@article {3085, title = {Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation.}, journal = {Microb Ecol}, volume = {76}, year = {2018}, month = {2018 Oct}, pages = {660-667}, abstract = {

Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40~days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater. In order to determine whether Methanosarcina species could be participating in U(VI) reduction in the subsurface, cell suspensions of Methanosarcina barkeri were incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically active M. barkeri cells; however, no U(VI) reduction was observed in inactive controls. These results demonstrate that Methanosarcina species could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth of Geobacter species. The results also suggest that Methanosarcina have the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.

}, keywords = {Acetates, Biodegradation, Environmental, Geobacter, Groundwater, Methane, Methanosarcina, Oxidation-Reduction, Uranium, Water Pollutants, Chemical}, issn = {1432-184X}, doi = {10.1007/s00248-018-1165-5}, author = {Holmes, Dawn E and Orelana, Roberto and Giloteaux, Ludovic and Wang, Li-Ying and Shrestha, Pravin and Williams, Kenneth and Lovley, Derek R and Rotaru, Amelia-Elena} } @article {1561, title = {4-methylphenol produced in freshwater sediment microcosms is not a bisphenol A metabolite.}, journal = {Chemosphere}, volume = {117}, year = {2014}, month = {2014 Dec}, pages = {521-6}, abstract = {

4-Methylphenol (4-MP), a putative bisphenol A (BPA) degradation intermediate, was detected at concentrations reaching 2.1 mg L(-1) in anoxic microcosms containing 10 mg L(-1) BPA and 5 g of freshwater sediment material collected from four geographically distinct locations and amended with nitrate, nitrite, ferric iron, or bicarbonate as electron acceptors. 4-MP accumulation was transient, and 4-MP degradation was observed under all redox conditions tested. 4-MP was not detected in microcosms not amended with BPA. Unexpectedly, incubations with (13)C-labeled BPA failed to produce (13)C-labeled 4-MP suggesting that 4-MP was not derived from BPA. The detection of 4-MP in live microcosms amended with lactate, but not containing BPA corroborated that BPA was not the source of 4-MP. These findings demonstrate that the transient formation of 4-MP as a possible BPA degradation intermediate must be interpreted cautiously, as microbial activity in streambed microcosms may generate 4-MP from sediment-associated organic material.

}, keywords = {Anaerobiosis, Benzhydryl Compounds, Biodegradation, Environmental, Chromatography, High Pressure Liquid, Cresols, Environmental Monitoring, Fresh Water, Gas Chromatography-Mass Spectrometry, Geologic Sediments, Phenols, Water Pollutants, Chemical}, issn = {1879-1298}, doi = {10.1016/j.chemosphere.2014.09.008}, author = {Im, Jeongdae and Prevatte, Carson W and Lee, Hong Geun and Campagna, Shawn R and L{\"o}ffler, Frank E} } @article {3138, title = {Field evidence of selenium bioreduction in a uranium-contaminated aquifer.}, journal = {Environ Microbiol Rep}, volume = {5}, year = {2013}, month = {2013 Jun}, pages = {444-52}, abstract = {

Removal of selenium from groundwater was documented during injection of acetate into a uranium-contaminated aquifer near Rifle, Colorado (USA). Bioreduction of aqueous selenium to its elemental form (Se0) concentrated it within mineralized biofilms affixed to tubing used to circulate acetate-amended groundwater. Scanning and transmission electron microscopy revealed close association between Se0 precipitates and cell surfaces, with Se0 aggregates having a diameter of 50-60 nm. Accumulation of Se0 within biofilms occurred over a three-week interval at a rate of c. 9 mg Se0 m(-2) tubing day(-1). Removal was inferred to result from the activity of a mixed microbial community within the biofilms capable of coupling acetate oxidation to the reduction of oxygen, nitrate and selenate. Phylogenetic analysis of the biofilm revealed a community dominated by strains of Dechloromonas sp. and Thauera sp., with isolates exhibiting genetic similarity to the latter known to reduce selenate to Se0. Enrichment cultures of selenate-respiring microorganisms were readily established using Rifle site groundwater and acetate, with cultures dominated by strains closely related to D. aromatica (96-99\% similarity). Predominance of Dechloromonas sp. in recovered biofilms and enrichments suggests this microorganism may play a role in the removal of selenium oxyanions present in Se-impacted groundwaters and sediments.

}, keywords = {Acetates, Betaproteobacteria, Biodegradation, Environmental, Biofilms, Colorado, Groundwater, Humans, Microbial Consortia, Oxidation-Reduction, Oxygen, Phylogeny, RNA, Ribosomal, 16S, Selenic Acid, Selenium, Selenium Compounds, Thauera, Uranium, Water Pollutants, Chemical}, issn = {1758-2229}, doi = {10.1111/1758-2229.12032}, author = {Williams, Kenneth H and Wilkins, Michael J and N{\textquoteright}Guessan, A Lucie and Arey, Bruce and Dodova, Elena and Dohnalkova, Alice and Holmes, Dawn and Lovley, Derek R and Long, Philip E} } @article {726, title = {Biodegradation of ethylene dibromide (1,2-dibromoethane [EDB]) in microcosms simulating in situ and biostimulated conditions.}, journal = {J Hazard Mater}, volume = {209-210}, year = {2012}, month = {2012 Mar 30}, pages = {92-8}, abstract = {Although 1,2-dibromoethane (EDB) is a common groundwater contaminant, there is the lack of knowledge surrounding EDB biodegradation, especially under aerobic conditions. We have performed an extensive microcosm study to investigate the biodegradation of EDB under simulated in situ and biostimulated conditions. The materials for soil microcosms were collected from an EDB-contaminated aquifer at the Massachusetts Military Reservation in Cape Cod, MA. This EDB plume has persisted for nearly 40 years in both aerobic and anaerobic EDB zones of the aquifer. Microcosms were constructed under environmentally relevant conditions (field EDB and DO concentrations; incubated at 12{\textdegree}C). The results showed that natural attenuation occurred under anaerobic conditions but not under aerobic conditions, explaining why aerobic EDB contamination is so persistent. EDB degradation rates were greater under biostimulated conditions for both the aerobic and anaerobic microcosms. Particularly for aerobic biostimulation, methane-amended microcosms degraded EDB, on average, at a first order rate eight times faster than unamended microcosms. The best performing replicate achieved an EDB degradation rate of 7.0 yr(-1) (half-life (t(1/2))=0.10 yr). Residual methane concentrations and the emergence of methanotrophic bacteria, measured by culture independent bacterial analysis, provided strong indications that EDB degradation in aerobic methane-amended microcosms occurred via cometabolic degradation. These results indicate the potential for enhanced natural attenuation of EDB and that methane could be considered co-substrate for EDB bioremediation for the EDB-contaminated groundwater in aerobic zone.}, keywords = {Aerobiosis, Anaerobiosis, Biodegradation, Environmental, Ethylene Dibromide, Water Microbiology, Water Pollutants, Chemical}, issn = {1873-3336}, doi = {10.1016/j.jhazmat.2011.12.067}, author = {McKeever, Robert and Sheppard, Diane and N{\"u}sslein, Klaus and Baek, Kyung-Hwa and Rieber, Khalil and Ergas, Sarina J and Forbes, Rose and Hilyard, Mark and Park, Chul} } @article {728, title = {Performance of a pilot-scale packed bed reactor for perchlorate reduction using a sulfur oxidizing bacterial consortium.}, journal = {Biotechnol Bioeng}, volume = {109}, year = {2012}, month = {2012 Mar}, pages = {637-46}, abstract = {A novel sulfur-utilizing perchlorate reducing bacterial consortium successfully treated perchlorate (ClO$_{4}$$^{-}$) in prior batch and bench-scale packed bed reactor (PBR) studies. This study examined the scale up of this process for treatment of water from a ClO $_{4}$$^{-}$ and RDX contaminated aquifer in Cape Cod Massachusetts. A pilot-scale upflow PBR (\~{}250-L) was constructed with elemental sulfur and crushed oyster shell packing media. The reactor was inoculated with sulfur oxidizing ClO$_{4}$$^{-}$ reducing cultures enriched from a wastewater seed. Sodium sulfite provided a good method of dissolved oxygen removal in batch cultures, but was found to promote the growth of bacteria that carry out sulfur disproportionation and sulfate reduction, which inhibited ClO$_{4}$$^{-}$ reduction in the pilot system. After terminating sulfite addition, the PBR successfully removed 96\% of the influent ClO$_{4}$$^{-}$ in the groundwater at an empty bed contact time (EBCT) of 12 h (effluent ClO$_{4}$$^{-}$ of 4.2 {\textmu}g L(-1)). Simultaneous ClO$_{4}$$^{-}$ and NO$_{3}$$^{-}$ reduction was observed in the lower half of the reactor before reactions shifted to sulfur disproportionation and sulfate reduction. Analyses of water quality profiles were supported by molecular analysis, which showed distinct groupings of ClO$_{4}$$^{-}$ and NO$_{3}$$^{-}$ degrading organisms at the inlet of the PBR, while sulfur disproportionation was the primary biological process occurring in the top potion of the reactor.}, keywords = {Bioreactors, Cluster Analysis, DNA, Bacterial, DNA, Ribosomal, Massachusetts, Microbial Consortia, Molecular Sequence Data, Oxidation-Reduction, Perchloric Acid, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Sulfites, Sulfur, Water Microbiology, Water Pollutants, Chemical, Water Purification}, issn = {1097-0290}, doi = {10.1002/bit.24354}, author = {Boles, Amber R and Conneely, Teresa and McKeever, Robert and Nixon, Paul and N{\"u}sslein, Klaus R and Ergas, Sarina J} } @article {453, title = {Electrode-based approach for monitoring in situ microbial activity during subsurface bioremediation.}, journal = {Environ Sci Technol}, volume = {44}, year = {2010}, month = {2010 Jan 1}, pages = {47-54}, abstract = {Current production by microorganisms colonizing subsurface electrodes and its relationship to substrate availability and microbial activity was evaluated in an aquifer undergoing bioremediation. Borehole graphite anodes were installed downgradient from a region of acetate injection designed to stimulate bioreduction of U(VI); cathodes consisted of graphite electrodes embedded at the ground surface. Significant increases in current density (< or =50 mA/m2) tracked delivery of acetate to the electrodes, dropping rapidly when acetate inputs were discontinued. An upgradient control electrode not exposed to acetate produced low, steady currents (< or =0.2 mA/m2). Elevated current was strongly correlated with uranium removal but minimal correlation existed with elevated Fe(II). Confocal laser scanning microscopy of electrodes revealed firmly attached biofilms, and analysis of 16S rRNA gene sequences indicated the electrode surfaces were dominated (67-80\%) by Geobacter species. This is the first demonstration that electrodes can produce readily detectable currents despite long-range (6 m) separation of anode and cathode, and these results suggest that oxidation of acetate coupled to electron transfer to electrodes by Geobacter species was the primary source of current. Thus it is expected that current production may serve as an effective proxy for monitoring in situ microbial activity in a variety of subsurface anoxic environments.}, keywords = {Electrodes, Environmental Monitoring, Environmental Remediation, Geobacter, RNA, Ribosomal, 16S, Water Pollutants, Chemical}, issn = {0013-936X}, doi = {10.1021/es9017464}, author = {Williams, Kenneth H and Nevin, Kelly P and Franks, Ashley and Englert, Andreas and Long, Philip E and Lovley, Derek R} } @article {448, title = {Stimulating the anaerobic degradation of aromatic hydrocarbons in contaminated sediments by providing an electrode as the electron acceptor.}, journal = {Environ Microbiol}, volume = {12}, year = {2010}, month = {2010 Apr}, pages = {1011-20}, abstract = {The possibility that electrodes might serve as an electron acceptor to simulate the degradation of aromatic hydrocarbons in anaerobic contaminated sediments was investigated. Initial studies with Geobacter metallireducens demonstrated that although toluene was rapidly adsorbed onto the graphite electrodes it was rapidly oxidized to carbon dioxide with the electrode serving as the sole electron acceptor. Providing graphite electrodes as an electron acceptor in hydrocarbon-contaminated sediments significantly stimulated the removal of added toluene and benzene. Rates of toluene and benzene removal accelerated with continued additions of toluene and benzene. [(14)C]-Toluene and [(14)C]-benzene were quantitatively recovered as [(14)C]-CO(2), demonstrating that even though the graphite adsorbed toluene and benzene they were degraded. Introducing an electrode as an electron acceptor also accelerated the loss of added naphthalene and [(14)C]-naphthalene was converted to [(14)C]-CO(2). The results suggest that graphite electrodes can serve as an electron acceptor for the degradation of aromatic hydrocarbon contaminants in sediments, co-localizing the contaminants, the degradative organisms and the electron acceptor. Once in position, they provide a permanent, low-maintenance source of electron acceptor. Thus, graphite electrodes may offer an attractive alternative for enhancing contaminant degradation in anoxic environments.}, keywords = {Anaerobiosis, Benzene, Carbon Dioxide, Electrodes, Geobacter, Geologic Sediments, Graphite, Naphthalenes, Oxidation-Reduction, Toluene, Water Pollutants, Chemical}, issn = {1462-2920}, doi = {10.1111/j.1462-2920.2009.02145.x}, author = {Zhang, Tian and Gannon, Sarah M and Nevin, Kelly P and Franks, Ashley E and Lovley, Derek R} } @article {1570, title = {Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers.}, journal = {Appl Microbiol Biotechnol}, volume = {85}, year = {2009}, month = {2009 Nov}, pages = {389-403}, abstract = {

Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5\% moisture content) along with 15 mg NH (4) (+) (kg soil)(-1) and 0.1 mg phenylacetylene(kg soil)(-1) provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

}, keywords = {Archaea, Bacteria, Base Sequence, DNA, DNA Primers, DNA, Archaeal, DNA, Bacterial, Global Warming, Greenhouse Effect, Inorganic Chemicals, Methane, Nitrites, Nitrogen, Nitrogen Oxides, Nitrous Oxide, Oxidation-Reduction, Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, RNA, Bacterial, RNA, Messenger, Soil, Water Pollutants, Chemical}, issn = {1432-0614}, doi = {10.1007/s00253-009-2238-7}, author = {Lee, Sung-Woo and Im, Jeongdae and Dispirito, Alan A and Bodrossy, Levente and Barcelona, Michael J and Semrau, Jeremy D} } @article {736, title = {Hydrogenotrophic denitrification and perchlorate reduction in ion exchange brines using membrane biofilm reactors.}, journal = {Biotechnol Bioeng}, volume = {104}, year = {2009}, month = {2009 Oct 15}, pages = {483-91}, abstract = {Halophilic (salt loving), hydrogenotrophic (H(2) oxidizing) denitrifying bacteria were investigated for treatment of nitrate (NO3-) and perchlorate (ClO4-) contaminated groundwater and ion exchange (IX) brines. Hydrogenotrophic denitrifying bacteria were enriched from a denitrifying wastewater seed under both halophilc and non-halophilc conditions. The cultures were inoculated into bench-scale membrane biofilm reactors (MBfRs) with an "outside in" configuration, with contaminated water supplied to the lumen of the membranes and H(2) supplied to the shell. Abiotic mass transfer tests showed that H(2) mass transfer coefficients were lower in brines than in tap water at highest Reynolds number, possibly due to increased transport of salts and decreased H(2) solubility at the membrane/liquid interface. An average NO3- removal efficiency of 93\% was observed for the MBfR operated in continuous flow mode with synthetic contaminated groundwater. Removal efficiencies of 30\% for NO3- and 42\% for ClO4- were observed for the MBfR operated with synthetic IX brine in batch operating mode with a reaction time of 53 h. Phylogenetic analysis focused on the active microbial community and revealed that halotolerant, NO3- -reducing bacteria of the bacterial classes Gamma-Proteobacteria and Sphingobacteria were the metabolically dominant members within the stabilized biofilm. This study shows that, despite decreased H(2) transfer under high salt conditions, hydrogenotrophic biological reduction may be successfully used for the treatment of NO3- and ClO- in a MBfR.}, keywords = {Bacteroidetes, Biofilms, Cluster Analysis, DNA, Bacterial, DNA, Ribosomal, Gammaproteobacteria, Hydrogen, Ion Exchange, Membranes, Molecular Sequence Data, Nitrites, Oxidation-Reduction, Perchloric Acid, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Water Pollutants, Chemical, Water Purification}, issn = {1097-0290}, doi = {10.1002/bit.22414}, author = {Sahu, Ashish K and Conneely, Teresa and N{\"u}sslein, Klaus and Ergas, Sarina J} } @article {743, title = {Arsenic sequestration by nitrate respiring microbial communities in urban lake sediments.}, journal = {Chemosphere}, volume = {70}, year = {2007}, month = {2007 Dec}, pages = {329-36}, abstract = {Changes in microbial community composition and activity were related to geochemical conditions favoring arsenic sequestration in sediments collected from the urban, arsenic-contaminated Upper Mystic Lake. After amendment with nitrate, >94\% total soluble arsenic is sequestered by Fe(III)-(oxy)hydroxides generated in live sediments. Of this sequestered arsenic, >75\% existed as As(III), indicating As redox state alone is not responsible for changes in mobility. Arsenic sequestration was concurrent with the microbial respiration of nitrate as indicated by steady state hydrogen concentration and the presence of organisms similar to nitrate-reducing, iron-oxidizing bacteria belonging to the genus Dechloromonas in 16S rDNA clone libraries.}, keywords = {Arsenic, Betaproteobacteria, Biodegradation, Environmental, DNA, Bacterial, DNA, Ribosomal, Fresh Water, Geologic Sediments, Massachusetts, Nitrates, Oxidation-Reduction, RNA, Ribosomal, 16S, Urbanization, Water Microbiology, Water Pollutants, Chemical}, issn = {0045-6535}, doi = {10.1016/j.chemosphere.2007.05.094}, author = {Gibney, Brian P and N{\"u}sslein, Klaus} } @article {502, title = {Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.}, journal = {BMC Genomics}, volume = {8}, year = {2007}, month = {2007}, pages = {180}, abstract = {BACKGROUND: Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known. RESULTS: The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold induced during benzoate oxidation. CONCLUSION: G. metallireducens appears to convert aromatic compounds to benzoyl-CoA, then to acetyl-CoA via fatty acid oxidation, and then to carbon dioxide via the TCA cycle. The enzyme responsible for dearomatizing the aromatic ring may be novel, and energetic investments at this step may be offset by a change in succinate metabolism. Analysis of a field isolate suggests that the pathways inferred for G. metallireducens may be applicable to modeling in situ bioremediation.}, keywords = {Biodegradation, Environmental, Citric Acid Cycle, Gene Expression Regulation, Bacterial, Genomics, Geobacter, Hydrocarbons, Aromatic, Microarray Analysis, Models, Chemical, Models, Genetic, Multigene Family, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Phylogeny, Soil Pollutants, Water Pollutants, Chemical}, issn = {1471-2164}, doi = {10.1186/1471-2164-8-180}, author = {Butler, Jessica E and He, Qiang and Nevin, Kelly P and He, Zhili and Zhou, Jizhong and Lovley, Derek R} } @article {529, title = {Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes.}, journal = {Appl Environ Microbiol}, volume = {71}, year = {2005}, month = {2005 Nov}, pages = {6870-7}, abstract = {The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current production, whereas the expression of the constitutively expressed housekeeping genes recA, rpoD, and proC remained relatively constant. Analysis of mRNA extracted from groundwater collected from a U(VI)-contaminated site undergoing in situ uranium bioremediation revealed a remarkable correspondence between acetate levels in the groundwater and levels of transcripts of gltA. The expression of gltA was also significantly greater in RNA extracted from groundwater beneath a highway runoff recharge pool that was exposed to calcium magnesium acetate in June, when acetate concentrations were high, than in October, when the levels had significantly decreased. It was also possible to detect gltA transcripts on current-harvesting anodes deployed in freshwater sediments. These results suggest that it is possible to monitor the in situ metabolic rate of Geobacteraceae by tracking the expression of the citrate synthase gene.}, keywords = {Acetates, Citrate (si)-Synthase, Deltaproteobacteria, DNA, Ribosomal, Electrodes, Ferric Compounds, Fresh Water, Geobacter, Geologic Sediments, Petroleum, Phylogeny, RNA, Ribosomal, 16S, Uranium, Water Pollutants, Chemical, Water Pollutants, Radioactive}, issn = {0099-2240}, doi = {10.1128/AEM.71.11.6870-6877.2005}, author = {Holmes, Dawn E and Nevin, Kelly P and O{\textquoteright}Neil, Regina A and Ward, Joy E and Adams, Lorrie A and Woodard, Trevor L and Vrionis, Helen A and Lovley, Derek R} } @article {528, title = {Remediation and recovery of uranium from contaminated subsurface environments with electrodes.}, journal = {Environ Sci Technol}, volume = {39}, year = {2005}, month = {2005 Nov 15}, pages = {8943-7}, abstract = {Previous studies have demonstrated that Geobacter species can effectively remove uranium from contaminated groundwater by reducing soluble U(VI) to the relatively insoluble U(IV) with organic compounds serving as the electron donor. Studies were conducted to determine whether electrodes might serve as an alternative electron donor for U(VI) reduction by a pure culture of Geobacter sulfurreducens and microorganisms in uranium-contaminated sediments. Electrodes poised at -500 mV (vs a Ag/AgCl reference) rapidly removed U(VI) from solution in the absence of cells. However, when the poise at the electrode was removed, all of the U(VI) returned to solution, demonstrating that the electrode did not reduce U(VI). If G. sulfurreducens was present on the electrode, U(VI) did not return to solution until the electrode was exposed to dissolved oxygen. This suggeststhat G. sulfurreducens on the electrode reduced U(VI) to U(IV) which was stably precipitated until reoxidized in the presence of oxygen. When an electrode was placed in uranium-contaminated subsurface sediments, U(VI) was removed and recovered from groundwater using poised electrodes. Electrodes emplaced in flow-through columns of uranium-contaminated sediments readily removed U(VI) from the groundwater, and 87\% of the uranium that had been removed was recovered from the electrode surface after the electrode was pulled from the sediments. These results suggest that microorganisms can use electrons derived from electrodes to reduce U(VI) and that it may be possible to remove and recover uranium from contaminated groundwater with poised electrodes.}, keywords = {Biodegradation, Environmental, Electrodes, Geobacter, Graphite, Soil Pollutants, Uranium, Water Pollutants, Chemical}, issn = {0013-936X}, author = {Gregory, Kelvin B and Lovley, Derek R} } @article {543, title = {In situ expression of nifD in Geobacteraceae in subsurface sediments.}, journal = {Appl Environ Microbiol}, volume = {70}, year = {2004}, month = {2004 Dec}, pages = {7251-9}, abstract = {In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 microM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.}, keywords = {Acetates, Biodegradation, Environmental, Culture Media, DNA, Ribosomal, Fresh Water, Gene Expression Regulation, Bacterial, Geobacter, Geologic Sediments, Nitrogenase, Petroleum, Phylogeny, Polymerase Chain Reaction, Quaternary Ammonium Compounds, Rec A Recombinases, RNA, Ribosomal, 16S, Water Pollutants, Chemical}, issn = {0099-2240}, doi = {10.1128/AEM.70.12.7251-7259.2004}, author = {Holmes, Dawn E and Nevin, Kelly P and Lovley, Derek R} } @article {561, title = {Biotechnological application of metal-reducing microorganisms.}, journal = {Adv Appl Microbiol}, volume = {53}, year = {2003}, month = {2003}, pages = {85-128}, keywords = {Archaea, Biodegradation, Environmental, Bioreactors, Environmental Microbiology, Geobacter, Gram-Negative Anaerobic Bacteria, Metals, Heavy, Water Pollutants, Chemical}, issn = {0065-2164}, author = {Lloyd, Jonathan R and Lovley, Derek R and Macaskie, Lynne E} } @article {575, title = {Anaerobic, sulfate-dependent degradation of polycyclic aromatic hydrocarbons in petroleum-contaminated harbor sediment.}, journal = {Environ Sci Technol}, volume = {36}, year = {2002}, month = {2002 Nov 15}, pages = {4811-7}, abstract = {It has previously been demonstrated that [14C]-labeled polycyclic aromatic hydrocarbons (PAHs) can be oxidized to 14CO2 in anoxic, PAH-contaminated, marine harbor sediments in which sulfate reduction is the terminal electron-accepting process. However, it has not previously been determined whether this degradation of [14C]-PAHs accurately reflects the degradation of the in situ pools of contaminant PAHs. In coal tar-contaminated sediments from Boston Harbor, [14C]-naphthalene was readily oxidized to 14CO2, but, after 95 d of incubation under anaerobic conditions, there was no significant decrease in the detectable pool of in situ naphthalene in these sediments. Therefore, to better evaluate the anaerobic biodegradation of the in situ PAH pools, the concentrations of these contaminants were monitored for ca. 1 year during which the sediments were incubated under conditions that mimicked those found in situ. There was loss of all of the PAHs that were monitored (2-5 ring congeners), including high molecular weight PAHs, such as benzo[a]pyrene, that have not previously been shown to be degraded under anaerobic conditions. There was no significant change in the PAH levels in the sediments amended with molybdate to inhibit sulfate-reducing bacteria or in sediments in which all microorganisms had been killed with glutaraldehyde. In some instances, over half of the detectable pools of in situ 2-3 ring PAHs were degraded. In general, the smaller PAHs were degraded more rapidly than the larger PAHs. A distinct exception in the Boston Harbor sediment was naphthalene which was degraded very slowly at a rate comparable to the larger PAHs. In a similar in situ-like study of fuel-contaminated sediments from Liepaja Harbor, Latvia, there was no decline in PAH levels in samples that were sulfate-depleted. However, when the Latvia sediments were supplemented with sufficient sodium sulfate or gypsum to elevate pore water levels of sulfate to approximately 14-25 mM there was a 90\% decline in the naphthalene and a 60\% decline in the 2-methylnaphthalene pool within 90 days. These studies demonstrate for the first time that degradation by anaerobic microorganisms can significantly impact the in situ pools of PAHs in petroleum-contaminated, anoxic, sulfate-reducing harbor sediments and suggest that the self-purification capacity of contaminated harbor sediments is greater than previously considered.}, keywords = {Bacteria, Anaerobic, Biodegradation, Environmental, Environmental Monitoring, Geologic Sediments, Molecular Weight, Petroleum, Polycyclic Hydrocarbons, Aromatic, Ships, Sulfur-Reducing Bacteria, Transportation, Water Pollutants, Chemical}, issn = {0013-936X}, author = {Rothermich, Mary M and Hayes, Lory A and Lovley, Derek R} } @article {577, title = {Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments.}, journal = {Environ Microbiol}, volume = {4}, year = {2002}, month = {2002 Sep}, pages = {510-6}, abstract = {Microbiological reduction of soluble U(VI) to insoluble U(IV) has been proposed as a remediation strategy for uranium-contaminated groundwater. Nitrate is a common co-contaminant with uranium. Nitrate inhibited U(VI) reduction in acetate-amended aquifer sediments collected from a uranium-contaminated site in New Mexico. Once nitrate was depleted, both U(VI) and Fe(III) were reduced concurrently. When nitrate was added to sediments in which U(VI) had been reduced, U(VI) reappeared in solution. Parallel studies with the dissimilatory Fe(III)-, U(VI)- and nitrate-reducing microorganism, Geobacter metallireducens, demonstrated that nitrate inhibited reduction of Fe(III) and U(VI) in cell suspensions of cells that had been grown with nitrate as the electron acceptor, but not in Fe(III)-grown cells. Suspensions of nitrate-grown G. metallireducens oxidized Fe(II) and U(IV) with nitrate as the electron acceptor. U(IV) oxidation was accelerated when Fe(II) was also added, presumably due to the Fe(III) being formed abiotically oxidizing U(IV). These studies demonstrate that although the presence of nitrate is not likely to be an impediment to the bioremediation of uranium contamination with microbial U(VI) reduction, it is necessary to reduce nitrate before U(VI) can be reduced. These results also suggest that anaerobic oxidation of U(IV) to U(VI) with nitrate serving as the electron acceptor may provide a novel strategy for solubilizing and extracting microbial U(IV) precipitates from the subsurface.}, keywords = {Ferric Compounds, Ferrous Compounds, Geologic Sediments, Nitrates, Oxidation-Reduction, Proteobacteria, Soil Pollutants, Solubility, Uranium, Water Pollutants, Chemical}, issn = {1462-2912}, author = {Finneran, Kevin T and Housewright, Meghan E and Lovley, Derek R} } @article {582, title = {Specific 16S rDNA sequences associated with naphthalene degradation under sulfate-reducing conditions in harbor sediments.}, journal = {Microb Ecol}, volume = {43}, year = {2002}, month = {2002 Jan}, pages = {134-45}, abstract = {Previous studies have demonstrated that naphthalene and other polycyclic aromatic hydrocarbons (PAHs) can be anaerobically oxidized with the reduction of sulfate in PAH-contaminated marine harbor sediments, including those in San Diego Bay. In order to learn more about the microorganisms that might be involved in anaerobic naphthalene degradation, the microorganisms associated with naphthalene degradation in San Diego Bay sediments were evaluated. A dilution-to-extinction enrichment culture strategy, designed to recover the most numerous culturable naphthalene-degrading sulfate reducers, resulted in the enrichment of microorganisms with 16S rDNA sequences in the d-Proteobacteria, which were closely related to a previously described pure culture of a naphthalene-degrading sulfate reducer, NaphS2, isolated from sediments in Germany. A more traditional enrichment culture approach, expected to enrich for the fastest-growing naphthalene-degrading sulfate reducers, yielded 16S rDNA sequences closely related to those found in the dilution-to-extinction enrichments and NaphS2. Analysis of 16S rDNA sequences in sediments from two sites in San Diego Bay that had been adapted for rapid naphthalene degradation by continual amendment with low levels of naphthalene suggested that the microbial community composition in the amended sediments differed from that present in the unamended sediments from the same sites. Most significantly, 6-8\% of the sequences recovered from 100 clones of each of the naphthalene-amended sediments were closely related to the 16S rDNA sequences in the enrichment cultures as well as the sequence of the pure culture, NaphS2. No sequences in this NaphS2 phylotype were recovered from the sediments that were not continually exposed to naphthalene. A PCR primer, which was designed based on these phylotype sequences, was used to amplify additional 16S rDNA sequences belonging to the NaphS2 phylotype from PAH-degrading sediments from Island End River (Boston), MA, and Liepaja Harbor, Latvia. Closely related sequences were also recovered from highly contaminated sediment from Tampa Bay, FL. These results suggest that microorganisms closely related to NaphS2 might be involved in naphthalene degradation in harbor sediments. This finding contrasts with the frequent observation that the environmentally relevant microorganisms cannot be readily recovered in pure culture and suggests that further study of the physiology of NaphS2 may provide insights into factors controlling the rate and extent of naphthalene degradation in marine harbor sediments.}, keywords = {Biodegradation, Environmental, DNA Primers, DNA, Bacterial, Geologic Sediments, Naphthalenes, Oxidation-Reduction, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Sulfur-Reducing Bacteria, Water Pollutants, Chemical}, issn = {0095-3628}, doi = {10.1007/s00248-001-1055-z}, author = {Hayes, L A and Lovley, Derek R} } @article {599, title = {Anaerobic degradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA).}, journal = {Environ Sci Technol}, volume = {35}, year = {2001}, month = {2001 May 1}, pages = {1785-90}, abstract = {The potential for anaerobic degradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) was investigated in laboratory incubations of sediments from a petroleum-contaminated aquifer and in aquatic sediments. The addition of humic substances (HS) stimulated the anaerobic degradation of MTBE in aquifer sediments in which Fe(III) was available as an electron acceptor. This is attributed to the fact that HS and other extracellular quinones can stimulate the activity of Fe(III)-reducing microorganisms by acting as an electron shuttle between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides. MTBE was not degraded in aquifer sediments without Fe(III) and HS. [14C]-MTBE added to aquatic sediments adapted for anaerobic MTBE degradation was converted to 14CO2 in the presence or absence of HS or the HS analog, anthraquione-2,6-disulfonate. Unamended aquatic sediments produced 14CH4 as well as 14CO2 from [14C]-MTBE. The aquatic sediments also rapidly consumed TBA under anaerobic conditions and converted [14C]-TBA to 14CH4 and 14CO2. An adaptation period of ca. 250-300 days was required prior to the most rapid anaerobic MTBE degradation in both sediment types, whereas TBA was metabolized in the aquatic sediments without a lag. These results demonstrate that, under the appropriate conditions, MTBE and TBA can be degraded in the absence of oxygen. This suggests that it may be possible to design strategies for the anaerobic remediation of MTBE in petroleum-contaminated subsurface environments.}, keywords = {Anaerobiosis, Biodegradation, Environmental, Carbon Dioxide, Geologic Sediments, Methane, Methyl Ethers, tert-Butyl Alcohol, Water Pollutants, Chemical}, issn = {0013-936X}, author = {Finneran, K T and Lovley, D R} } @article {591, title = {Bioremediation. Anaerobes to the rescue.}, journal = {Science}, volume = {293}, year = {2001}, month = {2001 Aug 24}, pages = {1444-6}, keywords = {Bacteria, Aerobic, Bacteria, Anaerobic, Biodegradation, Environmental, Euryarchaeota, Ferric Compounds, Genome, Archaeal, Genome, Bacterial, Hydrocarbons, Aromatic, Hydrocarbons, Chlorinated, Metals, Methane, Nitrates, Oxidation-Reduction, Oxygen, Soil Microbiology, Sulfates, Sulfur-Reducing Bacteria, Water Pollutants, Chemical}, issn = {0036-8075}, doi = {10.1126/science.1063294}, author = {Lovley, D R} } @article {614, title = {Reduction of Fe(III), Mn(IV), and toxic metals at 100 degrees C by Pyrobaculum islandicum.}, journal = {Appl Environ Microbiol}, volume = {66}, year = {2000}, month = {2000 Mar}, pages = {1050-6}, abstract = {It has recently been noted that a diversity of hyperthermophilic microorganisms have the ability to reduce Fe(III) with hydrogen as the electron donor, but the reduction of Fe(III) or other metals by these organisms has not been previously examined in detail. When Pyrobaculum islandicum was grown at 100 degrees C in a medium with hydrogen as the electron donor and Fe(III)-citrate as the electron acceptor, the increase in cell numbers of P. islandicum per mole of Fe(III) reduced was found to be ca. 10-fold higher than previously reported. Poorly crystalline Fe(III) oxide could also serve as the electron acceptor for growth on hydrogen. The stoichiometry of hydrogen uptake and Fe(III) oxide reduction was consistent with the oxidation of 1 mol of hydrogen resulting in the reduction of 2 mol of Fe(III). The poorly crystalline Fe(III) oxide was reduced to extracellular magnetite. P. islandicum could not effectively reduce the crystalline Fe(III) oxide minerals goethite and hematite. In addition to using hydrogen as an electron donor for Fe(III) reduction, P. islandicum grew via Fe(III) reduction in media in which peptone and yeast extract served as potential electron donors. The closely related species P. aerophilum grew via Fe(III) reduction in a similar complex medium. Cell suspensions of P. islandicum reduced the following metals with hydrogen as the electron donor: U(VI), Tc(VII), Cr(VI), Co(III), and Mn(IV). The reduction of these metals was dependent upon the presence of cells and hydrogen. The metalloids arsenate and selenate were not reduced. U(VI) was reduced to the insoluble U(IV) mineral uraninite, which was extracellular. Tc(VII) was reduced to insoluble Tc(IV) or Tc(V). Cr(VI) was reduced to the less toxic, less soluble Cr(III). Co(III) was reduced to Co(II). Mn(IV) was reduced to Mn(II) with the formation of manganese carbonate. These results demonstrate that biological reduction may contribute to the speciation of metals in hydrothermal environments and could account for such phenomena as magnetite accumulation and the formation of uranium deposits at ca. 100 degrees C. Reduction of toxic metals with hyperthermophilic microorganisms or their enzymes might be applied to the remediation of metal-contaminated waters or waste streams.}, keywords = {Chromium, Cobalt, Energy Metabolism, Ferric Compounds, Geological Phenomena, Geology, Iron, Manganese, Metals, Heavy, Oxidation-Reduction, Technetium, Thermoproteaceae, Uranium, Water Pollutants, Chemical}, issn = {0099-2240}, author = {Kashefi, K and Lovley, D R} } @article {616, title = {Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer.}, journal = {Int J Syst Bacteriol}, volume = {49 Pt 4}, year = {1999}, month = {1999 Oct}, pages = {1615-22}, abstract = {In an attempt to understand better the micro-organisms involved in anaerobic degradation of aromatic hydrocarbons in the Fe(III)-reducing zone of petroleum-contaminated aquifers, Fe(III)-reducing micro-organisms were isolated from contaminated aquifer material that had been adapted for rapid oxidation of toluene coupled to Fe(III) reduction. One of these organisms, strain H-5T, was enriched and isolated on acetate/Fe(III) medium. Strain H-5T is a Gram-negative strict anaerobe that grows with various simple organic acids such as acetate, propionate, lactate and fumarate as alternative electron donors with Fe(III) as the electron acceptor. In addition, strain H-5T also oxidizes long-chain fatty acids such as palmitate with Fe(III) as the sole electron acceptor. Strain H-5T can also grow by fermentation of citrate or fumarate in the absence of an alternative electron acceptor. The primary end-products of citrate fermentation are acetate and succinate. In addition to various forms of soluble and insoluble Fe(III), strain H-5T grows with nitrate, Mn(IV), fumarate and the humic acid analogue 2,6-anthraquinone disulfonate as alternative electron acceptors. As with other organisms that can oxidize organic compounds completely with the reduction of Fe(III), cell suspensions of strain H-5T have absorbance maxima indicative of a c-type cytochrome(s). It is proposed that strain H-5T represents a novel genus in the Holophaga-Acidobacterium phylum and that it should be named Geothrix fermentans sp. nov., gen. nov.}, keywords = {Biodegradation, Environmental, DNA, Bacterial, DNA, Ribosomal, Ferric Compounds, Geologic Sediments, Gram-Negative Anaerobic Bacteria, Molecular Sequence Data, Oxidation-Reduction, Petroleum, Phylogeny, RNA, Ribosomal, 16S, Water Microbiology, Water Pollutants, Chemical, Water Supply}, issn = {0020-7713}, author = {Coates, J D and Ellis, D J and Gaw, C V and Lovley, D R} } @article {628, title = {Anaerobic degradation of polycyclic aromatic hydrocarbons and alkanes in petroleum-contaminated marine harbor sediments.}, journal = {Appl Environ Microbiol}, volume = {63}, year = {1997}, month = {1997 Sep}, pages = {3589-93}, abstract = {Although polycyclic aromatic hydrocarbons (PAHs) have usually been found to persist under strict anaerobic conditions, in a previous study an unusual site was found in San Diego Bay in which two PAHs, naphthalene and phenanthrene, were oxidized to carbon dioxide under sulfate-reducing conditions. Further investigations with these sediments revealed that methylnaphthalene, fluorene, and fluoranthene were also anaerobically oxidized to carbon dioxide in these sediments, while pyrene and benzo[a]pyrene were not. Studies with naphthalene indicated that PAH oxidation was sulfate dependent. Incubating the sediments with additional naphthalene for 1 month resulted in a significant increase in the oxidation of [14C]naphthalene. In sediments from a less heavily contaminated site in San diego Bay where PAHs were not readily degraded, naphthalene degradation could be stimulated through inoculation with active PAH-degrading sediments from the most heavily contaminated site. Sediments from the less heavily contaminated site that had been adapted for rapid anaerobic degradation of high concentrations of benzene did not oxidize naphthalene, suggesting that the benzene- and naphthalene-degrading populations were different. When fuels containing complex mixtures of alkanes were added to sediments from the two sites, there was significant degradation in the alkanes. [14C]hexadecane was also anaerobically oxidized to 14CO2 in these sediments. Molybdate, a specific inhibitor of sulfate reduction, inhibited hexadecane oxidation. These results demonstrate that a wide variety of hydrocarbon contaminants can be degraded under sulfate-reducing conditions in hydrocarbon-contaminated sediments, and they suggest that it may be possible to use sulfate reduction rather than aerobic respiration as a treatment strategy for hydrocarbon-contaminated dredged sediments.}, keywords = {Alkanes, Anaerobiosis, Biodegradation, Environmental, California, Naphthalenes, Oxidation-Reduction, Petroleum, Polycyclic Hydrocarbons, Aromatic, Sulfates, Water Microbiology, Water Pollutants, Chemical}, issn = {0099-2240}, author = {Coates, J D and Woodward, J and Allen, J and Philp, P and Lovley, D R} } @article {643, title = {Stimulated anoxic biodegradation of aromatic hydrocarbons using Fe(III) ligands.}, journal = {Nature}, volume = {370}, year = {1994}, month = {1994 Jul 14}, pages = {128-31}, abstract = {Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing the bioavailability of Fe(III) by adding suitable ligands provides a potential alternative to oxygen addition for the bioremediation of petroleum-contaminated aquifers.}, keywords = {Benzene, Biodegradation, Environmental, Ferric Compounds, Hydrocarbons, Ligands, Methane, Nitrilotriacetic Acid, Oxidation-Reduction, Toluene, Water Pollutants, Chemical}, issn = {0028-0836}, doi = {10.1038/370128a0}, author = {Lovley, D R and Woodward, J C and Chapelle, F H} }