe) at a stoichiometric excess Fe (III) over electron donor. Increasing amounts of ferrihydrite significantly increased the time for complete TCE degradation from 8 days (control sand) to 28 days (excess Fe). Acid extractable Fe (II) increased and magnetite formed during incubation, confirming Fe (III) reduction. At constant total Fe in the sand, TCE dechlorination time varied with Fe mineralogy between 8 days (no Fe added) to >120 days (Fe-containing bentonite). In general, poorly crystalline Fe (III) minerals inhibited TCE dechlorination whereas crystalline Fe (III) minerals such as goethite or hematite had no effect. The TCE inhibition time was positively correlated to the Fe (II) determined after 122 days and to the surface area of the Fe (III) minerals. Only a fraction of total Fe (III) is reduced, likely because of solubility constraints and/or coating of Fe (III) minerals by Fe (II) minerals. Iron extraction tests based on Fe (III) reduction using NH2OH(.)HCl predict the competitive inhibition of TCE degradation in these model systems. This study shows that Fe mineralogy rather that total Fe content determines the competitive inhibition of TCE dechlorination.

Effects of sulfate reduction on the bacterial community and kinetic parameters of a dechlorinating culture under chemostat growth conditions

Results are presented from a chemostat study where the reductive dehalogenation of PCE was evaluated in the absence and presence of sulfate. Two chemostats inoculated with the Point Mugu culture, which contains strains of Dehalococcoides mccartyi, were operated at a 50 day HRT and fed PCE (1.12 mM) and lactate (4.3 mM). The control chemostat (PM-5L, no sulfate), achieved pseudo-steady-state transformation of PCE to ethene (98%) and VC (2%) at 2.4 nM of H(2). Batch kinetic tests with chemostat harvested cells showed the maximum rate (k(max)X) value for each dehalogenation step remained fairly constant, while hupL clone library analyses showed maintenance of a diverse D. mccartyi community. Sulfate (1 mM) was introduced to the second chemostat, PM-2L. Effective sulfate reduction was achieved 110 days later, resulting in 600 μM of total sulfide. PCE dechlorination efficiency decreased following complete sulfate reduction, yielding ethene (25%), VC (67%), and cis-DCE (8%). VC dechlorination was most affected, with k(max)X values decreasing by a factor of 50. The decrease was associated with the enrichment of the Cornell group of D. mccartyi and decline of the Pinellas group. Long-term exposure to sulfides and/or competition for H(2) may have been responsible for the community shift.

Evaluation of biodegradable plastics as solid hydrogen donors for the reductive dechlorination of fthalide by Dehalobacter species

Biodegradable plastics (BPs) were evaluated for their applicability as sustainable and solid H(2) donors for microbial reductive dechlorination of 4,5,6,7-tetrachlorophthalide (fthalide). After a screening test of several BPs, the starch-based plastic (SP) that produced the highest levels of H(2) was selected for its use as the sole H(2) donor in this reaction. Fthalide dechlorination was successfully accomplished by combining an H(2)-producing SP culture and a KFL culture containing Dehalobacter species, supplemented with 0.13% and 0.5% SP, respectively. The efficiency of H(2) use in dechlorination was evaluated in a combined culture containing the KFL culture and strain Clostridium sp. Ma13, a new isolate that produces H(2) from SP. Results obtained with this culture indicated increased H(2)-fraction for fthalide dechlorination much more in this culture than in compared with a KFL culture supplemented with 20mM lactate, which are 0.75 H(2)·glucose(-1) and 0.015 H(2)·lactate(-1) in mol ratio, respectively.

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants.

Geothrix fermentans secretes two different redox-active compounds to utilize electron acceptors across a wide range of redox potentials

The current understanding of dissimilatory metal reduction is based primarily on isolates from the proteobacterial genera Geobacter and Shewanella. However, environments undergoing active Fe(III) reduction often harbor less-well-studied phyla that are equally abundant. In this work, electrochemical techniques were used to analyze respiratory electron transfer by the only known Fe(III)-reducing representative of the Acidobacteria, Geothrix fermentans. In contrast to previously characterized metal-reducing bacteria, which typically reach maximal rates of respiration at electron acceptor potentials of 0 V versus standard hydrogen electrode (SHE), G. fermentans required potentials as high as 0.55 V to respire at its maximum rate. In addition, G. fermentans secreted two different soluble redox-active electron shuttles with separate redox potentials (-0.2 V and 0.3 V). The compound with the lower midpoint potential, responsible for 20 to 30% of electron transfer activity, was riboflavin. The behavior of the higher-potential compound was consistent with hydrophilic UV-fluorescent molecules previously found in G. fermentans supernatants. Both electron shuttles were also produced when cultures were grown with Fe(III), but not when fumarate was the electron acceptor. This study reveals that Geothrix is able to take advantage of higher-redox-potential environments, demonstrates that secretion of flavin-based shuttles is not confined to Shewanella, and points to the existence of high-potential-redox-active compounds involved in extracellular electron transfer. Based on differences between the respiratory strategies of Geothrix and Geobacter, these two groups of bacteria could exist in distinctive environmental niches defined by redox potential.

Zymographic differentiation of [NiFe]-hydrogenases 1, 2 and 3 of Escherichia coli K-12

Background

When grown under anaerobic conditions, Escherichia coli K-12 is able to synthesize three active [NiFe]-hydrogenases (Hyd1-3). Two of these hydrogenases are respiratory enzymes catalysing hydrogen oxidation, whereby Hyd-1 is oxygen-tolerant and Hyd-2 is considered a standard oxygen-sensitive hydrogenase. Hyd-3, together with formate dehydrogenase H (Fdh-H), forms the formate hydrogenlyase (FHL) complex, which is responsible for H₂ evolution by intact cells. Hydrogen oxidation activity can be assayed for all three hydrogenases using benzyl viologen (BV; E_o′ = -360 mV) as an artificial electron acceptor; however ascribing activities to specific isoenzymes is not trivial. Previously, an in-gel assay could differentiate Hyd-1 and Hyd-2, while Hyd-3 had long been considered too unstable to be visualized on such native gels. This study identifies conditions allowing differentiation of all three enzymes using simple in-gel zymographic assays.

Results

Using a modified in-gel assay hydrogen-dependent BV reduction catalyzed by Hyd-3 has been described for the first time. High hydrogen concentrations facilitated visualization of Hyd-3 activity. The activity was membrane-associated and although not essential for visualization of Hyd-3, the activity was maximal in the presence of a functional Fdh-H enzyme. Furthermore, through the use of nitroblue tetrazolium (NBT; E_o′ = -80 mV) it was demonstrated that Hyd-1 reduces this redox dye in a hydrogen-dependent manner, while neither Hyd-2 nor Hyd-3 could couple hydrogen oxidation to NBT reduction. Hydrogen-dependent reduction of NBT was also catalysed by an oxygen-sensitive variant of Hyd-1 that had a supernumerary cysteine residue at position 19 of the small subunit substituted for glycine. This finding suggests that tolerance toward oxygen is not the main determinant that governs electron donation to more redox-positive electron acceptors such as NBT.

Conclusions

The utilization of particular electron acceptors at different hydrogen concentrations and redox potentials correlates with the known physiological functions of the respective hydrogenase. The ability to rapidly distinguish between oxygen-tolerant and standard [NiFe]-hydrogenases provides a facile new screen for the discovery of novel enzymes. A reliable assay for Hyd-3 will reinvigorate studies on the characterisation of the hydrogen-evolving FHL complex.

Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi

Six obligately anaerobic bacterial isolates (195(T), CBDB1, BAV1, VS, FL2 and GT) with strictly organohalide-respiring metabolisms were obtained from chlorinated solvent-contaminated aquifers, contaminated and uncontaminated river sediments or anoxic digester sludge. Cells were non-motile with a disc-shaped morphology, 0.3-1 µm in diameter and 0.1-0.2 µm thick, and characteristic indentations on opposite flat sides of the cell. Growth occurred in completely synthetic, reduced medium amended with a haloorganic electron acceptor (mostly chlorinated but also some brominated compounds), hydrogen as electron donor, acetate as carbon source, and vitamins. No other growth-supporting redox couples were identified. Aqueous hydrogen consumption threshold concentrations were <1 nM. Growth ceased when vitamin B(12) was omitted from the medium. Addition of sterile cell-free supernatant of Dehalococcoides-containing enrichment cultures enhanced dechlorination and growth of strains 195 and FL2, suggesting the existence of so-far unidentified stimulants. Dechlorination occurred between pH 6.5 and 8.0 and over a temperature range of 15-35 °C, with an optimum growth temperature between 25 and 30 °C. The major phospholipid fatty acids were 14 : 0 (15.7 mol%), br15 : 0 (6.2 mol%), 16 : 0 (22.7 mol%), 10-methyl 16 : 0 (25.8 mol%) and 18 : 0 (16.6 mol%). Unusual furan fatty acids including 9-(5-pentyl-2-furyl)-nonanoate and 8-(5-hexyl-2-furyl)-octanoate were detected in strains FL2, BAV1 and GT, but not in strains 195(T) and CBDB1. The 16S rRNA gene sequences of the six isolates shared more than 98 % identity, and phylogenetic analysis revealed an affiliation with the phylum Chloroflexi and more than 10 % sequence divergence from other described isolates. The genome sizes and G+C contents ranged from 1.34 to 1.47 Mbp and 47 to 48.9 mol% G+C, respectively. Based on 16S rRNA gene sequence comparisons, genome-wide average nucleotide identity and phenotypic characteristics, the organohalide-respiring isolates represent a new genus and species, for which the name Dehalococcoides mccartyi gen. nov., sp. nov. is proposed. Isolates BAV1 ( = ATCC BAA-2100  = JCM 16839  = KCTC 5957), FL2 ( = ATCC BAA-2098  = DSM 23585  = JCM 16840  = KCTC 5959), GT ( = ATCC BAA-2099  = JCM 16841  = KCTC 5958), CBDB1, 195(T) ( = ATCC BAA-2266(T)  = KCTC 15142(T)) and VS are considered strains of Dehalococcoides mccartyi, with strain 195(T) as the type strain. The new class Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov. are described to accommodate the new taxon.

Use of γ-hexachlorocyclohexane as a terminal electron acceptor by an anaerobic enrichment culture

The use of γ-hexachlorocyclohexane (HCH) as a terminal electron acceptor via organohalide respiration was demonstrated for the first time with an enrichment culture grown in a sulfate-free HEPES-buffered anaerobic mineral salts medium. The enrichment culture was initially developed with soil and groundwater from an industrial site contaminated with HCH isomers, chlorinated benzenes, and chlorinated ethenes. When hydrogen served as the electron donor, 79-90% of the electron equivalents from hydrogen were used by the enrichment culture for reductive dechlorination of the γ-HCH, which was provided at a saturation concentration of approximately 10 mg/L. Benzene and chlorobenzene were the only volatile transformation products detected, accounting for 25% and 75% of the γ-HCH consumed (on a molar basis), respectively. The enrichment culture remained active with only hydrogen as the electron donor and γ-HCH as the electron acceptor through several transfers to fresh mineral salts medium for more than one year. Addition of vancomycin to the culture significantly slowed the rate of γ-HCH dechlorination, suggesting that a Gram-positive organism is responsible for the reduction of γ-HCH. Analysis of the γ-HCH dechlorinating enrichment culture did not detect any known chlororespiring genera, including Dehalobacter. In bicarbonate-buffered medium, reductive dechlorination of γ-HCH was accompanied by significant levels of acetogenesis as well as methanogenesis.

Enhanced reductive dechlorination of polychlorinated biphenyl impacted sediment by bioaugmentation with a dehalorespiring bacterium

Anaerobic reductive dehalogenation of commercial PCBs such as Aroclor 1260 has a critical role of transforming highly chlorinated congeners to less chlorinated congeners that are then susceptible to aerobic degradation. The efficacy of bioaugmentation with the dehalorespiring bacterium Dehalobium chlorocoercia DF1 was tested in 2-L laboratory mesocosms containing sediment contaminated with weathered Aroclor 1260 (1.3 ppm) from Baltimore Harbor, MD. Total penta- and higher chlorinated PCBs decreased by approximately 56% (by mass) in bioaugmented mesocosms after 120 days compared with no activity observed in unamended controls. Bioaugmentation with DF-1 enhanced the dechlorination of doubly flanked chlorines and stimulated the dechlorination of single flanked chlorines as a result of an apparent synergistic effect on the indigenous population. Addition of granulated activated carbon had a slight stimulatory effect indicating that anaerobic reductive dechlorination of PCBs at low concentrations was not inhibited by a high background of inorganic carbon that could affect bioavailability. The total number of dehalorespiring bacteria was reduced by approximately half after 60 days. However, a steady state level was maintained that was greater than the indigenous population of putative dehalorespiring bacteria in untreated sediments and DF1 was maintained within the indigenous population after 120 days. The results of this study demonstrate that bioaugmentation with dehalorespiring bacteria has a stimulatory effect on the dechlorination of weathered PCBs and supports the feasibility of using in situ bioaugmentation as an environmentally less invasive and lower cost alternate to dredging for treatment of PCB impacted sediments.

Biotransformation of nitrosamines and precursor secondary amines under methanogenic conditions

The biotransformation potential of six nitrosamines and their precursor secondary amines by a mixed methanogenic culture was investigated. Among the six nitrosamines tested, N-nitrosodimethylamine (NDMA), N-nitrosomethylethylamine (NMEA), and N-nitrosopyrrolidine (NPYR) were almost completely degraded but only when degradable electron donors were available. On the contrary, N-nitrosodiethylamine (NDEA), N-nitrosodipropylamine (NDPA), and N-nitrosodibutylamine (NDBA) were not degraded. Three precursor secondary amines, corresponding to the three biodegradable nitrosamines, were also completely utilized even with very low levels of available electron donors. The secondary amine precursors of the three, nonbiodegradable nitrosamines were also recalcitrant. A bioassay conducted to elucidate the biotransformation pathway of NDMA in the mixed methanogenic culture using H(2) as the electron donor showed that NDMA was utilized as an electron acceptor and transformed to dimethylamine (DMA), which in turn was degraded to ammonia and methane. The H(2) threshold concentration for NDMA bioreduction ranged between 0.0017 and 0.031 atm. Such a high H(2) threshold concentration suggests that in mixed methanogenic cultures, NDMA reducers are weak competitors to other, H(2)-consuming microbial species, such as homoacetogens and methanogens. Thus, complete removal of nitrosamines in anaerobic digestion systems, where the H(2) partial pressure is typically below 10(-4) atm, is difficult to achieve.

Dechlorination of trichloroethene in a continuous-flow bioelectrochemical reactor: effect of cathode potential on rate, selectivity, and electron transfer mechanisms

The exciting discovery that dechlorinating bacteria can use polarized graphite cathodes as direct electron donors in the reductive dechlorination has prompted investigations on the development of novel bioelectrochemical remediation approaches. In this work, we investigated the performance of a bioelectrochemical reactor for the treatment of trichloroethene (TCE). The reactor was continuously operated for about 570 days, at different potentiostatically controlled cathode potentials, ranging from -250 mV to -750 mV vs standard hydrogen electrode. The rate and extent of TCE dechlorination, as well as the competition for the available electrons, were highly dependent on the set cathode potential. When the cathode was controlled at -250 mV, no abiotic hydrogen production occurred and TCE dechlorination (predominantly to cis-DCE and VC), most probably sustained via direct extracellular electron transfer, proceeded at an average rate of 15.5 ± 1.2 μmol e(-)/L d. At this cathode, potential methanogenesis was almost completely suppressed and dechlorination accounted for 94.7 ± 0.1% of the electric current (15.0 ± 0.8 μA) flowing in the system. A higher rate of TCE dechlorination (up to 64 ± 2 μmol e(-)/L d) was achieved at cathode potentials lower than -450 mV, though in the presence of a very active methanogenesis which accounted for over 60% of the electric current. Remarkably, the bioelectrochemical reactor displayed a stable and reproducible performance even without the supply of organic carbon sources with the feed, confirming long-term viability.

Influence of ferric iron on complete dechlorination of trichloroethylene (TCE) to ethene: Fe(III) reduction does not always inhibit complete dechlorination

The effects of Fe(III) reduction on TCE, cis-DCE, and VC dechlorination were studied in both contaminated aquifer material and enrichment cultures. The results from sediment batch experiments demonstrated that Fe(III) reduction did not inhibit complete dechlorination. TCE was reduced concurrently with Fe(III) in the first 40 days of the incubations. While all incubations (plus and minus Fe(III)) generated approximately the same mass of ethene within the experimental time frame, Fe(III) speciation (ferrihydrite versus Fe(III)-NTA) had an impact on daughter product distribution and dechlorination kinetics. 16S rRNA gene clone library sequencing identified Dehalococcoides and Geobacteraceae as dominant populations, which included G. lovleyi like organisms. Quantitative PCR targeting 16S rRNA genes and Reductive Dehalogenase genes (tceA, bvcA, vcrA) indicated that Dehalococcoides and Geobacteraceae were enriched concurrently in the TCE-degrading, Fe(III)-reducing sediments. Enrichment cultures demonstrated that soluble Fe(III) had a greater impact on cis-DCE and VC reduction than solid-phase Fe(III). Geobacteraceae and Dehalococcoides were also coenriched in the liquid cultures, and the Dehalococcoides abundance in the presence of Fe(III) was not significantly different from those in the cultures without Fe(III). Hydrogen reached steady-state concentrations most amenable to complete dechlorination very quickly when Fe(III) was present in the culture, suggesting that Fe(III) reduction may actually help dechlorination. This was contrasted to hydrogen levels in nitrate-amended enrichments, in which hydrogen concentration was too low for any chlororespiration.

Global transcriptome analysis of the tetrachloroethene-dechlorinating bacterium Desulfitobacterium hafniense Y51 in the presence of various electron donors and terminal electron acceptors

Desulfitobacterium hafniense Y51 is a dechlorinating bacterium that encodes an unusually large set of O-demethylase paralogs and specialized respiratory systems including specialized electron donors and acceptors. To use this organism in bioremediation of tetrachloroethene (PCE) or trichloroethene (TCE) pollution, expression patterns of its 5,060 genes were determined under different conditions using 60-mer probes in DNA microarrays. PCE, TCE, fumarate, nitrate, and dimethyl sulfoxide (DMSO) respiration all sustain the growth of strain Y51. Global transcriptome analyses were thus performed using various electron donor and acceptor couples (respectively, pyruvate and either fumarate, TCE, nitrate, or DMSO, and vanillate/fumarate). When TCE is used as terminal electron acceptor, resulting in its detoxification, a series of electron carriers comprising a cytochrome bd-type quinol oxidase (DSY4055-4056), a ferredoxin (DSY1451), and four Fe-S proteins (DSY1626, DSY1629, DSY0733, DSY3309) are upregulated, suggesting that the products of these genes are involved in PCE oxidoreduction. Interestingly, the PCE dehalogenase cluster (pceABCT) is constitutively expressed in the media tested, with pceT being upregulated and pceC downregulated in pyruvate/TCE-containing medium. In addition, another dehalogenation enzyme (DSY1155 coding for a putative chlorophenol reductive dehalogenase), is induced 225-fold in that medium, despite not being involved in PCE respiration. Remarkably since the reducing equivalents formed during pyruvate conversion to acetyl-CoA are channeled to electron acceptors including halogenated compounds, pyruvate induces expression of a pyruvate:ferredoxin oxidoreductase. This study paves the way to understanding the physiology of D. hafniense, optimizing this microbe as a bioremediation agent, and designing bioarray sensors to monitor the presence of dechlorinating organisms in the environment.

Sequential reductive and oxidative biodegradation of chloroethenes stimulated in a coupled bioelectro-process

This article for the first time demonstrates successful application of electrochemical processes to stimulate sequential reductive/oxidative microbial degradation of perchloroethene (PCE) in mineral medium and in contaminated groundwater. In a flow-through column system, hydrogen generation at the cathode supported reductive dechlorination of PCE to cis-dichloroethene (cDCE), vinyl chloride (VC), and ethene (ETH). Electrolytically generated oxygen at the anode allowed subsequent oxidative degradation of the lower chlorinated metabolites. Aerobic cometabolic degradation of cDCE proved to be the bottleneck for complete metabolite elimination. Total removal of chloroethenes was demonstrated for a PCE load of approximately 1.5 μmol/d. In mineral medium, long-term operation with stainless steel electrodes was demonstrated for more than 300 days. In contaminated groundwater, corrosion of the stainless steel anode occurred, whereas DSA (dimensionally stable anodes) proved to be stable. Precipitation of calcareous deposits was observed at the cathode, resulting in a higher voltage demand and reduced dechlorination activity. With DSA and groundwater from a contaminated site, complete degradation of chloroethenes in groundwater was obtained for two months thus demonstrating the feasibility of the sequential bioelectro-approach for field application.

Redox control and hydrogen production in sediment caps using carbon cloth electrodes

Sediment caps that degrade contaminants can improve their ability to contain contaminants relative to sand and sorbent-amended caps, but few methods to enhance contaminant degradation in sediment caps are available. The objective of this study was to determine if, carbon electrodes emplaced within a sediment cap at poised potential could create a redox gradient and provide electron donor for the potential degradation of contaminants. In a simulated sediment cap overlying sediment from the Anacostia River (Washington, DC), electrochemically induced redox gradients were developed within 3 days and maintained over the period of the test (∼100 days). Hydrogen and oxygen were produced by water electrolysis at the electrode surfaces and may serve as electron donor and acceptor for contaminant degradation. Electrochemical and geochemical factors that may influence hydrogen production were studied. Hydrogen production displayed zero order kinetics with ∼75% Coulombic efficiency. Rates were proportional to the applied potential between 2.5 and 5 V and not greatly affected by pH. Hydrogen production was promoted by increasing ionic strength and in the presence of natural organic matter. Carbon electrode-stimulated degradation of tetrachlorobenzene in a batch reactor was dependent on applied voltage and production of hydrogen to a concentration above the threshold for biological dechlorination. These findings suggest that electrochemical reactive capping can potentially be used to create "reactive" sediments caps capable of promoting chemical or biological transformations of contaminants within the cap.

Geochemical constraints on the diversity and activity of H2 -oxidizing microorganisms in diffuse hydrothermal fluids from a basalt- and an ultramafic-hosted vent

Mixing processes of reduced hydrothermal fluids with oxygenated seawater and fluid-rock reactions contribute to the chemical signatures of diffuse venting and likely determine the geochemical constraints on microbial life. We examined the influence of fluid chemistry on microbial diversity and activity by sampling diffuse fluids emanating through mussel beds at two contrasting hydrothermal vents. The H(2) concentration was very low at the basalt-hosted Clueless site, and mixing models suggest O(2) availability throughout much of the habitat. In contrast, effluents from the ultramafic-hosted Quest site were considerably enriched in H(2) , while O(2) is likely limited to the mussel layer. Only two different hydrogenase genes were identified in clone libraries from the H(2) -poor Clueless fluids, but these fluids exhibited the highest H(2) uptake rates in H(2) -spiked incubations (oxic conditions, at 18 °C). In contrast, a phylogenetically diverse H(2) -oxidizing potential was associated with distinct thermal conditions in the H(2) -rich Quest fluids, but under oxic conditions, H(2) uptake rates were extremely low. Significant stimulation of CO(2) fixation rates by H(2) addition was solely illustrated in Quest incubations (P-value <0.02), but only in conjunction with anoxic conditions (at 18 °C). We conclude that the factors contributing toward differences in the diversity and activity of H(2) oxidizers at these sites include H(2) and O(2) availability.

Comparison of lactate, formate, and propionate as hydrogen donors for the reductive dehalogenation of trichloroethene in a continuous-flow column

A continuous-flow column study was conducted to analyze the reductive dehalogenation of trichloroethene (TCE) with aquifer material with high content of iron oxides. The column was bioaugmented with the Point Mugu (PM) culture, which is a mixed microbial enrichment culture capable of completely transforming TCE to ethene (ETH). We determined whether lactate, formate, or propionate fermentation resulted in more effective dehalogenation. Reductive dehalogenation, fermentation, and sulfate, Fe(III), and Mn(IV) reduction were all exhibited within the column. Different steady-states of dehalogenation were achieved based on the concentration of substrates added, with effective transformation to ETH obtained when ample electron donor equivalents were provided. Most of the metabolic reducing equivalents were channeled to sulfate, Fe(III), and Mn(IV) reduction. When similar electron reducing equivalents were added, the most effective dehalogenation was achieved with formate, with 14% of the electron equivalents going towards dehalogenation reactions, compared to 6.5% for lactate and 9.6% for propionate. Effective dehalogenation was maintained over 1000 days of column operation. Over 90% of electron equivalents added could be accounted for by the different electron accepting processes in the column, with 50% associated with soluble and precipitated Fe(II) and Mn(II). Bulk Fe(III) and Mn(IV) reduction was rather associated with lactate and propionate addition than formate addition. Sulfate reduction was a competing electron acceptor reaction with all three electron donors. DNA was extracted from solid coupon samples obtained during the course of the experiment and analyzed using 16S rRNA gene clone libraries and quantitative PCR. Lactate and propionate addition resulted in a significant increase in Geobacter, Spirochaetes, and Desulfitobacterium phylotypes relative to "Dehalococcoides" when compared to formate addition. Results from the molecular biological analyses support chemical observations that a greater percentage of the electron donor addition was channeled to Fe(III) reduction when lactate and propionate were added compared to formate, and formate was more effective than lactate in supporting dehalogenation. The results demonstrate the importance of electron donor selection and competing electron acceptor reactions when implementing reductive dehalogenation remediation technologies.

Unique ecophysiology among U(VI)-reducing bacteria as revealed by evaluation of oxygen metabolism in Anaeromyxobacter dehalogenans strain 2CP-C

Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2x10(7)+/-8.6x10(6) to 1.0x10(8)+/-2.2x10(7) cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3x10(4)+/-1.1x10(4) cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [micro=(-0.09xpO2)+0.051; R2=0.923] was observed between the instantaneous specific growth rate micro and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. dehalogenans from other known U(VI)-reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.

Energetic constraints on H2-dependent terminal electron accepting processes in anoxic environments: a review of observations and model approaches

Microbially mediated terminal electron accepting processes (TEAPs) to a large extent control the fate of redox reactive elements and associated reactions in anoxic soils, sediments, and aquifers. This review focuses on thermodynamic controls and regulation of H2-dependent TEAPs, case studies illustrating this concept, and the quantitative description of thermodynamic controls in modeling. Other electron transfer processes are considered where appropriate. The work reviewed shows that thermodynamics and microbial kinetics are connected near thermodynamic equilibrium. Free energy thresholds for terminal respiration are physiologically based and often near -20 kJ mol(-1), depending on the mechanism of ATP generation; more positive free energy values have been reported under "starvation conditions" for methanogenesis and lower values for TEAPs that provide more energy. H2-dependent methanogenesis and sulfate reduction are under direct thermodynamic control in soils and sediments and generally approach theoretical minimum energy thresholds. If H2 concentrations are lowered by thermodynamically more potent TEAPs, these processes are inhibited. This principle is also valid for TEAPS providing more free energy, such as denitrification and arsenate reduction, but electron donor concentration cannot be lowered so that the processes reach theoretical energy thresholds. Thermodynamics and kinetics have been integrated by combining traditional descriptions of microbial kinetics with the equilibrium constant K and reaction quotient Q of a process, taking into account process-specific threshold energies. This approach is dynamically evolving toward a general concept of microbially driven electron transfer in anoxic environments and has been used successfully in applications ranging from bioreactor regulation to groundwater and sediment biogeochemistry.

Variations in expression of carbon isotope fractionation of chlorinated ethenes during biologically enhanced PCE dissolution close to a source zone

The stable carbon isotope values of tetrachloroethene (PCE) and its degradation products were monitored during studies of biologically enhanced dissolution of PCE dense nonaqueous phase liquid (DNAPL) to determine the effect of PCE dissolution on observed isotope values. The degradation of PCE was monitored in a 2-dimensional model aquifer and in a pilot test cell (PTC) at Dover Air Force Base, both with emplaced PCE DNAPL sources. Within the plume down gradient from the source, the isotopic fractionation of dissolved PCE and its degradation products were consistent with those observed in biodegradation laboratory studies. However, close to the source zone significant shifts in the isotope values of dissolved PCE were not observed in either the model aquifer or PTC due to the constant input of newly dissolved, non fractionated PCE, and the small isotopic fractionation associated with PCE reductive dechlorination by the mixed microbial culture used. Therefore the identification of reductive dechlorination in the presence of PCE DNAPL was based upon the appearance of daughter products and the isotope values of those daughter products. An isotope model was developed to simulate isotope values of PCE during the dissolution and degradation of PCE adjacent to a DNAPL source zone. With the exception of very high degradation rate constants (>1/day) stable carbon isotope values of PCE estimated by the model remained within error of the isotope value of the PCE DNAPL, consistent with measured isotope values in the model aquifer and in the PTC.

Properties of a trichlorodibenzo-p-dioxin-dechlorinating mixed culture with a Dehalococcoides as putative dechlorinating species

An anaerobic mixed culture enriched over 16 transfers (1/10) from Saale river sediment reductively dehalogenated 1,2,4- and 1,2,3-trichlorodibenzo-p-dioxin (TrCDD) to di- and monochlorinated congeners in the presence of pyruvate (or lactate) and fumarate as cosubstrates. Besides TrCDD, tetrachloroethene and 1,2,3-trichlorobenzene were dechlorinated. Dioxin dehalogenation was sensitive to pasteurization, but was not remarkably influenced by inhibitors of methanogens, sulfate-reducing bacteria or Gram-positive bacteria. The rate of 1,3-dichlorodibenzo-p-dioxin formation increased with rising initial concentrations of 1,2,4-TrCDD (1-250 microM) from 0.05 to 5.4 micromol l(-1) day(-1). Two isolates, belonging to Sulfurospirillum and Trichococcus, did not show reductive dehalogenation. 16S rDNA-targeted methods further revealed the presence of Acetobacterium, Desulfitobacterium, Desulfuromonas and Dehalococcoides. Nested polymerase chain reaction (PCR) indicated the presence of Dehalococcoides in highest most probable number (MPN) dilutions that were positive for dioxin dechlorination.

Application of electrolysis to stimulate microbial reductive PCE dechlorination and oxidative VC biodegradation

A novel approach was applied to stimulate biodegradation of chloroethenes bya coupled bioelectro-process. In a flow-through column system, microbial dechlorination of tetrachloroethene to cis-dichloroethene, vinyl chloride, and ethene was stimulated by hydrogen produced by water electrolysis. Dechlorinating bacteria (Dehalococcoides spp. and Desulfitobacterium spp.) and also methanogens and homoacetogens were detected in the anaerobic column. Simultaneously, oxidative biodegradation of lower chlorinated metabolites (vinyl chloride) was stimulated by electrolytic oxygen formation in the corresponding aerobic column. The process was stable for more than 100 days and an average removal of approximately 23 micromol/d PCE and 72 micromo/d vinyl chloride was obtained with a current density of 0.05 mA/cm2. Abiotic electrochemical degradation of the contaminants was not observed. Microbial dechlorination correlated with the current densities in the applied range of 0.01-0.05 mA/cm2. The results are promising for environmental applications, since with electrolysis hydrogen and oxygen can be supplied continuously to chloroethene degrading microorganisms, and the supply rates can be easily controlled by adjusting the electric current.

pH control for enhanced reductive bioremediation of chlorinated solvent source zones

Enhanced reductive dehalogenation is an attractive treatment technology for in situ remediation of chlorinated solvent DNAPL source areas. Reductive dehalogenation is an acid-forming process with hydrochloric acid and also organic acids from fermentation of the electron donors typically building up in the source zone during remediation. This can lead to groundwater acidification thereby inhibiting the activity of dehalogenating microorganisms. Where the soils' natural buffering capacity is likely to be exceeded, the addition of an external source of alkalinity is needed to ensure sustained dehalogenation. To assist in the design of bioremediation systems, an abiotic geochemical model was developed to provide insight into the processes influencing the groundwater acidity as dehalogenation proceeds, and to predict the amount of bicarbonate required to maintain the pH at a suitable level for dehalogenating bacteria (i.e., >6.5). The model accounts for the amount of chlorinated solvent degraded, site water chemistry, electron donor, alternative terminal electron-accepting processes, gas release and soil mineralogy. While calcite and iron oxides were shown to be the key minerals influencing the soil's buffering capacity, for the extensive dehalogenation likely to occur in a DNAPL source zone, significant bicarbonate addition may be necessary even in soils that are naturally well buffered. Results indicated that the bicarbonate requirement strongly depends on the electron donor used and availability of competing electron acceptors (e.g., sulfate, iron (III)). Based on understanding gained from this model, a simplified model was developed for calculating a preliminary design estimate of the bicarbonate addition required to control the pH for user-specified operating conditions.

Biochemistry, physiology and biotechnology of sulfate-reducing bacteria

Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The production of biosulfide by SRB has led to immobilization of toxic metals and reduction of textile dyes, although the process remains unresolved, SRB play a role in anaerobic methane oxidation which not only contributes to carbon cycle activities but also depletes an important industrial energy reserve.

Tropospheric H(2) budget and the response of its soil uptake under the changing environment

Molecular hydrogen (H(2)) is an indirect greenhouse gas present at the trace level in the atmosphere. So far, the sum of its sources and sinks is close to equilibrium, but its large-scale utilization as an alternative energy carrier would alter its atmospheric burden. The magnitude of the emissions associated with a future H(2)-based economy is difficult to predict and remains a matter of debate. Previous attempts to predict the impact that a future H(2)-based economy would exert on tropospheric chemistry were realized by considering a steady rate of microbial-mediated soil uptake, which is currently responsible of ~80% of the tropospheric H(2) losses. Although soil uptake, also known as dry deposition is the most important sink for tropospheric H(2), microorganisms involved in the activity remain elusive. Given that microbial-mediated H(2) soil uptake is influenced by several environmental factors, global change should exert a significant effect on the activity and then, assuming a steady H(2) soil uptake rate for the future may be mistaken. Here, we present an overview of tropospheric H(2) sources and sinks with an emphasis on microbial-mediated soil uptake process. Future researches are proposed to investigate the influence that global change would exert on H(2) dry deposition and to identify microorganisms involved H(2) soil uptake activity.

Complete dechlorination of tetrachloroethylene by use of an anaerobic Clostridium bifermentans DPH-1 and zero-valent iron

A laboratory test was conducted to examine the combined effect of an anaerobic Clostridium bifermentans DPH-1 and addition of zero-valent iron (Fe0) on the reductive dechlorination of tetrachloroethylene (PCE). In addition, the dechlorination of cis-1,2-dichloroethylene (cDCE) produced from PCE was examined using Fe0. The cDCE produced was completely dechlorinated to non-toxic end products, mostly, ethylene by a subsequent chemical reductive process. Production of ethylene was dramatically increased with increase of initial cDCE concentration in the range of 10.3 microM to 928 microM (1.0-90 mg l(-1)) and the velocity constant was calculated to be 0.38 day(-1). On the other hand, the combined use of strain DPH-1 and Fe0 showed the most significant effect on the initial PCE dechlorination, but cohesion of Fe0 was found to inhibit the dechlorination rate of PCE. It is thought that phosphoric acid iron contained in a medium forms film on the surface of iron particle, so oxidation of iron is inhibited.

Acidogenic sequencing batch reactor start-up procedures for induction of 2,4,6-trichlorophenol dechlorination

Dechlorination of 2,4,6-trichlorophenol to 4-chlorophenol under acidogenic conditions (pH 5.6-6.5) was successfully induced by manipulating the start-up procedure of an acidogenic sequencing batch reactor (SBR). A stepwise pH reduction from neutral to acidic level during start-up was crucial for inducing dechlorination. Once induced, dechlorination can proceed at pH as low as 5.6 before inhibition occurs. Optimum pH for maximum dechlorination rate ranged from 6.0 to 6.3. High primary (sucrose) to secondary (2,4,6-trichlorophenol) substrate ratio failed to induce dechlorination. Instead, dechlorination occurred at primary to secondary substrate ratios of less than 103M/M. A specific maximum trichlorophenol loading rate of 60micromol/g MLVSSd was achieved before inhibition appeared with onset of acidogenic reactor failure. T-RFLP profile analysis gave evidence that the start-up procedure resulted in the selection of an appropriate microbial community, which resulted in the successful development of an acidogenic consortium capable of degrading 2,4,6-trichlorophenol.

Variability in microbial carbon isotope fractionation of tetra- and trichloroethene upon reductive dechlorination

The variability of stable carbon isotope fractionation upon reductive dechlorination of tetra- and trichloroethene by several microbial strains was investigated to examine the uncertainties related to the in situ application of compound specific isotope analysis (CSIA) of chlorinated ethenes. Carbon isotope fractionation was investigated with a set of microorganisms representative for the currently known diversity of dehalorespirers: Dehalococcoides ethenogenes strain 195, Desulfitobacterium sp. strain Viet1, Desulfuromonas michiganensis and Geobacter lovleyi sp. strain SZ and compared to the previous reports using Sulfurospirillum spp. and Desulfitobacterium sp. strain PCE-S. Carbon isotope fractionation of tetrachloroethene (PCE) and trichlorethene (TCE) was highly variable ranging from the absence of significant fractionation to carbon isotope fractionation (epsilonC) of 16.7 and 3.5-18.9 for PCE and TCE, respectively. Fractionation of both compounds by D. ethenogenes strain 195 (PCE: epsilonC=6.0; TCE: epsilonC=13.7) was similar to the literature data for mixed cultures containing Dehalococcoides spp. D. michiganensis (PCE: no significant fractionation; TCE: epsilonC=3.5) and G. lovleyi sp. strain SZ (PCE no significant fractionation; TCE: epsilonC=8.5) generated the lowest fractionation of all studied strains. Desulfitobacterium sp. strain Viet1 (PCE: epsilonC=16.7) gave the highest enrichment factor for PCE.

Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes

DNA and RNA transcripts, particularly of genes of functional importance in the reductively dechlorinating microbe Dehalococcoides, are increasingly being studied as potential molecular bioindicators of reductive dechlorination. Ideally, mRNA bioindicators would be informative both qualitatively (with respect to dechlorination end point and substrate range) and quantitatively (with respectto activity rates). Here, we examined pseudo-steady-state mRNA levels in Dehalococcoides-containing microcosms continuously fed PCE at various loading rates. We characterized gene transcript abundance of potential Dehalococcoides bioindicators of reductive dechlorination, including 16S rRNA, and genes encoding an annotated formate dehydrogenase (Fdh), the hydrogenase (H2ase) Hup, and the reductive dehalogenases (RDases) TceA, DET1559, PceA, and DET1545. Increases in steady PCE loading rate led to corresponding increases in PCE respiration rate (1.5 +/- 0.1, 2.5 +/- 0.3, 4.8 +/- 0.1, and 9.2 +/- 0.5 micromol/L/hr). We also observed that pseudo-steady-state expression levels of most functional targets increase linearly over PCE respiration rates of 1.5-4.8 micromol/L/hr, with Fdh, Hup, and TceA transcripts increasing by approximately 2 x 10(10) copies per mL of culture for every micromol/L/hr increase in chloroethene respiration rate, and DET1559 and PceAtranscripts increasing by approximately9 x 10(9) copies per mL of culture, butthat increased respiration rates of 9.2 micromol/L/hr did not necessarily lead to corresponding increases in transcript levels.

Biodegradation of perfluorinated compounds

The information available in the literature provides evidence for the biodegradation of some poly- and per-fluorinated compounds, but such biodegradation is incomplete and may not result in mineralization. Recent publications have demonstrated that 8:2 fluorotelomer alcohol, for example, can be degraded by bacteria from soil and wastewater treatment plants to perfluorooctanoic acid. Similarly, 2-N-ethyl(perfluorooctane sulfonamido)ethanol can be degraded by wastewater treatment sludge to perfluorooctanesulfonate. It is presently unclear whether these two products are degraded further. Therefore, the question remains as to whether there is a potential for defluorination and biodegradation of PFCs that contributes significantly to their environmental fate. The lack of mineralization observed is probably caused by the stability of the C-F bond, although there are examples of microbially catalyzed defluorination reactions. As is the case with reductive dechlorination or debromination, reductive defluorination is energetically favorable under anaerobic conditions and releases more energy than that available from sulfate reduction or methanogenesis. Consequently, we should consider the possibility that bacteria will adapt to utilize this source of energy, although evolving mechanisms to overcome the kinetic barriers to degradation of these compounds may take some time. The fact that such reactions are absent for some PFCs, to date, may be because too little time has passed for microorganisms to adapt to these potential substrates. Hence, the situation may be comparable to that of chlorinated organic compounds several decades ago. For many years, organochlorine compounds were considered to be catabolically recalcitrant; today, reductive chlorination reactions of many organochlorines, including PCBs and dioxins, are regularly observed in anaerobic environments. Hence, it is opportune and important to continue studying the potential degradation of perfluorinated compounds in carefully designed experiments with either microbial populations from contaminated sites or cultures of bacteria known to dehalogenate chlorinated compounds.

Growth with high planktonic biomass in Shewanella oneidensis fuel cells

Shewanella oneidensis MR-1 grew for over 50 days in microbial fuel cells, incompletely oxidizing lactate to acetate with high recovery of the electrons derived from this reaction as electricity. Electricity was produced with lactate or hydrogen and current was comparable to that of electricigens which completely oxidize organic substrates. However, unlike fuel cells with previously described electricigens, in which cells are primarily attached to the anode, at least as many of the S. oneidensis cells were planktonic as were attached to the anode. These results demonstrate that S. oneidensis may conserve energy for growth with an electrode serving as an electron acceptor and suggest that multiple strategies for electron transfer to fuel cell anodes exist.

A simple pore water hydrogen diffusion syringe sampler

Molecular hydrogen (H(2)) is an important intermediate product and electron donor in microbial metabolism. Concentrations of dissolved H(2) are often diagnostic of the predominant terminal electron-accepting processes in ground water systems or aquatic sediments. H(2) concentrations are routinely measured in ground water monitoring wells but are rarely measured in saturated aquatic sediments due to a lack of simple and practical sampling methods. This report describes the design and development (including laboratory and field testing) of a simple, syringe-based H(2) sampler in (1) saturated, riparian sediments, (2) surface water bed sediments, and (3) packed intervals of a fractured bedrock borehole that are inaccessible by standard pumped methods.

Detection and quantification of Geobacter lovleyi strain SZ: implications for bioremediation at tetrachloroethene- and uranium-impacted sites

Geobacter lovleyi strain SZ reduces hexavalent uranium, U(VI), to U(IV) and is the first member of the metal-reducing Geobacter group capable of using tetrachloroethene (PCE) as a growth-supporting electron acceptor. Direct and nested PCR with specific 16S rRNA gene-targeted primer pairs distinguished strain SZ from other known chlorinated ethene-dechlorinating bacteria and closely related Geobacter isolates, including its closest cultured relative, G. thiogenes. Detection limits for direct and nested PCR were approximately 1 x 10(6) and 1 x 10(4) 16S rRNA gene copies per mul of template DNA, respectively. A quantitative real-time PCR (qPCR) approach increased the sensitivity to as few as 30 16S rRNA gene copies per mul of template DNA but was less specific. Melting curve analysis and comparison of the shapes of amplification plots identified false-positive signals and distinguished strain SZ from G. thiogenes when analyzed separately. These indicators were less reliable when target (strain SZ) DNA and nontarget (G. thiogenes) DNA with high sequence similarity were mixed, indicating that the development of qPCR protocols should not only evaluate specificity but also explore the effects of nontarget DNA on the accuracy of quantification. Application of specific tools detected strain SZ-like amplicons in PCE-dechlorinating consortia, including the bioaugmentation consortium KB-1, and two chlorinated ethene-impacted groundwater samples. Strain SZ-like amplicons were also detected in 13 of 22 groundwater samples following biostimulation at the uranium- and chlorinated solvent-contaminated Integrated Field-Scale Subsurface Research Challenge (IFC) site in Oak Ridge, TN. The numbers of strain SZ-like cells increased from below detection to 2.3 x 10(7) +/- 0.1 x 10(7) per liter groundwater, suggesting that strain SZ-like organisms contribute to contaminant transformation. The G. lovleyi strain SZ-specific tools will be useful for monitoring bioremediation efforts at uranium- and/or chlorinated solvent-impacted sites such as the Oak Ridge IFC site.

Benzoate-driven dehalogenation of chlorinated ethenes in microbial cultures from a contaminated aquifer

Microbial dehalogenation of tetrachloroethene (PCE) and cis-dichloroethene (cis-DCE) was studied in cultures from a continuous stirred tank reactor initially inoculated with aquifer material from a PCE-contaminated site. Cultures amended with hydrogen and acetate readily dechlorinated PCE and cis-DCE; however, this transformation was incomplete and resulted in the accumulation of chlorinated intermediates and only small amounts of ethene within 60 days of incubation. Conversely, microbial PCE and cis-DCE dechlorination in cultures with benzoate and acetate resulted in the complete transformation to ethene within 30 days. Community fingerprinting by denaturing gradient gel electrophoresis (DGGE) revealed the predominance of phylotypes closely affiliated with Desulfitobacterium, Dehalococcoides, and Syntrophus species. The Dehalococcoides culture VZ, obtained from small whitish colonies in cis-DCE dechlorinating agarose cultures, revealed an irregular cell diameter between 200 and 500 nm, and a spherical or biconcave disk-shaped morphology. These organisms were identified as responsible for the dechlorination of cis-DCE to ethene in the PCE-dechlorinating consortia, operating together with the Desulfitobacterium as PCE-to-cis-DCE dehalogenating bacterium and with a Syntrophus species as potential hydrogen-producing partner in cultures with benzoate.