@article {3045, title = {H Is a Major Intermediate in Corrosion of Iron.}, journal = {mBio}, volume = {14}, year = {2023}, month = {2023 Apr 25}, pages = {e0007623}, abstract = {

Desulfovibrio vulgaris has been a primary pure culture sulfate reducer for developing microbial corrosion concepts. Multiple mechanisms for how it accepts electrons from Fe have been proposed. We investigated Fe oxidation with a mutant of in which hydrogenase genes were deleted. The hydrogenase mutant grew as well as the parental strain with lactate as the electron donor, but unlike the parental strain, it was not able to grow on H. The parental strain reduced sulfate with Fe as the sole electron donor, but the hydrogenase mutant did not. H accumulated over time in Fe cultures of the hydrogenase mutant and sterile controls but not in parental strain cultures. Sulfide stimulated H production in uninoculated controls apparently by both reacting with Fe to generate H and facilitating electron transfer from Fe to H. Parental strain supernatants did not accelerate H production from Fe, ruling out a role for extracellular hydrogenases. Previously proposed electron transfer between Fe and via soluble electron shuttles was not evident. The hydrogenase mutant did not reduce sulfate in the presence of Fe and either riboflavin or anthraquinone-2,6-disulfonate, and these potential electron shuttles did not stimulate parental strain sulfate reduction with Fe as the electron donor. The results demonstrate that primarily accepts electrons from Fe via H as an intermediary electron carrier. These findings clarify the interpretation of previous corrosion studies and suggest that H-mediated electron transfer is an important mechanism for iron corrosion under sulfate-reducing conditions. Microbial corrosion of iron in the presence of sulfate-reducing microorganisms is economically significant. There is substantial debate over how microbes accelerate iron corrosion. Tools for genetic manipulation have only been developed for a few Fe(III)-reducing and methanogenic microorganisms known to corrode iron and in each case those microbes were found to accept electrons from Fe via direct electron transfer. However, iron corrosion is often most intense in the presence of sulfate-reducing microbes. The finding that Desulfovibrio vulgaris relies on H to shuttle electrons between Fe and cells revives the concept, developed in some of the earliest studies on microbial corrosion, that sulfate reducers consumption of H is a major microbial corrosion mechanism. The results further emphasize that direct Fe-to-microbe electron transfer has yet to be rigorously demonstrated in sulfate-reducing microbes.

}, keywords = {Corrosion, Desulfovibrio, Desulfovibrio vulgaris, Hydrogenase, Iron, Lactic Acid, Oxidation-Reduction, Sulfates}, issn = {2150-7511}, doi = {10.1128/mbio.00076-23}, author = {Woodard, Trevor L and Ueki, Toshiyuki and Lovley, Derek R} } @article {3082, title = {The Hydrogen Economy of Methanosarcina barkeri: Life in the Fast Lane.}, journal = {J Bacteriol}, volume = {200}, year = {2018}, month = {2018 Oct 15}, abstract = {

Two recent studies (T. D. Mand, G. Kulkarni, and W. W. Metcalf, J. Bacteriol 200:e00342-18, 2018, https://doi.org/10.1128/JB.00342-18, and G. Kulkarni, T. D. Mand, and W. W. Metcalf, mBio 9:e01256-18, 2018, https://doi.org/10.1128/mBio.01256-18) analyzed an impressive array of hydrogenase-deficient mutant strains of not only to describe H-based growth but also to demonstrate the conservation of energy with intracellular hydrogen cycling, a novel strategy for creating a proton motive force to support ATP synthesis.

}, keywords = {Hydrogen, Hydrogenase, Methane, Methanosarcina barkeri, Proton-Motive Force}, issn = {1098-5530}, doi = {10.1128/JB.00445-18}, author = {Lovley, Derek R} } @article {3097, title = {Happy together: microbial communities that hook up to swap electrons.}, journal = {ISME J}, volume = {11}, year = {2017}, month = {2017 Feb}, pages = {327-336}, abstract = {

The discovery of direct interspecies electron transfer (DIET) and cable bacteria has demonstrated that microbial cells can exchange electrons over long distances (μm-cm) through electrical connections. For example, in the presence of cable bacteria electrons are rapidly transported over centimeter distances, coupling the oxidation of reduced sulfur compounds in anoxic sediments to oxygen reduction in overlying surficial sediments. Bacteria and archaea wired for DIET are found in anaerobic methane-producing and methane-consuming communities. Electrical connections between gut microbes and host cells have also been proposed. Iterative environmental and defined culture studies on methanogenic communities revealed the importance of electrically conductive pili and c-type cytochromes in natural electrical grids, and demonstrated that conductive carbon materials and magnetite can substitute for these biological connectors to facilitate DIET. This understanding has led to strategies to enhance and stabilize anaerobic digestion. Key unknowns warranting further investigation include elucidation of the archaeal electrical connections facilitating DIET-based methane production and consumption; and the mechanisms for long-range electron transfer through cable bacteria. A better understanding of mechanisms for cell-to-cell electron transfer could facilitate the hunt for additional electrically connected microbial communities with omics approaches and could advance spin-off applications such as the development of sustainable bioelectronics materials and bioelectrochemical technologies.

}, keywords = {Archaea, Bacteria, Electron Transport, Methane, Microbial Consortia, Microbial Interactions, Models, Biological, Oxidation-Reduction}, issn = {1751-7370}, doi = {10.1038/ismej.2016.136}, author = {Lovley, Derek R} } @article {3095, title = {How to Sustainably Feed a Microbe: Strategies for Biological Production of Carbon-Based Commodities with Renewable Electricity.}, journal = {Front Microbiol}, volume = {7}, year = {2016}, month = {2016}, pages = {1879}, abstract = {

As interest and application of renewable energy grows, strategies are needed to align the asynchronous supply and demand. Microbial metabolisms are a potentially sustainable mechanism for transforming renewable electrical energy into biocommodities that are easily stored and transported. Acetogens and methanogens can reduce carbon dioxide to organic products including methane, acetic acid, and ethanol. The library of biocommodities is expanded when engineered metabolisms of acetogens are included. Typically, electrochemical systems are employed to integrate renewable energy sources with biological systems for production of carbon-based commodities. Within these systems, there are three prevailing mechanisms for delivering electrons to microorganisms for the conversion of carbon dioxide to reduce organic compounds: (1) electrons can be delivered to microorganisms via H produced separately in a electrolyzer, (2) H produced at a cathode can convey electrons to microorganisms supported on the cathode surface, and (3) a cathode can directly feed electrons to microorganisms. Each of these strategies has advantages and disadvantages that must be considered in designing full-scale processes. This review considers the evolving understanding of each of these approaches and the state of design for advancing these strategies toward viability.

}, issn = {1664-302X}, doi = {10.3389/fmicb.2016.01879}, author = {Butler, Caitlyn S and Lovley, Derek R} } @article {472, title = {Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation.}, journal = {Microbiology}, volume = {154}, year = {2008}, month = {2008 Sep}, pages = {2589-99}, abstract = {Analysis of the genome of Geobacter sulfurreducens revealed four genes encoding putative symporters with homology to ActP, an acetate transporter in Escherichia coli. Three of these genes, aplA, aplB and aplC, are highly similar (over 90 \% identical) and fell within a tight phylogenetic cluster (Group I) consisting entirely of Geobacter homologues. Transcript levels for all three genes increased in response to acetate limitation. The fourth gene, aplD, is phylogenetically distinct (Group II) and its expression was not influenced by acetate availability. Deletion of any one of the three genes in Group I did not significantly affect acetate-dependent growth, suggesting functional redundancy. Attempts to recover mutants in which various combinations of two of these genes were deleted were unsuccessful, suggesting that at least two of these three transporter genes are required to support growth. Closely related Group I apl genes were found in the genomes of other Geobacter species whose genome sequences are available. Furthermore, related genes could be detected in genomic DNA extracted from a subsurface environment undergoing in situ uranium bioremediation. The transporter genes recovered from the subsurface were most closely related to Group I apl genes found in the genomes of cultured Geobacter species that were isolated from contaminated subsurface environments. The increased expression of these genes in response to acetate limitation, their high degree of conservation among Geobacter species and the ease with which they can be detected in environmental samples suggest that Group I apl genes of the Geobacteraceae may be suitable biomarkers for acetate limitation. Monitoring the expression of these genes could aid in the design of strategies for acetate-mediated in situ bioremediation of uranium-contaminated groundwater.}, keywords = {Acetates, Biodegradation, Environmental, DNA, Bacterial, Escherichia coli, Escherichia coli Proteins, Gene Deletion, Gene Expression, Genes, Bacterial, Genome, Bacterial, Geobacter, Membrane Transport Proteins, Phylogeny, Uranium}, issn = {1350-0872}, doi = {10.1099/mic.0.2008/017244-0}, author = {Risso, Carla and Meth{\'e}, Barbara A and Elifantz, Hila and Holmes, Dawn E and Lovley, Derek R} } @article {507, title = {Heat-shock sigma factor RpoH from Geobacter sulfurreducens.}, journal = {Microbiology}, volume = {153}, year = {2007}, month = {2007 Mar}, pages = {838-46}, abstract = {Recent studies with Myxococcus xanthus have suggested that homologues of the Escherichia coli heat-shock sigma factor, RpoH, may not be involved in the heat-shock response in this delta-proteobacterium. The genome of another delta-proteobacterium, Geobacter sulfurreducens, which is considered to be a representative of the Fe(III)-reducing Geobacteraceae that predominate in a diversity of subsurface environments, contains an rpoH homologue. Characterization of the G. sulfurreducens rpoH homologue revealed that it was induced by a temperature shift from 30 degrees C to 42 degrees C and that an rpoH-deficient mutant was unable to grow at 42 degrees C. The predicted heat-shock genes, hrcA, grpE, dnaK, groES and htpG, were heat-shock inducible in an rpoH-dependent manner, and comparison of promoter regions of these genes identified the consensus sequences for the -10 and -35 promoter elements. In addition, DNA elements identical to the CIRCE consensus sequence were found in promoters of rpoH, hrcA and groES, suggesting that these genes are regulated by a homologue of the repressor HrcA, which is known to bind the CIRCE element. These results suggest that the G. sulfurreducens RpoH homologue is the heat-shock sigma factor and that heat-shock response in G. sulfurreducens is regulated positively by RpoH as well as negatively by the HrcA/CIRCE system.}, keywords = {Adaptation, Physiological, Base Sequence, Binding Sites, Consensus Sequence, DNA, Bacterial, Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Heat-Shock Proteins, Hot Temperature, Molecular Sequence Data, Promoter Regions, Genetic, RNA, Bacterial, RNA, Messenger, Sigma Factor, Transcription, Genetic}, issn = {1350-0872}, doi = {10.1099/mic.0.2006/000638-0}, author = {Ueki, Toshiyuki and Lovley, Derek R} } @article {523, title = {Harvesting energy from the marine sediment-water interface II. Kinetic activity of anode materials.}, journal = {Biosens Bioelectron}, volume = {21}, year = {2006}, month = {2006 May 15}, pages = {2058-63}, abstract = {Here, we report a comparative study on the kinetic activity of various anodes of a recently described microbial fuel cell consisting of an anode imbedded in marine sediment and a cathode in overlying seawater. Using plain graphite anodes, it was demonstrated that a significant portion of the anodic current results from oxidation of sediment organic matter catalyzed by microorganisms colonizing the anode and capable of directly reducing the anode without added exogenous electron-transfer mediators. Here, graphite anodes incorporating microbial oxidants are evaluated in the laboratory relative to plain graphite with the goal of increasing power density by increasing current density. Anodes evaluated include graphite modified by adsorption of anthraquinone-1,6-disulfonic acid (AQDS) or 1,4-naphthoquinone (NQ), a graphite-ceramic composite containing Mn2+ and Ni2+, and graphite modified with a graphite paste containing Fe3O4 or Fe3O4 and Ni2+. It was found that these anodes possess between 1.5- and 2.2-fold greater kinetic activity than plain graphite. Fuel cells were deployed in a coastal site near Tuckerton, NJ (USA) that utilized two of these anodes. These fuel cells generated ca. 5-fold greater current density than a previously characterized fuel cell equipped with a plain graphite anode, and operated at the same site.}, keywords = {Electrochemistry, Electrodes, Energy-Generating Resources, Ferumoxytol, Geologic Sediments, Kinetics, Oceans and Seas, Seawater}, issn = {0956-5663}, doi = {10.1016/j.bios.2006.01.033}, author = {Lowy, Daniel A and Tender, Leonard M and Zeikus, J Gregory and Park, Doo Hyun and Lovley, Derek R} } @article {580, title = {Harnessing microbially generated power on the seafloor.}, journal = {Nat Biotechnol}, volume = {20}, year = {2002}, month = {2002 Aug}, pages = {821-5}, abstract = {In many marine environments, a voltage gradient exists across the water sediment interface resulting from sedimentary microbial activity. Here we show that a fuel cell consisting of an anode embedded in marine sediment and a cathode in overlying seawater can use this voltage gradient to generate electrical power in situ. Fuel cells of this design generated sustained power in a boat basin carved into a salt marsh near Tuckerton, New Jersey, and in the Yaquina Bay Estuary near Newport, Oregon. Retrieval and analysis of the Tuckerton fuel cell indicates that power generation results from at least two anode reactions: oxidation of sediment sulfide (a by-product of microbial oxidation of sedimentary organic carbon) and oxidation of sedimentary organic carbon catalyzed by microorganisms colonizing the anode. These results demonstrate in real marine environments a new form of power generation that uses an immense, renewable energy reservoir (sedimentary organic carbon) and has near-immediate application.}, keywords = {Bacteria, Bioelectric Energy Sources, Biotechnology, Carbon, Conservation of Energy Resources, DNA, Ribosomal, Electricity, Electrodes, Environmental Microbiology, Geologic Sediments, Molecular Sequence Data, New Jersey, Oceans and Seas, Oregon, Oxidation-Reduction, RNA, Bacterial, RNA, Ribosomal, 16S, Sulfides}, issn = {1087-0156}, doi = {10.1038/nbt716}, author = {Tender, Leonard M and Reimers, Clare E and Stecher, Hilmar A and Holmes, Dawn E and Bond, Daniel R and Lowy, Daniel A and Pilobello, Kanoelani and Fertig, Stephanie J and Lovley, Derek R} } @article {589, title = {A hydrogen-based subsurface microbial community dominated by methanogens.}, journal = {Nature}, volume = {415}, year = {2002}, month = {2002 Jan 17}, pages = {312-5}, abstract = {The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90\% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth{\textquoteright}s subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.}, keywords = {Bacteria, DNA, Archaeal, DNA, Bacterial, Ecosystem, Euryarchaeota, Exobiology, Hydrogen, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Water Microbiology}, issn = {0028-0836}, doi = {10.1038/415312a}, author = {Chapelle, Francis H and O{\textquoteright}Neill, Kathleen and Bradley, Paul M and Meth{\'e}, Barbara A and Ciufo, Stacy A and Knobel, LeRoy L and Lovley, Derek R} }