Search

Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5 were obtained from the metagenome of a cathode-associated community enriched within a microbial electrosynthesis system (MES). The draft genome sequences provide insight into the functional potential of these microorganisms within an MES and a foundation for future comparative analyses.

Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial taxa to capture electrons from a cathode and fix carbon. Yet the metabolic capacity of multispecies microbial communities on electrosynthetic biocathodes remains unknown. We assembled 13 genomes from a high-performing electroacetogenic culture, and mapped their transcriptional activity from a range of conditions. This allowed us to create a metabolic model of the primary community members (Acetobacterium, Sulfurospirillum, and Desulfovibrio). Acetobacterium was the primary carbon fixer, and a keystone member of the community. Based on transcripts upregulated near the electrode surface, soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were essential conduits for electron flow from the electrode into the electrosynthetic community. A nitrogenase gene cluster with an adjacent ferredoxin and one of two Rnf complexes within the genome of the Acetobacterium were also upregulated on the electrode. Nitrogenase is known to serve as a hydrogenase, thereby it would contribute to hydrogen production by the biocathode. Oxygenases of microaerobic members of the community throughout the cathode chamber, including Sulfurospirillum and Rhodobacteraceae, were expressed. While the reactors were maintained anaerobically, this gene expression would support anaerobic growth and thus electrosynthesis by scrubbing small amounts of O2 out of the reactor. These molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Microbial electrosynthesis is the biocathode-driven production of chemicals from CO2 and has the promise to be a sustainable, carbon-consuming technology. To date, microbial electrosynthesis of acetate, the first step in order to generate liquid fuels from CO2, has been characterized by low rates and yields. To improve performance, a previously established acetogenic biocathode was operated in semi-batch mode at a poised potential of -590 mV vs SHE for over 150 days beyond its initial development. Rates of acetate production reached a maximum of 17.25 mM day(-1) (1.04 g L(-1) d(-1)) with accumulation to 175 mM (10.5 g L(-1)) over 20 days. Hydrogen was also produced at high rates by the biocathode, reaching 100 mM d(-1) (0.2 g L(-1) d(-1)) and a total accumulation of 1164 mM (2.4 g L(-1)) over 20 days. Phylogenetic analysis of the active electrosynthetic microbiome revealed a similar community structure to what was observed during an earlier stage of development of the electroacetogenic microbiome. Acetobacterium spp. dominated the active microbial population on the cathodes. Also prevalent were Sulfurospirillum spp. and an unclassified Rhodobacteraceae. Taken together, these results demonstrate the stability, resilience, and improved performance of electrosynthetic biocathodes following long-term operation. Furthermore, sustained product formation at faster rates by a carbon-capturing microbiome is a key milestone addressed in this study that advances microbial electrosynthesis systems toward commercialization.

Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor stability and performance. Understanding why this organism is present and elucidating its genetic repertoire provide a genomic and ecological foundation for future studies where Sulfurospirillum are found, especially in electrode-associated communities. Metabolic comparisons and in-depth analysis of unique genes revealed potential ecological niche-specific capabilities within the Sulfurospirillum genus. The functional similarities common to all genomes, i.e., core genome, and unique gene clusters found only in a single genome were identified. Based upon 16S rRNA gene phylogenetic analysis and average nucleotide identity, the Sulfurospirillum draft genome was found to be most closely related to Sulfurospirillum cavolei. Characterization of the draft genome described herein provides pathway-specific details of the metabolic significance of the newly described Sulfurospirillum cavolei MES and, importantly, yields insight to the ecology of the genus as a whole. Comparison of eleven sequenced Sulfurospirillum genomes revealed a total of 6246 gene clusters in the pan-genome. Of the total gene clusters, 18.5% were shared among all eleven genomes and 50% were unique to a single genome. While most Sulfurospirillum spp. reduce nitrate to ammonium, five of the eleven Sulfurospirillum strains encode for a nitrous oxide reductase (nos) cluster with an atypical nitrous-oxide reductase, suggesting a utility for this genus in reduction of the nitrous oxide, and as a potential sink for this potent greenhouse gas.

The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack., IMPORTANCE While the Synechococcus/Prochlorococcus-type cyanobacteria are widely distributed in the world’s oceans, a subgroup has established its niche within marine sponge tissues. Recently, the first genome of sponge-associated cyanobacteria, “Candidatus Synechococcus spongiarum,” was described. The sequencing of three representatives of different clades within this cyanobacterial group has enabled us to investigate intraspecies diversity, as well as to give a more comprehensive understanding of the common symbiotic features that adapt “Ca. Synechococcus spongiarum” to its life within the sponge host.

A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic binning of a metagenome sequenced from a microbial electrosynthesis system (MES) actively producing acetate and hydrogen. The genome contains the nosZDFLY genes, which are involved in nitrous oxide reduction, suggesting the potential role of this strain in denitrification.

Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (∼ 5). Hydrogen production by biocathodes poised at -600 mV vs. SHE increased >100-fold and acetate production ceased at acidic pH, but ∼ 5-15 mM (catholyte volume)/day acetate and >1,000 mM/day hydrogen were attained at pH ∼ 6.5 following repeated exposure to acidic pH. Cyclic voltammetry revealed a 250 mV decrease in hydrogen overpotential and a maximum current density of 12.2 mA/cm2 at -765 mV (0.065 mA/cm2 sterile control at -800 mV) by the Acetobacterium-dominated community. Supplying -800 mV to the microbiome after repeated exposure to acidic pH resulted in up to 2.6 kg/m3/day hydrogen (≈ 2.6 gallons gasoline equivalent), 0.7 kg/m3/day formate, and 3.1 kg/m3/day acetate ( = 4.7 kg CO2 captured).

The demand for chemicals and fuels will continue to grow simultaneously with the costly requirement to treat solid waste, wastewater, and regarding climate change, carbon dioxide. A dual benefit is at hand if waste could be converted to valuable chemicals. The application of stable chemical producing microbiomes adapted to these waste streams may turn this challenge into an opportunity.

The demand for chemicals and fuels will continue to grow simultaneously with the costly requirement to treat solid waste, wastewater, and regarding climate change, carbon dioxide. A dual benefit is at hand if waste could be converted to valuable chemicals. The application of stable chemical producing microbiomes adapted to these waste streams may turn this challenge into an opportunity.

A microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at −590 mV versus the standard hydrogen electrode (SHE) with CO 2 as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariant Archaea population of Methanobacterium spp. and a shifting Bacteria population. Acetobacterium spp. were the most abundant Bacteria on the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from −1 (per cathode liquid volume) and was concomitantly produced with acetate and hydrogen. Acetogenesis increased to >4 mM day −1 (accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to >11 mM day −1 (versus 0.045 mM day −1 abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of −460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility.

The search for microorganisms that are capable of catalyzing the reduction of an electrode within a fuel cell has primarily been focused on bacteria that operate mesobiotically. Bacteria that function optimally under extreme conditions are beginning to be examined because they may serve as more effective catalysts (higher activity, greater stability, longer life, capable of utilizing a broader range of fuels) in microbial fuel cells. An examination of marine sediment from temperate waters (Charleston, SC) proved to be a good source of thermophilic electrode-reducing bacteria. Electric current normalized to the surface area of graphite electrodes was approximately ten times greater when sediment fuel cells were incubated at 60 degrees C (209 to 254 mA/m(2)) vs 22 degrees C (10 to 22 mA/m(2)). Electricity-generating communities were selected in sediment fuel cells and then maintained without sediment or synthetic electron-carrying mediators in single-chambered fuel cells. Current was generated when cellulose or acetate was added as a substrate to the cells. The 16S ribosomal ribonucleic acid genes from the heavy biofilms that formed on the graphite anodes of acetate-fed fuel cells were cloned and sequenced. The preponderance of the clones (54 of 80) was most related to a Gram-positive thermophile, Thermincola carboxydophila (99% similarity). The remainder of clones from the community was most related to T. carboxydophila, or uncultured Firmicutes and Deferribacteres. Overall, the data indicate that temperate aquatic sediments are a good source of thermophilic electrode-reducing bacteria.

Microbial fuel cells (MFCs) are bioelectrochemical devices capable of converting chemical energy to electrical energy using bacteria as the catalysts. Mechanisms of microbial electron transfer to solid electrode surfaces are not well defined in most electrochemically-active microorganisms, particularly for Gram-positive bacteria. In this study, we investigated the electrochemical characteristics of the Gram-positive, thermophilic bacterium Thermincola ferriacetica strain Z-0001. This organism was capable of transferring electrons from acetate to the anode of an MFC to generate an electric current. T. ferriacetica exhibited rapid recovery of current following medium exchanges, recovering to near-maximum current output in less than three hours. The recovery of electrons from acetate was 97% in air-cathode MFCs inoculated with T. ferriacetica. Further insights into the anode reduction by these biofilms were gained through cyclic voltammetry (CV). A continuous steady-state current was reached above −0.1 V vs.Ag/AgCl reference electrode in CV scans of an established T. ferriacetica biofilm. A catalytic wave with a midpoint potential consistently near −0.28 V indicated a continuous electron-transporting interface between the attached microbial biofilm and the electrode surface. Additionally, no significant peaks were observed when scanning cell-free spent medium from active MFCs. These data suggest that T. ferriacetica directly transfers electrons to an electrode through a mechanism that is tightly associated with the biofilm that forms on the electrode. This is the first mechanistic insight into how Gram-positive extracellular electron transfer might occur without the addition of soluble electron shuttling mediators. These mechanistic evaluations will be essential for the improvement and application of such biocatalysts in microbial fuel cells and other bioelectrochemical systems.