scholarly journals Anaerobic Benzene Oxidation by Geobacter Species

2012 ◽  
Vol 78 (23) ◽  
pp. 8304-8310 ◽  
Author(s):  
Tian Zhang ◽  
Timothy S. Bain ◽  
Kelly P. Nevin ◽  
Melissa A. Barlett ◽  
Derek R. Lovley
Keyword(s):  
Electron Donor ◽  
Electron Acceptor ◽  
Model Organism ◽  
Benzene Oxidation ◽  
Geobacter Metallireducens ◽  
Contaminated Aquifer ◽  
Content Type ◽  
Benzene Degradation ◽  
Contaminated Aquifers ◽  
Genetically Manipulated

ABSTRACTThe abundance ofGeobacterspecies in contaminated aquifers in which benzene is anaerobically degraded has led to the suggestion that someGeobacterspecies might be capable of anaerobic benzene degradation, but this has never been documented. A strain ofGeobacter, designated strain Ben, was isolated from sediments from the Fe(III)-reducing zone of a petroleum-contaminated aquifer in which there was significant capacity for anaerobic benzene oxidation. Strain Ben grew in a medium with benzene as the sole electron donor and Fe(III) oxide as the sole electron acceptor. Furthermore, additional evaluation ofGeobacter metallireducensdemonstrated that it could also grow in benzene-Fe(III) medium. In both strain Ben andG. metallireducensthe stoichiometry of benzene metabolism and Fe(III) reduction was consistent with the oxidation of benzene to carbon dioxide with Fe(III) serving as the sole electron acceptor. With benzene as the electron donor, and Fe(III) oxide (strain Ben) or Fe(III) citrate (G. metallireducens) as the electron acceptor, the cell yields of strain Ben andG. metallireducenswere 3.2 × 109and 8.4 × 109cells/mmol of Fe(III) reduced, respectively. Strain Ben also oxidized benzene with anthraquinone-2,6-disulfonate (AQDS) as the sole electron acceptor with cell yields of 5.9 × 109cells/mmol of AQDS reduced. Strain Ben serves as model organism for the study of anaerobic benzene metabolism in petroleum-contaminated aquifers, andG. metallireducensis the first anaerobic benzene-degrading organism that can be genetically manipulated.

scholarly journals Direct Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri

2014 ◽  
Vol 80 (15) ◽  
pp. 4599-4605 ◽  
Author(s):  
Amelia-Elena Rotaru ◽  
Pravin Malla Shrestha ◽  
Fanghua Liu ◽  
Beatrice Markovaite ◽  
Shanshan Chen ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Model Organism ◽  
Methanosarcina Barkeri ◽  
Physical Contact ◽  
Acetate Metabolism ◽  
Geobacter Metallireducens ◽  
Content Type ◽  
Direct Interspecies Electron Transfer ◽  
Interspecies Electron Transfer ◽  
Effective Form

ABSTRACTDirect interspecies electron transfer (DIET) is potentially an effective form of syntrophy in methanogenic communities, but little is known about the diversity of methanogens capable of DIET. The ability ofMethanosarcina barkerito participate in DIET was evaluated in coculture withGeobacter metallireducens. Cocultures formed aggregates that shared electrons via DIET during the stoichiometric conversion of ethanol to methane. Cocultures could not be initiated with a pilin-deficientG. metallireducensstrain, suggesting that long-range electron transfer along pili was important for DIET. Amendments of granular activated carbon permitted the pilin-deficientG. metallireducensisolates to share electrons withM. barkeri, demonstrating that this conductive material could substitute for pili in promoting DIET. WhenM. barkeriwas grown in coculture with the H2-producingPelobacter carbinolicus, incapable of DIET,M. barkeriutilized H2as an electron donor but metabolized little of the acetate thatP. carbinolicusproduced. This suggested that H2, but not electrons derived from DIET, inhibited acetate metabolism.P. carbinolicus-M. barkericocultures did not aggregate, demonstrating that, unlike DIET, close physical contact was not necessary for interspecies H2transfer.M. barkeriis the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H2or electrons derived from DIET for CO2reduction. Furthermore,M. barkeriis genetically tractable, making it a model organism for elucidating mechanisms by which methanogens make biological electrical connections with other cells.

Rapid Benzene Degradation in Methanogenic Sediments from a Petroleum-Contaminated Aquifer

1998 ◽  
Vol 64 (5) ◽  
pp. 1937-1939 ◽  
Author(s):  
Jonathan M. Weiner ◽  
Derek R. Lovley
Keyword(s):  
Natural Attenuation ◽  
Electron Acceptors ◽  
Contaminated Aquifer ◽  
Benzene Degradation ◽  
Contaminated Aquifers

ABSTRACT In methanogenic sediments from a petroleum-contaminated aquifer, [14C]benzene was converted to14CH4 and 14CO2 without an apparent lag. Phenol, acetate, and propionate were intermediates in benzene mineralization. These results suggest that alternative electron acceptors need not be available for there to be significant natural attenuation of benzene in some petroleum-contaminated aquifers.

scholarly journals Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3786-3791 ◽  
Author(s):  
Shungui Zhou ◽  
Guiqin Yang ◽  
Qin Lu ◽  
Min Wu
Keyword(s):  
Forest Soil ◽  
Electron Donor ◽  
Electron Acceptor ◽  
Type Species ◽  
Geobacter Sulfurreducens ◽  
Phenotypic Characterization ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A novel Fe(III)-reducing bacterium, designated GSS01T, was isolated from a forest soil sample using a liquid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS01T were strictly anaerobic, Gram-stain-negative, motile, non-spore-forming and slightly curved rod-shaped. Growth occurred at 16–40 °C and optimally at 30 °C. The DNA G+C content was 60.9 mol%. The major respiratory quinone was MK-8. The major fatty acids were C16 : 0, C18 : 0 and C16 : 1ω7c/C16 : 1ω6c. Strain GSS01T was able to grow with ferrihydrite, Fe(III) citrate, Mn(IV), sulfur, nitrate or anthraquinone-2,6-disulfonate, but not with fumarate, as sole electron acceptor when acetate was the sole electron donor. The isolate was able to utilize acetate, ethanol, glucose, lactate, butyrate, pyruvate, benzoate, benzaldehyde, m-cresol and phenol but not toluene, p-cresol, propionate, malate or succinate as sole electron donor when ferrihydrite was the sole electron acceptor. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSS01T was most closely related to Geobacter sulfurreducens PCAT (98.3 % sequence similarity) and exhibited low similarities (94.9–91.8 %) to the type strains of other species of the genus Geobacter . The DNA–DNA relatedness between strain GSS01T and G. sulfurreducens PCAT was 41.4±1.1 %. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS01T is believed to represent a novel species of the genus Geobacter , and the name Geobacter soli sp. nov. is proposed. The type strain is GSS01T ( = KCTC 4545T = MCCC 1K00269T).

scholarly journals Anaerobic Benzene Oxidation via Phenol in Geobacter metallireducens

2013 ◽  
Vol 79 (24) ◽  
pp. 7800-7806 ◽  
Author(s):  
Tian Zhang ◽  
Pier-Luc Tremblay ◽  
Akhilesh Kumar Chaurasia ◽  
Jessica A. Smith ◽  
Timothy S. Bain ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Geobacter Sulfurreducens ◽  
Environmental Significance ◽  
Geobacter Metallireducens ◽  
Content Type ◽  
Benzene Degradation ◽  
Metabolic Route ◽  
Benzene Hydroxylation ◽  
Anaerobic Benzene Degradation ◽  
Anaerobic Conversion

ABSTRACTAnaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated inGeobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (<0.5 μM) of phenol accumulated in cultures ofGeobacter metallireducensanaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures ofGeobacter sulfurreducens, aGeobacterspecies that cannot metabolize benzene. The phenol produced inG. metallireducenscultures was labeled with18O during growth in H218O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in whichGeobacterspecies are considered to play an important role in anaerobic benzene degradation.

scholarly journals A NovelShewanellaIsolate Enhances Corrosion by Using Metallic Iron as the Electron Donor with Fumarate as the Electron Acceptor

2018 ◽  
Vol 84 (20) ◽  
Author(s):  
Jo Philips ◽  
Niels Van den Driessche ◽  
Kim De Paepe ◽  
Antonin Prévoteau ◽  
Jeffrey A. Gralnick ◽  
...  
Keyword(s):  
Corrosion Rate ◽  
Electron Donor ◽  
Electron Acceptor ◽  
Metallic Iron ◽  
Hydrogen Generation ◽  
Formation Rate ◽  
Fold Increase ◽  
Hydrogen Formation ◽  
Content Type ◽  
Reducing Properties

ABSTRACTThe involvement ofShewanellaspp. in biocorrosion is often attributed to their Fe(III)-reducing properties, but they could also affect corrosion by using metallic iron as an electron donor. Previously, we isolatedShewanellastrain 4t3-1-2LB from an acetogenic community enriched with Fe(0) as the sole electron donor. Here, we investigated its use of Fe(0) as an electron donor with fumarate as an electron acceptor and explored its corrosion-enhancing mechanism. Without Fe(0), strain 4t3-1-2LB fermented fumarate to succinate and CO2, as was shown by the reaction stoichiometry and pH. With Fe(0), strain 4t3-1-2LB completely reduced fumarate to succinate and increased the Fe(0) corrosion rate (7.0 ± 0.6)-fold in comparison to that of abiotic controls (based on the succinate-versus-abiotic hydrogen formation rate). Fumarate reduction by strain 4t3-1-2LB was, at least in part, supported by chemical hydrogen formation on Fe(0). Filter-sterilized spent medium increased the hydrogen generation rate only 1.5-fold, and thus extracellular hydrogenase enzymes appear to be insufficient to explain the enhanced corrosion rate. Electrochemical measurements suggested that strain 4t3-1-2LB did not excrete dissolved redox mediators. Exchanging the medium and scanning electron microscopy (SEM) imaging indicated that cells were attached to Fe(0). It is possible that strain 4t3-1-2LB used a direct mechanism to withdraw electrons from Fe(0) or favored chemical hydrogen formation on Fe(0) through maintaining low hydrogen concentrations. In coculture with anAcetobacteriumstrain, strain 4t3-1-2LB did not enhance acetogenesis from Fe(0). This work describes a strong corrosion enhancement by aShewanellastrain through its use of Fe(0) as an electron donor and provides insights into its corrosion-enhancing mechanism.IMPORTANCEShewanellaspp. are frequently found on corroded metal structures. Their role in microbial influenced corrosion has been attributed mainly to their Fe(III)-reducing properties and, therefore, has been studied with the addition of an electron donor (lactate).Shewanellaspp., however, can also use solid electron donors, such as cathodes and potentially Fe(0). In this work, we show that the electron acceptor fumarate supported the use of Fe(0) as the electron donor byShewanellastrain 4t3-1-2LB, which caused a (7.0 ± 0.6)-fold increase of the corrosion rate. The corrosion-enhancing mechanism likely involved cell surface-associated components in direct contact with the Fe(0) surface or maintenance of low hydrogen levels by attached cells, thereby favoring chemical hydrogen formation by Fe(0). This work sheds new light on the role ofShewanellaspp. in biocorrosion, while the insights into the corrosion-enhancing mechanism contribute to the understanding of extracellular electron uptake processes.

scholarly journals Dissimilatory Nitrate Reduction to Ammonium (DNRA) and Denitrification Pathways Are Leveraged by Cyclic AMP Receptor Protein (CRP) Paralogues Based on Electron Donor/Acceptor Limitation in Shewanella loihica PV-4

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Shuangyuan Liu ◽  
Jingcheng Dai ◽  
Hehong Wei ◽  
Shuyang Li ◽  
Pei Wang ◽  
...  
Keyword(s):  
Global Warming ◽  
Carbon Source ◽  
Cyclic Amp ◽  
Electron Donor ◽  
Electron Acceptor ◽  
Nitrite Reductase ◽  
Nitrate Reduction ◽  
Receptor Protein ◽  
Content Type ◽  
Dissimilatory Nitrate Reduction

ABSTRACT Under anoxic conditions, many bacteria, including Shewanella loihica strain PV-4, could use nitrate as an electron acceptor for dissimilatory nitrate reduction to ammonium (DNRA) and/or denitrification. Previous and current studies have shown that DNRA is favored under higher ambient carbon-to-nitrogen (C/N) ratios, whereas denitrification is upregulated under lower C/N ratios, which is consistent with our bioenergetics calculations. Interestingly, computational analyses indicate that the common cyclic AMP receptor protein (designated CRP1) and its paralogue CRP2 might both be involved in the regulation of two competing dissimilatory nitrate reduction pathways, DNRA and denitrification, in S. loihica PV-4 and several other denitrifying Shewanella species. To explore the regulatory mechanism underlying the dissimilatory nitrate reduction (DNR) pathways, nitrate reduction of a series of in-frame deletion mutants was analyzed under different C/N ratios. Deletion of crp1 could accelerate the reduction of nitrite to NO under both low and high C/N ratios. CRP1 is not required for denitrification and actually suppresses production of NO and N2O gases. Deletion of either of the NO-forming nitrite reductase genes nirK or crp2 blocked production of NO gas. Furthermore, real-time PCR and electrophoretic mobility shift assays (EMSAs) demonstrated that the transcription levels of DNRA-relevant genes such as nap-β (napDABGH), nrfA, and cymA were upregulated by CRP1, while nirK transcription was dependent on CRP2. There are tradeoffs between the different physiological roles of nitrate/lactate, as nitrogen nutrient/carbon source and electron acceptor/donor and CRPs may leverage dissimilatory nitrate reduction pathways for maximizing energy yield and bacterial survival under ambient environmental conditions. IMPORTANCE Some microbes utilize different dissimilatory nitrate reduction (DNR) pathways, including DNR to ammonia (DNRA) and denitrification pathways, for anaerobic respiration in response to ambient carbon/nitrogen ratio changes. Large-scale industrial nitrogen fixation and fertilizer application raise the concern of emission of N2O, a stable gas with potent global warming potential, as consequence of microbial respiration, thereby aggravating global warming and climate change. However, little is known about the molecular mechanism underlying the choice of two competing DNR pathways. We demonstrate that the global regulator CRP1, which is widely encoded in bacteria, is required for DNRA in S. loihica PV-4 strain, while the CRP2 paralogue is required for transcription of the nitrite reductase gene nirK for denitrification. Sufficient carbon source lead to the predominance of DNRA, while carbon source/electron donor deficiency may result in an incomplete denitrification process, raising the concern of high levels of N2O emission from nitrate-rich and carbon source-poor waters and soils.

scholarly journals Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1T

2017 ◽  
Vol 83 (12) ◽  
Author(s):  
Peng Peng ◽  
Ying Zheng ◽  
Jasper J. Koehorst ◽  
Peter J. Schaap ◽  
Alfons J. M. Stams ◽  
...  
Keyword(s):  
Electron Donor ◽  
Electron Acceptor ◽  
Inorganic Compounds ◽  
Environmental Pollutants ◽  
Amino Acid Sequences ◽  
Halogenated Compounds ◽  
Metabolic Potential ◽  
Haloacid Dehalogenase ◽  
Content Type ◽  
Donor And Acceptor

ABSTRACT Haloalkanoates are environmental pollutants that can be degraded aerobically by microorganisms producing hydrolytic dehalogenases. However, there is a lack of information about the anaerobic degradation of haloalkanoates. Genome analysis of Pseudomonas chloritidismutans AW-1T, a facultative anaerobic chlorate-reducing bacterium, showed the presence of two putative haloacid dehalogenase genes, the l-DEX gene and dehI, encoding an l-2-haloacid dehalogenase (l-DEX) and a halocarboxylic acid dehydrogenase (DehI), respectively. Hence, we studied the concurrent degradation of haloalkanoates and chlorate as a yet-unexplored trait of strain AW-1T. The deduced amino acid sequences of l-DEX and DehI revealed 33 to 37% and 26 to 86% identities with biochemically/structurally characterized l-DEX and the d- and dl-2-haloacid dehalogenase enzymes, respectively. Physiological experiments confirmed that strain AW-1T can grow on chloroacetate, bromoacetate, and both l- and d-α-halogenated propionates with chlorate as an electron acceptor. Interestingly, growth and haloalkanoate degradation were generally faster with chlorate as an electron acceptor than with oxygen as an electron acceptor. In line with this, analyses of l-DEX and DehI dehalogenase activities using cell-free extract (CFE) of strain AW-1T grown on dl-2-chloropropionate under chlorate-reducing conditions showed up to 3.5-fold higher dehalogenase activity than the CFE obtained from AW-1T cells grown on dl-2-chloropropionate under aerobic conditions. Reverse transcription-quantitative PCR showed that the l-DEX gene was expressed constitutively independently of the electron donor (haloalkanoates or acetate) or acceptor (chlorate or oxygen), whereas the expression of dehI was induced by haloalkanoates. Concurrent degradation of organic and inorganic halogenated compounds by strain AW-1T represents a unique metabolic capacity in a single bacterium, providing a new piece of the puzzle of the microbial halogen cycle. IMPORTANCE Halogenated organic and inorganic compounds are important environmental pollutants that have carcinogenic and genotoxic effects on both animals and humans. Previous research studied the degradation of organic and inorganic halogenated compounds separately but not concurrently. This study shows concurrent degradation of halogenated alkanoates and chlorate as an electron donor and acceptor, respectively, coupled to growth in a single bacterium, Pseudomonas chloritidismutans AW-1T. Hence, besides biogenesis of molecular oxygen from chlorate reduction enabling a distinctive placement of strain AW-1T between aerobic and anaerobic microorganisms, we can now add another unique metabolic potential of this bacterium to the roster. The degradation of different halogenated compounds under anoxic conditions by a single bacterium is also of interest for the natural halogen cycle in different aquatic and terrestrial ecosystems where ample natural production of halogenated compounds has been documented.

scholarly journals Shewanella spp. Use Acetate as an Electron Donor for Denitrification but Not Ferric Iron or Fumarate Reduction

2013 ◽  
Vol 79 (8) ◽  
pp. 2818-2822 ◽  
Author(s):  
Sukhwan Yoon ◽  
Robert A. Sanford ◽  
Frank E. Löffler
Keyword(s):  
Electron Donor ◽  
Electron Acceptor ◽  
Iron Reduction ◽  
Ferric Iron ◽  
Acetate Oxidation ◽  
Content Type ◽  
Anoxic Conditions ◽  
Fumarate Reduction

ABSTRACTLactate but not acetate oxidation was reported to support electron acceptor reduction byShewanellaspp. under anoxic conditions. We demonstrate that the denitrifiersShewanella loihicastrain PV-4 andShewanella denitrificansOS217 utilize acetate as an electron donor for denitrification but not for fumarate or ferric iron reduction.

scholarly journals Combined Application of PCR-Based Functional Assays for the Detection of Aromatic-Compound-Degrading Anaerobes

2011 ◽  
Vol 77 (14) ◽  
pp. 5056-5061 ◽  
Author(s):  
Kevin Kuntze ◽  
Carsten Vogt ◽  
Hans-Hermann Richnow ◽  
Matthias Boll
Keyword(s):  
Gene Targeting ◽  
Aromatic Compound ◽  
Functional Gene ◽  
Content Type ◽  
Benzene Degradation ◽  
Functional Assays ◽  
Combined Application ◽  
Contaminated Aquifers ◽  
The Individual

ABSTRACTTo explore the reliability of assays that detect aromatic-compound-degrading anaerobes, a combination of three functional-gene-targeting assays was applied to microcosms from benzene-contaminated aquifers. Results of the assays were consistent and suggest that species related to the generaAzoarcusandGeobacterdominated benzene degradation at the individual sites.

scholarly journals Evaluation of a Genome-ScaleIn SilicoMetabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

2012 ◽  
Vol 78 (24) ◽  
pp. 8735-8742 ◽  
Author(s):  
Yilin Fang ◽  
Michael J. Wilkins ◽  
Steven B. Yabusaki ◽  
Mary S. Lipton ◽  
Philip E. Long
Keyword(s):  
Proteomic Analysis ◽  
In Silico ◽  
Field Experiments ◽  
Metabolic Model ◽  
Geobacter Metallireducens ◽  
Content Type ◽  
Proteomic Data ◽  
Subsurface Environment ◽  
A Genome ◽  
Genome Scale

ABSTRACTAccurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within anin silicomodel using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model ofGeobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-basedin silicomodelof G. metallireducensrelates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637G. metallireducensproteins detected during the 2008 experiment were associated with specific metabolic reactions in thein silicomodel. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through thein silicomodel reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in thein silicomodel that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

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