@article {3052, title = {Microbe Profile: : a model for novel physiologies of biogeochemical and technological significance.}, journal = {Microbiology (Reading)}, volume = {168}, year = {2022}, month = {2022 Feb}, abstract = {

has served as the initial model for a substantial number of newly recognized microbial physiologies that play an important role in biogeochemical cycling of carbon, metals and nutrients. The strategies used by for microbial interaction with minerals, contaminants, other microbes and electrodes have led to new technologies for bioremediation, bioenergy conversion and the sustainable production of {\textquoteright}green{\textquoteright} electronics.

}, keywords = {Biodegradation, Environmental, Electron Transport, Geobacter, Microbial Interactions, Oxidation-Reduction}, issn = {1465-2080}, doi = {10.1099/mic.0.001138}, author = {Lovley, Derek R} } @article {3084, title = { Strains Expressing Poorly Conductive Pili Reveal Constraints on Direct Interspecies Electron Transfer Mechanisms.}, journal = {mBio}, volume = {9}, year = {2018}, month = {2018 Jul 10}, abstract = {

Cytochrome-to-cytochrome electron transfer and electron transfer along conduits of multiple extracellular magnetite grains are often proposed as strategies for direct interspecies electron transfer (DIET) that do not require electrically conductive pili (e-pili). However, physical evidence for these proposed DIET mechanisms has been lacking. To investigate these possibilities further, we constructed strain Aro-5, in which the wild-type pilin gene was replaced with the pilin gene that was previously shown to yield poorly conductive pili in strain Aro-5. strain Aro-5 did not reduce Fe(III) oxide and produced only low current densities, phenotypes consistent with expression of poorly conductive pili. Like strain Aro-5, strain Aro-5 displayed abundant outer surface cytochromes. Cocultures initiated with wild-type as the electron-donating strain and strain Aro-5 as the electron-accepting strain grew via DIET. However, Aro-5/ wild-type cocultures did not. Cocultures initiated with the Aro-5 strains of both species grew only when amended with granular activated carbon (GAC), a conductive material known to be a conduit for DIET. Magnetite could not substitute for GAC. The inability of the two Aro-5 strains to adapt for DIET in the absence of GAC suggests that there are physical constraints on establishing DIET solely through cytochrome-to-cytochrome electron transfer or along chains of magnetite. The finding that DIET is possible with electron-accepting partners that lack highly conductive pili greatly expands the range of potential electron-accepting partners that might participate in DIET. DIET is thought to be an important mechanism for interspecies electron exchange in natural anaerobic soils and sediments in which methane is either produced or consumed, as well as in some photosynthetic mats and anaerobic digesters converting organic wastes to methane. Understanding the potential mechanisms for DIET will not only aid in modeling carbon and electron flow in these geochemically significant environments but will also be helpful for interpreting meta-omic data from as-yet-uncultured microbes in DIET-based communities and for designing strategies to promote DIET in anaerobic digesters. The results demonstrate the need to develop a better understanding of the diversity of types of e-pili in the microbial world to identify potential electron-donating partners for DIET. Novel methods for recovering as-yet-uncultivated microorganisms capable of DIET in culture will be needed to further evaluate whether DIET is possible without e-pili in the absence of conductive materials such as GAC.

}, keywords = {Cytochromes, Electron Transport, Ferric Compounds, Fimbriae, Bacterial, Geobacter, Microbial Interactions, Oxidation-Reduction}, issn = {2150-7511}, doi = {10.1128/mBio.01273-18}, author = {Ueki, Toshiyuki and Nevin, Kelly P and Rotaru, Amelia-Elena and Wang, Li-Ying and Ward, Joy E and Woodard, Trevor L and 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 {3133, title = {Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.}, journal = {Nat Commun}, volume = {4}, year = {2013}, month = {2013}, pages = {2809}, abstract = {

Syntrophic associations are central to microbial communities and thus have a fundamental role in the global carbon cycle. Despite biochemical approaches describing the physiological activity of these communities, there has been a lack of a mechanistic understanding of the relationship between complex nutritional and energetic dependencies and their functioning. Here we apply a multi-omic modelling workflow that combines genomic, transcriptomic and physiological data with genome-scale models to investigate dynamics and electron flow mechanisms in the syntrophic association of Geobacter metallireducens and Geobacter sulfurreducens. Genome-scale modelling of direct interspecies electron transfer reveals insights into the energetics of electron transfer mechanisms. While G. sulfurreducens adapts to rapid syntrophic growth by changes at the genomic and transcriptomic level, G. metallireducens responds only at the transcriptomic level. This multi-omic approach enhances our understanding of adaptive responses and factors that shape the evolution of syntrophic communities.

}, keywords = {Adaptation, Biological, Biological Evolution, Electron Transport, Genome, Bacterial, Geobacter, Microbial Interactions, Models, Biological, Symbiosis, Transcriptome}, issn = {2041-1723}, doi = {10.1038/ncomms3809}, author = {Nagarajan, Harish and Embree, Mallory and Rotaru, Amelia-Elena and Shrestha, Pravin M and Feist, Adam M and Palsson, Bernhard {\O} and Lovley, Derek R and Zengler, Karsten} } @article {3141, title = {When is a microbial culture "pure"? Persistent cryptic contaminant escapes detection even with deep genome sequencing.}, journal = {mBio}, volume = {4}, year = {2013}, month = {2013 Mar 12}, pages = {e00591-12}, abstract = {

UNLABELLED: Geobacter sulfurreducens strain KN400 was recovered in previous studies in which a culture of the DL1 strain of G. sulfurreducens served as the inoculum in investigations of microbial current production at low anode potentials (-400 mV versus Ag/AgCl). Differences in the genome sequences of KN400 and DL1 were too great to have arisen from adaptive evolution during growth on the anode. Previous deep sequencing (80-fold coverage) of the DL1 culture failed to detect sequences specific to KN400, suggesting that KN400 was an external contaminant inadvertently introduced into the anode culturing system. In order to evaluate this further, a portion of the gene for OmcS, a c-type cytochrome that both KN400 and DL1 possess, was amplified from the DL1 culture. HiSeq-2000 Illumina sequencing of the PCR product detected the KN400 sequence, which differs from the DL1 sequence at 14 bp, at a frequency of ca. 1 in 10(5) copies of the DL1 sequence. A similar low frequency of KN400 was detected with quantitative PCR of a KN400-specific gene. KN400 persisted at this frequency after intensive restreaking of isolated colonies from the DL1 culture. However, a culture in which KN400 could no longer be detected was obtained by serial dilution to extinction in liquid medium. The KN400-free culture could not grow on an anode poised at -400 mV. Thus, KN400 cryptically persisted in the culture dominated by DL1 for more than a decade, undetected by even deep whole-genome sequencing, and was only fortuitously uncovered by the unnatural selection pressure of growth on a low-potential electrode.

IMPORTANCE: Repeated streaking of isolated colonies on solidified medium remains a common strategy for obtaining pure cultures, especially of difficult-to-cultivate microorganisms such as strict anaerobes. The results presented here demonstrate that verifying the purity of cultures obtained in this manner may be difficult because extremely rare variants can persist, undetectable with even deep genomic DNA sequencing. The only way to ensure that a culture is pure is to cultivate it from an initial single cell, which may be technically difficult for many environmentally significant microbes.

}, keywords = {Coinfection, Electrodes, Genes, Bacterial, Genotype, Geobacter, High-Throughput Nucleotide Sequencing, Microbial Interactions, Polymerase Chain Reaction}, issn = {2150-7511}, doi = {10.1128/mBio.00591-12}, author = {Shrestha, Pravin Malla and Nevin, Kelly P and Shrestha, Minita and Lovley, Derek R} } @article {404, title = {Interspecies electron transfer via hydrogen and formate rather than direct electrical connections in cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens.}, journal = {Appl Environ Microbiol}, volume = {78}, year = {2012}, month = {2012 Nov}, pages = {7645-51}, abstract = {

Direct interspecies electron transfer (DIET) is an alternative to interspecies H(2)/formate transfer as a mechanism for microbial species to cooperatively exchange electrons during syntrophic metabolism. To understand what specific properties contribute to DIET, studies were conducted with Pelobacter carbinolicus, a close relative of Geobacter metallireducens, which is capable of DIET. P. carbinolicus grew in coculture with Geobacter sulfurreducens with ethanol as the electron donor and fumarate as the electron acceptor, conditions under which G. sulfurreducens formed direct electrical connections with G. metallireducens. In contrast to the cell aggregation associated with DIET, P. carbinolicus and G. sulfurreducens did not aggregate. Attempts to initiate cocultures with a genetically modified strain of G. sulfurreducens incapable of both H(2) and formate utilization were unsuccessful, whereas cocultures readily grew with mutant strains capable of formate but not H(2) uptake or vice versa. The hydrogenase mutant of G. sulfurreducens compensated, in cocultures, with significantly increased formate dehydrogenase gene expression. In contrast, the transcript abundance of a hydrogenase gene was comparable in cocultures with that for the formate dehydrogenase mutant of G. sulfurreducens or the wild type, suggesting that H(2) was the primary electron carrier in the wild-type cocultures. Cocultures were also initiated with strains of G. sulfurreducens that could not produce pili or OmcS, two essential components for DIET. The finding that P. carbinolicus exchanged electrons with G. sulfurreducens via interspecies transfer of H(2)/formate rather than DIET demonstrates that not all microorganisms that can grow syntrophically are capable of DIET and that closely related microorganisms may use significantly different strategies for interspecies electron exchange.

}, keywords = {Coculture Techniques, Deltaproteobacteria, Electricity, Electron Transport, Electrons, Formates, Geobacter, Hydrogen, Microbial Interactions}, issn = {1098-5336}, doi = {10.1128/AEM.01946-12}, author = {Rotaru, Amelia-Elena and Shrestha, Pravin M and Liu, Fanghua and Ueki, Toshiyuki and Nevin, Kelly and Summers, Zarath M and Lovley, Derek R} } @article {431, title = {Direct exchange of electrons within aggregates of an evolved syntrophic coculture of anaerobic bacteria.}, journal = {Science}, volume = {330}, year = {2010}, month = {2010 Dec 3}, pages = {1413-5}, abstract = {Microbial consortia that cooperatively exchange electrons play a key role in the anaerobic processing of organic matter. Interspecies hydrogen transfer is a well-documented strategy for electron exchange in dispersed laboratory cultures, but cooperative partners in natural environments often form multispecies aggregates. We found that laboratory evolution of a coculture of Geobacter metallireducens and Geobacter sulfurreducens metabolizing ethanol favored the formation of aggregates that were electrically conductive. Sequencing aggregate DNA revealed selection for a mutation that enhances the production of a c-type cytochrome involved in extracellular electron transfer and accelerates the formation of aggregates. Aggregate formation was also much faster in mutants that were deficient in interspecies hydrogen transfer, further suggesting direct interspecies electron transfer.}, keywords = {Anaerobiosis, Bacterial Proteins, Biological Evolution, Culture Media, Cytochrome c Group, Electron Transport, Electrons, Ethanol, Fimbriae Proteins, Geobacter, Hydrogen, Microbial Consortia, Microbial Interactions, Mutation, Oxidation-Reduction, Selection, Genetic}, issn = {1095-9203}, doi = {10.1126/science.1196526}, author = {Summers, Zarath M and Fogarty, Heather E and Leang, Ching and Franks, Ashley E and Malvankar, Nikhil S and Lovley, Derek R} }