Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium.

We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation

Novel syntrophic populations dominate an ammonia-tolerant methanogenic microbiome

Biogas reactors operating with protein-rich substrates have high methane potential and industrial value; however, they are highly susceptible to process failure because of the accumulation of ammonia. High ammonia levels cause a decline in acetate-utilizing methanogens and instead promote the conversion of acetate via a two-step mechanism involving syntrophic acetate oxidation (SAO) to H2 and CO2, followed by hydrogenotrophic methanogenesis. Despite the key role of syntrophic acetate-oxidizing bacteria (SAOB), only a few culturable representatives have been characterized. Here we show that the microbiome of a commercial, ammonia-tolerant biogas reactor harbors a deeply branched, uncultured phylotype (unFirm_1) accounting for approximately 5% of the 16S rRNA gene inventory and sharing 88% 16S rRNA gene identity with its closest characterized relative. Reconstructed genome and quantitative metaproteomic analyses imply unFirm_1’s metabolic dominance and SAO capabilities, whereby the key enzymes required for acetate oxidation are among the most highly detected in the reactor microbiome. While culturable SAOB were identified in genomic analyses of the reactor, their limited proteomic representation suggests that unFirm_1 plays an important role in channeling acetate toward methane. Notably, unFirm_1-like populations were found in other high-ammonia biogas installations, conjecturing a broader importance for this novel clade of SAOB in anaerobic fermentations

Better, Faster, Stronger: Evolving Geobacter Species For Enhanced Capabilities

The bacterial family of Geobacteraceae is comprised of many members including both Geobacter and Pelobacterspecies. The Geobacteraceae are the predominant Fe(III) reducing organisms in the subsurface due to their capacity for extracellular electron transfer, and play an important role in both the carbon and iron cycles in sedimentary environments. Their metal reducing capabilities can be applied to groundwater bioremediation and to the production of electrical current in microbial fuel cells. Although many members of this family are well known for their novel electron transfer mechanisms, there are also species that are capable of syntrophic growth, coupling the oxidation of certain organics with the production of byproducts, which in turn support the growth of partner microbes. It is a rare occurrence that a pure culture is applied for use in a large-scale bioreactor or in the sediment during in situ bioremediation. That being true, the study of the Geobacteraceae in pure culture and in microbial communities has far reaching significance. Laboratory evolution techniques were used to determine whether Geobacter species could evolve enhanced fitness in novel environments within a laboratory setting, offering insight into how these versatile microbes change with their environments. G. sulfurreducens was adapted for enhanced growth on lactate as a novel carbon and energy source, and the metabolic, regulatory, and genomic changes due to this adaptation were documented. Enhanced growth on lactate could be applied to the bioremediation of harmful metal contaminants by offering a more efficient and cost effective growth substrate relative to the current one used to stimulate the growth of Geobacter species in the subsurface. Laboratory adaptation techniques were also used to determine whether two differentGeobacter species could grow together in coculture, and by what mechanisms the two species would interact. This latter study advances the field of interspecies electron transfer, by offering a novel mechanism of electron transfer between microbial cells. This is relevant to the mechanisms that may be used in situ, such as in biofilms, microbial mats, or wastewater granules

Better, faster, stronger: Evolving Geobacter species for enhanced capabilities

The bacterial family of Geobacteraceae is comprised of many members including both Geobacter and Pelobacter species. The Geobacteraceae are the predominant Fe(III) reducing organisms in the subsurface due to their capacity for extracellular electron transfer, and play an important role in both the carbon and iron cycles in sedimentary environments. Their metal reducing capabilities can be applied to groundwater bioremediation and to the production of electrical current in microbial fuel cells. Although many members of this family are well known for their novel electron transfer mechanisms, there are also species that are capable of syntrophic growth, coupling the oxidation of certain organics with the production of byproducts, which in turn support the growth of partner microbes. It is a rare occurrence that a pure culture is applied for use in a large-scale bioreactor or in the sediment during in situ bioremediation. That being true, the study of the Geobacteraceae in pure culture and in microbial communities has far reaching significance. Laboratory evolution techniques were used to determine whether Geobacter species could evolve enhanced fitness in novel environments within a laboratory setting, offering insight into how these versatile microbes change with their environments. G. sulfurreducens was adapted for enhanced growth on lactate as a novel carbon and energy source, and the metabolic, regulatory, and genomic changes due to this adaptation were documented. Enhanced growth on lactate could be applied to the bioremediation of harmful metal contaminants by offering a more efficient and cost effective growth substrate relative to the current one used to stimulate the growth of Geobacter species in the subsurface. Laboratory adaptation techniques were also used to determine whether two different Geobacter species could grow together in coculture, and by what mechanisms the two species would interact. This latter study advances the field of interspecies electron transfer, by offering a novel mechanism of electron transfer between microbial cells. This is relevant to the mechanisms that may be used in situ, such as in biofilms, microbial mats, or wastewater granules

Microbial Electrosynthesis:Feeding Microbes Electricity to Convert carbon Dioxide and Water to Multi Carbon Extracellular Organic Compounds

The possibility of providing the acetogenic microorganism Sporomusa ovata with electrons delivered directly to the cells with a graphite electrode for the reduction of carbon dioxide to organic compounds was investigated. Biofilms of S. ovata growing on graphite cathode surfaces consumed electrons with the reduction of carbon dioxide to acetate and small amounts of 2-oxobutyrate. Electrons appearing in these products accounted for over 85% of the electrons consumed. These results demonstrate that microbial production of multicarbon organic compounds from carbon dioxide and water with electricity as the energy source is feasible. Importance Reducing carbon dioxide to multicarbon organic chemicals and fuels with electricity has been identified as an attractive strategy to convert solar energy that is harvested intermittently with photovoltaic technology and store it as covalent chemical bonds. The organic compounds produced can then be distributed via existing infrastructure. Nonbiological electrochemical reduction of carbon dioxide has proven problematic. The results presented here suggest that microbiological catalysts may be a robust alternative, and when coupled with photovoltaics, current-driven microbial carbon dioxide reduction represents a new form of photosynthesis that might convert solar energy to organic products more effectively than traditional biomass-based strategies

Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Co-Culture of Anaerobic Bacteria

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

Interspecies electron transfer via H2 and formate rather than direct electrical connections in co-cultures of Pelobacter carbinolicus and Geobacter sulfurreducens

Direct interspecies electron transfer (DIET) is an alternative to interspecies H2/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 co-culture with Geobacter sulfurreducens with ethanol as electron donor and fumarate as 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 co-cultures with a genetically modified strain of G. sulfurreducens incapable of both H2 and formate utilization were unsuccessful, whereas co-cultures readily grew with mutant strains capable of formate but not H2 uptake, or vice-versa. The hydrogenase mutant of G. sulfurreducens compensated, in co-cultures, with significantly increased formate-dehydrogenase gene expression. In contrast, the transcript abundance of a hydrogenase gene was comparable in co-cultures with the formate dehydrogenase mutant of G. sulfurreducens or wild-type, suggesting that H2 was the primary electron carrier in the wild-type co-cultures. Co-cultures 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 H2/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

Transcriptomic and genetic analysis of direct Interspecies electron transfer

The possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H2 interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in co-cultures in which Geobacter sulfurreducens was the electron-accepting partner for either Geobacter metallireducens, which performs DIET, or Pelobacter carbinolicus, which relies on HIT. Transcript abundance for G. sulfurreducens uptake hydrogenase genes were 7-fold lower in co-cultures with G. metallireducens than with P. carbinolicus, consistent with DIET and HIT, respectively, in the two co-cultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET, but not HIT, was 240-fold higher in the co-cultures with G. metallireducens than with P. carbinolicus. The pilin gene pilA was moderately expressed despite a mutation that might be expected to repress pilA expression. Lower transcript abundance for G. sulfurreducens genes associated with acetate metabolism in the co-cultures with P. carbinolicus was consistent with repression of these genes by the H2 during HIT. Genes for biogenesis of pili and flagella and several c-type cytochrome genes were among the most highly expressed in G. metallireducens. Mutant strains that lacked the ability to produce pili or flagella or outer-surface c-type cytochrome Gmet_2896 were not able to form co-cultures with G. sulfurreducens. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more complex environments

Interspecies Electron Transfer via Hydrogen and Formate Rather than Direct Electrical Connections in Cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens

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