The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features

Energetically exploiting lignocellulose-rich residues in anaerobic digestion technologies: from bioreactors to proteogenomics

The biogas produced through anaerobic digestion (AD) of renewable feedstocks is one of the promising alternatives to replace fossil-derived energy. Even though lignocellulosic biomass is the most abundant biomass on earth, only a small fraction is being used towards resources recovery, leaving a great potential unexploited. In this study, the combination of state-of-art genomic techniques and engineered systems were used to further advance the knowledge on biogas production from lignocellulosic-rich residues and the microbiome involved in the anaerobic digestion hereof. A long-term adapted anaerobic microbiome capable of degrading wheat straw as the sole substrate was investigated using protein stable isotope probing (protein-SIP). The results indicated that a diverse microbial community, primarily composed of Firmicutes and Methanogens, played crucial roles in cellulose degradation and methane production. Notably, Defluviitoga tunisiensis, Syntrophothermus lipocalidus, and Pelobacter carbinolicus were identified as direct metabolizers of cellulose, while Dehalobacterium assimilated labelled carbon through cross-feeding. This study provides direct evidence of primary cellulose degraders and sheds light on their genomic composition. By harnessing the potential of lignocellulosic biomass and understanding the microbial communities involved, we can promote sustainable biogas production, contributing to energy security and environmental preservation.

Fe(III) oxide microparticles modulate extracellular electron transfer in anodic biofilms dominated by bacteria of the Pelobacter genus

Exo-electrogenic microorganisms have been extensively studied for their ability to transfer electrons with solid surfaces using a large variety of metabolic pathways. Most of the studies on these microorganisms consist in the replacement of solid electron acceptors such as Fe(III) oxides found in nature by electrodes with the objective of generating harvestable current in devices such as microbial fuel cells. In this study we show how the presence of solid ferric oxide (Fe₂O₃) particles in the inoculum during bio-anode development influences extracellular electron transfer to the electrode. Amplification and sequencing of the 16S rRNA (V4-V5 region) show bacteria and archaea communities with a large predominance of the Pelobacter genus, which is known to be phylogenetically close to the Geobacter genus, regardless of the presence or absence of ferric oxide in the inoculum. Data indicate that the bacteria at the bio-anode surface can preferentially utilize solid ferric oxide as terminal electron acceptors instead of the anode, though extracellular electron transfer to the anode can be restored by removing the particles. Mixed inoculum commonly used to develop bioanodes may produce similar bacterial communities with divergent electrochemical responses due to the presence of alternate electron acceptors, with direct implications for microbial fuel cell performance.

Interspecies Formate Exchange Drives Syntrophic Growth of Syntrophotalea carbinolica and Methanococcus maripaludis

The complete remineralization of organic matter in anoxic environments relies on communities of microorganisms that ferment organic acids and alcohols to CH₄. This is accomplished through syntrophic association of H₂ or formate producing bacteria and methanogenic archaea, where exchange of these intermediates enables growth of both organisms. While these communities are essential to Earth's carbon cycle, our understanding of the dynamics of H₂ or formate exchanged is limited. Here, we establish a model partnership between Syntrophotalea carbinolica and Methanococcus maripaludis. Through sequencing a transposon mutant library of M. maripaludis grown with ethanol oxidizing S. carbinolica, we found that genes encoding the F₄₂₀-dependent formate dehydrogenase (Fdh) and F₄₂₀-dependent methylene-tetrahydromethanopterin dehydrogenase (Mtd) are important for growth. Competitive growth of M. maripaludis mutants defective in either H₂ or formate metabolism verified that, across multiple substrates, interspecies formate exchange was dominant in these communities. Agitation of these cultures to facilitate diffusive loss of H₂ to the culture headspace resulted in an even greater competitive advantage for M. maripaludis strains capable of oxidizing formate. Finally, we verified that an M. maripaludis Δmtd mutant had a defect during syntrophic growth. Together, these results highlight the importance of formate exchange for the growth of methanogens under syntrophic conditions. IMPORTANCE In the environment, methane is typically generated by fermentative bacteria and methanogenic archaea working together in a process called syntrophy. Efficient exchange of small molecules like H₂ or formate is essential for growth of both organisms. However, difficulties in determining the relative contribution of these intermediates to methanogenesis often hamper efforts to understand syntrophic interactions. Here, we establish a model syntrophic coculture composed of S. carbinolica and the genetically tractable methanogen M. maripaludis. Using mutant strains of M. maripaludis that are defective for either H₂ or formate metabolism, we determined that interspecies formate exchange drives syntrophic growth of these organisms. Together, these results advance our understanding of the degradation of organic matter in anoxic environments.

Desulfuromonas sp. 'CSMB_57', isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals

One of the most abundant and ubiquitous taxa observed in eastern Australian coal seams is an uncultured Desulfuromonas species and part of the Coal Seam Microbiome dataset assigned as 'CSMB_57'. Despite this abundance and ubiquity, knowledge about this taxon is limited. The present study aimed to generate an enrichment culture of Desulfuromonas sp. 'CSMB_57' using culturing strategies that exploit its sulphur-reducing capabilities by utilizing a polysulfide solution in a liquid medium. Using dilution to extinction methods, a highly enriched culture was successfully generated. The full-length 16S rRNA sequence revealed that all closely related taxa were observed in subsurface environments suggesting that D. sp. 'CSMB_57' may be a subsurface specialist. Subsequently, the DNA from the enrichment culture was sequenced and the genome of D. sp. 'CSMB_57' was assembled. Genomic annotation revealed a high number of CRISPR arrays for viral defence, a large array of ABC transporters for amino acid and peptide uptake, as well as genes likely associated with syntrophy such as genes associated with type-IVa pilus, often used for direct interspecies electron transfer, and multiple hydrogenases capable of producing hydrogen. From the various genomic observations, a conceptual ecological model was developed that explores its possible syntrophic roles with hydrogenotrophic methanogens and acetogenic bacteria within coal-seam environments.

Shift of DNRA bacterial community composition in sediment cores of the Pearl River Estuary and the impact of environmental factors

Dissimilatory nitrate reduction to ammonia (DNRA) process, competing with denitrification and anaerobic ammonia oxidation (anammox) for nitrate, is an important nitrogen retention pathway in the environment. Previous studies on DNRA bacterial diversity and composition focused on the surface sediments in estuaries, but studies on the deep sediments are limited, and the linkage between DNRA community structure and complex estuarine environment remains unclear. In this study, through high-throughput sequencing of nrfA gene followed by high-resolution sample inference, we examined spatially and temporally the composition and diversity of DNRA bacteria along a salinity gradient in five sediment cores of the Pearl River Estuary (PRE). We found a higher diversity and richness of DNRA bacteria in sediments with lower organic carbon, where sea water intersects fresh water. Moreover, the DNRA bacterial communities had the specific spatially distribution coupling with their metabolic difference along the salinity gradient of the Pearl River Estuary, but no obvious difference along the sediment depth. The distribution of DNRA bacteria in the PRE was largely driven by various environmental factors, including salinity, Oxidation-Reduction Potential (ORP), ammonium, nitrate and C_org/NO₃^-. Furthermore, dominant DNRA bacteria were found to be the key populations of DNRA communities in the PRE sediments by network analysis. Collectively, our results showed that niche difference of DNRA bacteria indeed occurs in the Pearl River Estuary.

Understanding Choline Bioavailability and Utilization: First Step Toward Personalizing Choline Nutrition

Choline is an essential macronutrient involved in neurotransmitter synthesis, cell-membrane signaling, lipid transport, and methyl-group metabolism. Nevertheless, the vast majority are not meeting the recommended intake requirement. Choline deficiency is linked to nonalcoholic fatty liver disease, skeletal muscle atrophy, and neurodegenerative diseases. The conversion of dietary choline to trimethylamine by gut microbiota is known for its association with atherosclerosis and may contribute to choline deficiency. Choline-utilizing bacteria constitutes less than 1% of the gut community and is modulated by lifestyle interventions such as dietary patterns, antibiotics, and probiotics. In addition, choline utilization is also affected by genetic factors, further complicating the impact of choline on health. This review overviews the complex interplay between dietary intakes of choline, gut microbiota and genetic factors, and the subsequent impact on health. Understanding of gut microbiota metabolism of choline substrates and interindividual variability is warranted in the development of personalized choline nutrition.

Simultaneous Genome Sequencing of Prosthecochloris ethylica and Desulfuromonas acetoxidans within a Syntrophic Mixture Reveals Unique Pili and Protein Interactions

Strains of Chloropseudomonas ethylica, 2-K, N2, and N3 are known to be composed of a syntrophic mixture of a green sulfur bacterium and a sulfur-reducing colorless component. Upon sequence analysis, the green sulfur photosynthetic bacterial component of strain N3 was dominant and was readily sequenced, but the less abundant sulfur-reducing bacterial component was apparent only when analyzed by metagenomic binning. Whole-genome comparison showed that the green bacterium belonged to the genus Prosthecochloris and apparently was a species for which there was no genome sequence on file. For comparison, we also sequenced the genome of Prosthecochloris sp. DSM 1685, which had previously been isolated from the 2-K mixture in pure culture and have shown that all three Prosthecochloris genomes belong to a new species, which we propose to be named Prosthecochloris ethylica comb. nov. Whole genomes were also sequenced for the isolated Desulfuromonas strains DSM 1675 (from strain 2-K) and DSM 1676 (from strain N2) and shown to be nearly identical to the genome found in the N3 mixture. The genome of the green sulfur bacterium contains large genes for agglutination proteins, similar to the ones proposed to be involved in larger photosynthetic consortia of Chlorochromatium aggregatum. In addition, we also identified several unique “tight adhesion (tad)” pili genes that are presumably involved in the formation of cell–cell interactions. The colorless component, on the other hand, contained a unique large multiheme cytochrome C and unique genes for e-pili (geopilin) formation, genetically clustered with a conserved ferredoxin gene, which are all expected to play an electron transfer role in the closed sulfur cycle in the syntrophic mixture. The findings from the simultaneous genome sequencing of the components of Cp. ethylica have implications for the phenomenon of direct interspecies interactions and coupled electron transfer in photosynthetic symbionts. The mechanisms for such interactions appear to be more common in the environment than originally anticipated.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO2, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.

Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut

The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut. We centre on several key methodological aspects for identifying the TMA-producing bacteria and report how these pathways can be identified in human gut microbiota through bioinformatics analysis of available bacterial genomes and gut metagenomes.

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment

Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope probing with high throughput sequencing of 16S rRNA genes and ¹³C₂-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm incubation with ¹³C₂-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. Together, our data provide a new insight on the diversity of choline utilizing organisms in coastal sediments and support a syntrophic relationship between Bacteria and Archaea as the dominant route for methanogenesis from choline in this environment.

Jellyfish Life Stages Shape Associated Microbial Communities, While a Core Microbiome Is Maintained Across All

The key to 650 million years of evolutionary success in jellyfish is adaptability: with alternating benthic and pelagic generations, sexual and asexual reproductive modes, multitudes of body forms and a cosmopolitan distribution, jellyfish are likely to have established a plenitude of microbial associations. Here we explored bacterial assemblages in the scyphozoan jellyfish Chrysaora plocamia (Lesson 1832). Life stages involved in propagation through cyst formation, i.e., the mother polyp, its dormant cysts (podocysts), and polyps recently excysted (excysts) from podocysts – were investigated. Associated bacterial assemblages were assessed using MiSeq Illumina paired-end tag sequencing of the V1V2 region of the 16S rRNA gene. A microbial core-community was identified as present through all investigated life stages, including bacteria with closest relatives known to be key drivers of carbon, nitrogen, phosphorus, and sulfur cycling. Moreover, the fact that half of C. plocamia’s core bacteria were also present in life stages of the jellyfish Aurelia aurita, suggests that this bacterial community might represent an intrinsic characteristic of scyphozoan jellyfish, contributing to their evolutionary success.

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition

Sediment bacterial communities play a critical role in biogeochemical cycling in lotic ecosystems. Despite their ecological significance, the effects of urban discharge on spatiotemporal distribution of bacterial communities are understudied. In this study, we examined the effect of urban discharge on the spatiotemporal distribution of stream sediment bacteria in a northeast Ohio stream. Water and sediment samples were collected after large storm events (discharge > 100 m) from sites along a highly impacted stream (Tinkers Creek, Cuyahoga River watershed, Ohio, USA) and two reference streams. Although alpha (α) diversity was relatively constant spatially, multivariate analysis of bacterial community 16S rDNA profiles revealed significant spatial and temporal effects on beta (β) diversity and community composition and identified a number of significant correlative abiotic parameters. Clustering of upstream and reference sites from downstream sites of Tinkers Creek combined with the dominant families observed in specific locales suggests that environmentally-induced species sorting had a strong impact on the composition of sediment bacterial communities. Distinct groupings of bacterial families that are often associated with nutrient pollution (i.e., Comamonadaceae, Rhodobacteraceae, and Pirellulaceae) and other contaminants (i.e., Sphingomonadaceae and Phyllobacteriaceae) were more prominent at sites experiencing higher degrees of discharge associated with urbanization. Additionally, there were marked seasonal changes in community composition, with individual taxa exhibiting different seasonal abundance patterns. However, spatiotemporal variation in stream conditions did not affect bacterial community functional profiles. Together, these results suggest that local environmental drivers and niche filtering from discharge events associated with urbanization shape the bacterial community structure. However, dispersal limitations and interactions among other species likely play a role as well.

A review on the bioenergetics of anaerobic microbial metabolism close to the thermodynamic limits and its implications for digestion applications

The exploration of the energetics of anaerobic digestion systems can reveal how microorganisms cooperate efficiently for cell growth and methane production, especially under low-substrate conditions. The establishment of a thermodynamically interdependent partnership, called anaerobic syntrophy, allows unfavorable reactions to proceed. Interspecies electron transfer and the concentrations of electron carriers are crucial for maintaining this mutualistic activity. This critical review summarizes the functional microorganisms and syntroph partners, particularly in the metabolic pathways and energy conservation of syntrophs. The kinetics and thermodynamics of propionate degradation to methane, reversibility of the acetate oxidation process, and estimation of microbial growth are summarized. The various routes of interspecies electron transfer, reverse electron transfer, and Poly-β-hydroxyalkanoate formation in the syntrophic community are also reviewed. Finally, promising and critical directions of future research are proposed. Fundamental insight in the activities and interactions involved in AD systems could serve as a guidance for engineered systems optimization and upgrade.

Acetylene Fuels TCE Reductive Dechlorination by Defined Dehalococcoides/Pelobacter Consortia

Acetylene (C2H2) can be generated in contaminated groundwater sites as a consequence of chemical degradation of trichloroethene (TCE) by in situ minerals, and C2H2 is known to inhibit bacterial dechlorination. In this study, we show that while high C2H2 (1.3 mM) concentrations reversibly inhibit reductive dechlorination of TCE by Dehalococcoides mccartyi isolates as well as enrichment cultures containing D. mccartyi sp., low C2H2 (0.4 mM) concentrations do not inhibit growth or metabolism of D. mccartyi. Cocultures of Pelobacter SFB93, a C2H2-fermenting bacterium, with D. mccartyi strain 195 or with D. mccartyi strain BAV1 were actively sustained by providing acetylene as the electron donor and carbon source while TCE or cis-DCE served as the electron acceptor. Inhibition by acetylene of reductive dechlorination and methanogenesis in the enrichment culture ANAS was observed, and the inhibition was removed by adding Pelobacter SFB93 into the consortium. Transcriptomic analysis of D. mccartyi strain 195 showed genes encoding for reductive dehalogenases (e.g., tceA) were not affected during the C2H2-inhibition, while genes encoding for ATP synthase, biosynthesis, and Hym hydrogenase were down-regulated during C2H2 inhibition, consistent with the physiological observation of lower cell yields and reduced dechlorination rates in strain 195. These results will help facilitate the optimization of TCE-bioremediation at contaminated sites containing both TCE and C2H2.

Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments

The fixation of dinitrogen (N₂) and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L⁻¹ d⁻¹ and from undetectable to 8.2 nmol N g⁻¹ d⁻¹ in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 μmol m⁻² d⁻¹ and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR) data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and oxygen concentration.

Degradation of acetaldehyde and its precursors by Pelobacter carbinolicus and P. acetylenicus

Pelobacter carbinolicus and P. acetylenicus oxidize ethanol in syntrophic cooperation with methanogens. Cocultures with Methanospirillum hungatei served as model systems for the elucidation of syntrophic ethanol oxidation previously done with the lost “Methanobacillus omelianskii” coculture. During growth on ethanol, both Pelobacter species exhibited NAD⁺-dependent alcohol dehydrogenase activity. Two different acetaldehyde-oxidizing activities were found: a benzyl viologen-reducing enzyme forming acetate, and a NAD⁺-reducing enzyme forming acetyl-CoA. Both species synthesized ATP from acetyl-CoA via acetyl phosphate. Comparative 2D-PAGE of ethanol-grown P. carbinolicus revealed enhanced expression of tungsten-dependent acetaldehyde: ferredoxin oxidoreductases and formate dehydrogenase. Tungsten limitation resulted in slower growth and the expression of a molybdenum-dependent isoenzyme. Putative comproportionating hydrogenases and formate dehydrogenase were expressed constitutively and are probably involved in interspecies electron transfer. In ethanol-grown cocultures, the maximum hydrogen partial pressure was about 1,000 Pa (1 mM) while 2 mM formate was produced. The redox potentials of hydrogen and formate released during ethanol oxidation were calculated to be E_H2 = -358±12 mV and E_HCOOH = -366±19 mV, respectively. Hydrogen and formate formation and degradation further proved that both carriers contributed to interspecies electron transfer. The maximum Gibbs free energy that the Pelobacter species could exploit during growth on ethanol was −35 to −28 kJ per mol ethanol. Both species could be cultivated axenically on acetaldehyde, yielding energy from its disproportionation to ethanol and acetate. Syntrophic cocultures grown on acetoin revealed a two-phase degradation: first acetoin degradation to acetate and ethanol without involvement of the methanogenic partner, and subsequent syntrophic ethanol oxidation. Protein expression and activity patterns of both Pelobacter spp. grown with the named substrates were highly similar suggesting that both share the same steps in ethanol and acetalydehyde metabolism. The early assumption that acetaldehyde is a central intermediate in Pelobacter metabolism was now proven biochemically.

Tn7

The bacterial transposon Tn7 is distinguished by the levels of control it displays over transposition and its capacity to utilize different kinds of target sites. Transposition is carried out using five transposon-encoded proteins, TnsA, TnsB, TnsC, TnsD, and TnsE, which facilitate transfer of the element while minimizing the chances of inactivating host genes by using two pathways of transposition. One of these pathways utilizes TnsD, which targets transposition into a single site found in bacteria ( attTn7 ), and a second utilizes TnsE, which preferentially directs transposition into plasmids capable of moving between bacteria. Control of transposition involves a heteromeric transposase that consists of two proteins, TnsA and TnsB, and a regulator protein TnsC. Tn7 also has the ability to inhibit transposition into a region already occupied by the element in a process called target immunity. Considerable information is available about the functional interactions of the Tn7 proteins and many of the protein–DNA complexes involved in transposition. Tn7-like elements that encode homologs of all five of the proteins found in Tn7 are common in diverse bacteria, but a newly appreciated larger family of elements appears to use the same core TnsA, TnsB, and TnsC proteins with other putative target site selector proteins allowing different targeting pathways.

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens

Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.

Prokaryotic carbonic anhydrases of Earth's environment

Carbonic anhydrase is a metalloenzyme catalyzing the reversible hydration of carbon dioxide to bicarbonate. Five independently evolved classes have been described for which one or more are found in nearly every cell type underscoring the general importance of this ubiquitous enzyme in Nature. The bulk of research to date has centered on the enzymes from mammals and plants with less emphasis on prokaryotes. Prokaryotic carbonic anhydrases play important roles in the ecology of Earth's biosphere including acquisition of CO2 for photosynthesis and the physiology of aerobic and anaerobic prokaryotes decomposing the photosynthate back to CO2 thereby closing the global carbon cycle. This review focuses on the physiology and biochemistry of carbonic anhydrases from prokaryotes belonging to the domains Bacteria and Archaea that play key roles in the ecology of Earth's biosphere.

Syntrophic growth with direct interspecies electron transfer as the primary mechanism for energy exchange

Direct interspecies electron transfer (DIET) through biological electrical connections is an alternative to interspecies H2 transfer as a mechanism for electron exchange in syntrophic cultures. However, it has not previously been determined whether electrons received via DIET yield energy to support cell growth. In order to investigate this, co-cultures of Geobacter metallireducens, which can transfer electrons to wild-type G. sulfurreducens via DIET, were established with a citrate synthase-deficient G. sulfurreducens strain that can receive electrons for respiration through DIET only. In a medium with ethanol as the electron donor and fumarate as the electron acceptor, co-cultures with the citrate synthase-deficient G. sulfurreducens strain metabolized ethanol as fast as co-cultures with wild-type, but the acetate that G. metallireducens generated from ethanol oxidation accumulated. The lack of acetate metabolism resulted in less fumarate reduction and lower cell abundance of G. sulfurreducens. RNAseq analysis of transcript abundance was consistent with a lack of acetate metabolism in G. sulfurreducens and revealed gene expression levels for the uptake hydrogenase, formate dehydrogenase, the pilus-associated c-type cytochrome OmcS and pili consistent with electron transfer via DIET. These results suggest that electrons transferred via DIET can serve as the sole energy source to support anaerobic respiration.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.

Proteins involved in electron transfer to Fe(III) and Mn(IV) oxides by Geobacter sulfurreducens and Geobacter uraniireducens

Whole-genome microarray analysis of Geobacter sulfurreducens grown on insoluble Fe(III) oxide or Mn(IV) oxide versus soluble Fe(III) citrate revealed significantly different expression patterns. The most upregulated genes, omcS and omcT, encode cell-surface c-type cytochromes, OmcS being required for Fe(III) and Mn(IV) oxide reduction. Other electron transport genes upregulated on both metal oxides included genes encoding putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc4 and Cbc5, periplasmic c-type cytochromes Dhc2 and PccF, outer membrane c-type cytochromes OmcC, OmcG and OmcV, multicopper oxidase OmpB, the structural components of electrically conductive pili, PilA-N and PilA-C, and enzymes that detoxify reactive oxygen/nitrogen species. Genes upregulated on Fe(III) oxide encode putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc3 and Cbc6, periplasmic c-type cytochromes, including PccG and PccJ, and outer membrane c-type cytochromes, including OmcA, OmcE, OmcH, OmcL, OmcN, OmcO and OmcP. Electron transport genes upregulated on Mn(IV) oxide encode periplasmic c-type cytochromes PccR, PgcA, PpcA and PpcD, outer membrane c-type cytochromes OmaB/OmaC, OmcB and OmcZ, multicopper oxidase OmpC and menaquinone-reducing enzymes. Genetic studies indicated that MacA, OmcB, OmcF, OmcG, OmcH, OmcI, OmcJ, OmcM, OmcV and PccH, the putative Cbc5 complex subunit CbcC and the putative Cbc3 complex subunit CbcV are important for reduction of Fe(III) oxide but not essential for Mn(IV) oxide reduction. Gene expression patterns for Geobacter uraniireducens were similar. These results demonstrate that the physiology of Fe(III)-reducing bacteria differs significantly during growth on different insoluble and soluble electron acceptors and emphasize the importance of c-type cytochromes for extracellular electron transfer in G. sulfurreducens.