Metabolism of methanogens

Leafcutter ants enhance microbial drought resilience in tropical forest soil

We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El-Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post-drought the microbiomes were similar to pre-drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post-drought. Drought increased CH4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH4 emissions in some soil types. CH4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.

Tracking investigation of archaeal composition and methanogenesis function from parental to offspring pigs

Archaea play a crucial role in microbial systems, including driving biochemical reactions and affecting host health by producing methane through hydrogen. The study of swine gut archaea has a positive significance in reducing methane emissions and improving feed utilization efficiency. However, the development and functional changes of archaea in the pig intestines have been overlooked for a long time. In this study, 54 fecal samples were collected from 36 parental pigs (18 boars and 18 pregnant/lactating sows), and 108 fecal samples from 18 offspring pigs during lactation, nursery, growing, and finishing stages were tracked and collected for metagenomic sequencing. We obtained 14 archaeal non-redundant metagenome-assembled genomes (MAGs). These archaea were classified as Methanobacteriota and Thermoplasmatota at the phylum level, and Methanobrevibacter, Methanosphaera, MX-02, and UBA71 at the genus level, involving hydrogenotrophic, methylotrophic, and acetoclastic pathways. The hydrogenotrophic pathway dominated the methanogenesis function, and the vast majority of archaea participated in it. Dietary changes profoundly affected the archaeal composition and methanogenesis function in pigs. The abundance of hydrogen-producing bacteria in parental pigs fed high-fiber diets was higher than that in offspring pigs fed low-fiber diets. The methanogenesis function was positively correlated with fiber decomposition functions and negatively correlated with the starch decomposition function. Increased abundance of sulfate reductase and fumarate reductase, as well as decreased acetate/propionate ratio, indicated that the upregulation of alternative hydrogen uptake pathways competing with methanogens may be the reason for the reduced methanogenesis function. These findings contribute to providing information and direction in the pig industry for the development of strategies to reduce methane emissions, improve feed efficiency, and maintain intestinal health.

Assessment of rapid initiators and long-lasting nutrients for developing biological permeable reactive barriers to treat mine-contaminated groundwater

The formation of mine-contaminated groundwater as a result of acidic mine drainage from the oxidation of sulfur-containing minerals entering the groundwater. Biological permeable reactive barrier (Bio-PRB) technology is excellent for the remediation of mine-contaminated groundwater. Usually, the organic substrates utilized in Bio-PRB are a combination of rapid initiators, which are readily bioavailable, and long-lasting nutrients, which are more difficult to degrade. Herein, we investigated the effectiveness of three rapid initiators and three long-lasting nutrients to remove sulfate from simulated mine-contaminated groundwater via simulated column experiments. The rapid initiators comprised crude glycerol, sodium acetate, and industrial syrup (IS), and the long-lasting nutrients included biodiesel emulsified oil, soybean oil emulsified oil, and high-carbon alcohol emulsified oil (HO). Microorganisms were stimulated using IS to create a sulfate reduction system owing to its high total organic carbon content (24.30 g L-1), achieving optimal sulfate removal rate (1.69 mmol dm-3 d-1). The fastest (2.93 mmol dm-3 d-1) and highest (88%) sulfate removal rates were achieved using HO, which is probably associated with the ability of HO to provide the most suitable C/N ratio (111.75) and induce the growth of sulfate-reducing bacteria (SRB) for substrate degradation. Conversely, a high concentration of sulfate reduction products inhibited SRB growth in the HO column. The addition of organic materials promoted SRB growth and various organic substrate-degrading bacteria. Furthermore, the competitive growth of methanogens (86.6%) may be responsible for the decrease in the relative abundance of SRB during the later stages of the experiment in the HO column.

Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome

Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.

Stems of Phragmites australis are buffering methane and carbon dioxide emissions

Internal concentrations in the culm nodes of Phragmites australis and fluxes of methane (CH₄) and carbon dioxide (CO₂) were recorded in the treatment bed of constructed wetland (CW) with subsurface wastewater horizontal flow. Fluxes of CH₄ and CO₂ from the CW treatment bed were in ranges of 0 to 490 μmol m^-2 h^-1 and from 0 to 4499 μmol m^-2 h^-1 for CH₄ and CO₂, respectively. The highest CH₄ soil fluxes were recorded in the unvegetated coarse gravel inflow zone of the CW treatment bed. The nearby inflow zone exhibited the highest CO₂ fluxes. Internal culm node concentrations of CH₄ and CO₂ were related to oxygen (O₂) stem concentrations and environmental conditions during diurnal courses. The concentrations of CH₄ and CO₂ gases were significantly correlated and opposing O₂ concentrations. Culm node parameters and shoot density of P. australis influenced internal gas concentrations and the buffering of CH₄ and CO₂ emissions. The effect of buffering CH₄ emissions is distinctive in the outflow zone of the treatment bed and is less important in the highly polluted inflow zone of the CW. Buffering of CH₄ and partially also CO₂ emissions by stems of P. australis is a process which affects the diurnal dynamics of CH₄ and CO₂ fluxes from common reed wetlands.

Interactions among heavy metals and methane-metabolizing microorganisms and their effects on methane emissions in Dajiuhu peatland

Peatlands play a crucial role in mediating the emissions of methane through active biogeochemical cycling of accumulated carbon driven by methane-metabolizing microorganisms; meanwhile, they serve as vital archives of atmospheric heavy metal deposition. Despite many edaphic factors confirmed as determinants to modulate the structure of methanotrophic and methanogenic communities, recognition of interactions among them is limited. In this study, peat soils were collected from Dajiuhu peatland to assess the presence of heavy metals, and methanotrophs and methanogens were investigated via high-throughput sequencing for functional genes mcrA and pmoA. Further analyses of the correlations between methane-related functional groups were conducted. The results demonstrated that both methane-metabolizing microorganisms and heavy metals have prominent vertical heterogeneity upward and downward along the depth of 20 cm. Pb, Cd, and Hg strongly correlated with methanotrophs and methanogens across all seasons and depths, serving as forceful factors in structural variations of methanogenic and methanotrophic communities. Particularly, Pb, Cd, and Hg were identified as excessive elements in Dajiuhu peatland. Furthermore, seasonal variations of networks among methane-related functional groups and environmental factors significantly affected the changes of methane fluxes across different seasons. Concretely, the complicated interactions were detrimental to methane emissions in the Dajiuhu peatland, leading to the minimum methane emissions in winter. Our study identified the key heavy metals affecting the composition of methane-metabolizing microorganisms and linkages between seasonal variations of methane emissions and interaction among heavy metals and methane-metabolizing microorganisms, which provided much new reference and theoretical basis for integrated management of natural peatlands.

Contrasting Fecal Methanogenic and Bacterial Profiles of Organic Dairy Cows Located in Northwest Washington Receiving Either a Mixed Diet of Pasture and TMR or Solely TMR

Currently, little is known regarding fecal microbial populations and their associations with methanogenic archaea in pasture-based dairy cattle. In this study, we assessed the fecal microbiome of organic dairy cows across different time points receiving a mixed diet of pasture and total mixed ration (TMR) or TMR only. We hypothesized that the fecal methanogenic community, as well as co-occurrence patterns with bacteria, change across diets. To test these hypotheses, we analyzed TMR and pasture samples, as well as the V3-V4 region of 16S rRNA of fecal samples collected over the course of a one-year study period from 209 cows located on an organic dairy in Northwest Washington. The inherent variability in pasture quality, quantity, availability, and animal preference can lead to diverse dietary intakes. Therefore, we conducted a k-means clustering analysis to identify samples from cows that were associated with either a pasture-based diet or a solely TMR diet. A total of 4 clusters were identified. Clusters 1 and 3 were mainly associated with samples primarily collected from cows with access to pasture of varying quality and TMR, cluster 2 was formed by samples from cows receiving only TMR, and cluster 4 was a mix of samples from cows receiving high-quality pasture and TMR or TMR only. Interestingly, we found little difference in the relative abundance of methanogens between the community clusters. There was evidence of differences in diversity between pasture associated bacterial communities and those associated with TMR. Cluster 4 had higher diversity and a less robust co-occurrence network based on Spearman correlations than communities representing TMR only or lower-quality pasture samples. These findings indicate that varied bacterial communities are correlated with the metabolic characteristics of different diets. The overall good pasture and TMR quality in this study, combined with the organic allowance for feeding high levels of TMR even during the grazing season, might have contributed to the lack of differences in the fecal archaeal community from samples associated with a mixed pasture and TMR diet, and a TMR only diet. Mitigation strategies to decrease methane emissions such as increasing concentrate to forage ratio, decreasing pasture maturity and adopting grazing systems targeting high quality pasture have been shown to be efficient for pasture-based systems. However, the allowance for organic dairy producers to provide up to an average of 70% of a ruminant's dry matter demand from dry matter fed (e.g., TMR), suggests that reducing enteric methane emissions may require the development of novel dietary strategies independent of pasture management.

Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea

SignificanceBiological carbon fixation provides opportunities to directly utilize CO₂ to synthesize a broad range of value-added compounds, potentially displacing petroleum feedstock use in industry. Chemoautotrophs are particularly interesting as their carbon fixation can be driven chemically by renewable H₂ in place of light, which can limit industrial fermentation of photosynthetic organisms. We describe the development of a methanogenic host, Methanococcus maripaludis, for metabolic engineering. Since redox cofactors used in upstream archaeal carbon fixation pathways are orthogonal to typical downstream biosynthetic pathways, it was necessary to engineer both NADH biosynthesis and turnover. In doing so, we are able to show that methanogenic archaea can, indeed, serve as a platform for the high-yield production of bioplastics and monomers from CO₂ and H₂.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

Microbial lipid biosynthesis from lignocellulosic biomass pyrolysis products

Lipids are a biorefinery platform to prepare fuel, food and health products. They are traditionally obtained from plants, but those of microbial origin allow for a better use of land and C resources, among other benefits. Several (thermo)chemical and biochemical strategies are used for the conversion of C contained in lignocellulosic biomass into lipids. In particular, pyrolysis can process virtually any biomass and is easy to scale up. Products offer cost-effective, renewable C in the form of readily fermentable molecules and other upgradable intermediates. Although the production of microbial lipids has been studied for 30 years, their incorporation into biorefineries was only described a few years ago. As pyrolysis becomes a profitable technology to depolymerize lignocellulosic biomass into assimilable C, the number of investigations on it raises significantly. This article describes the challenges and opportunities resulting from the combination of lignocellulosic biomass pyrolysis and lipid biosynthesis with oleaginous microorganisms. First, this work presents the basics of the individual processes, and then it shows state-of-the-art processes for the preparation of microbial lipids from biomass pyrolysis products. Advanced knowledge on separation techniques, structure analysis, and fermentability is detailed for each biomass pyrolysis fraction. Finally, the microbial fatty acid platform comprising biofuel, human food and animal feed products, and others, is presented. Literature shows that the microbial lipid production from anhydrosugars, like levoglucosan, and short-chain organic acids, like acetic acid, is straightforward. Indeed, processes achieving nearly theoretical yields form the latter have been described. Some authors have shown that lipid biosynthesis from different lignin sources is biochemically feasible. However, it still imposes major challenges regarding strain performance. No report on the fermentation of pyrolytic lignin is yet available. Research on the microbial uptake of pyrolytic humins remains vacant. Microorganisms that make use of methane show promising results at the proof-of-concept level. Overall, despite some issues need to be tackled, it is now possible to conceive new versatile biorefinery models by combining lignocellulosic biomass pyrolysis products and robust oleaginous microbial cell factories.

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention

Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.

Effect of Cobalt, Nickel, and Selenium/Tungsten Deficiency on Mesophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Trace elements (TEs) are vital for anaerobic digestion (AD), due to their role as cofactors in many key enzymes. The aim of this study was to evaluate the effects of specific TE deficiencies on mixed microbial communities during AD of soluble polymer-free substrates, thus focusing on AD after hydrolysis. Three mesophilic (37 °C) continuous stirred-tank biogas reactors were depleted either of Co, Ni, or a combination of Se and W, respectively, by discontinuing their supplementation. Ni and Se/W depletion led to changes in methane kinetics, linked to progressive volatile fatty acid (VFA) accumulation, eventually resulting in process failure. No significant changes occurred in the Co-depleted reactor, indicating that the amount of Co present in the substrate in absence of supplementation was sufficient to maintain process stability. Archaeal communities remained fairly stable independent of TE concentrations, while bacterial communities gradually changed with VFA accumulation in Ni- and Se-/W-depleted reactors. Despite this, the communities remained relatively similar between these two reactors, suggesting that the major shifts in composition likely occurred due to the accumulating VFAs. Overall, the results indicate that Ni and Se/W depletion primarily lead to slower metabolic activities of methanogenic archaea and their syntrophic partners, which then has a ripple effect throughout the microbial community due to a gradual accumulation of intermediate fermentation products.

Biohythane production via single-stage anaerobic fermentation using entrapped hydrogenic and methanogenic bacteria

This study demonstrates the continuous biohythane production in a single-stage anaerobic digester using a biomass mixture of separately entrapped hydrogenic and methanogenic bacteria (H₂- and CH₄-producing bacteria, respectively). The entrapped hydrogenic/methanogenic bacteria biomass ratios of 1/4, 2/3, 3/2 and 4/1 were tested and shown to have a great effect on the single-stage biohythane production performance. At steady-states, the cultivations had biohythane production rates in the range of 381-480 mL/L-d, with H₂ content in biohythane (HCH) varying from 1% to 75% (v/v) and chemical oxygen demand removal efficiencies (TCOD_re) of 57.6-81.9%. Biomass ratio 2/3 (weight ratio 1/1.5) resulted in peak biohythane production with H₂ and CH₄ production rates being 64.6 and 395 mL/L-d, respectively, HCH 15% and TCOD_re 74.4%. The novelty of this work is to show the potential of producing biohythane from an innovative single-stage dark fermentation system using entrapped hydrogenic and methanogenic bacteria.

Enhancement of methane production and antibiotic resistance genes reduction by ferrous chloride during anaerobic digestion of swine manure

In this study, effects of ferrous chloride (FeCl₂) addition on methane production and antibiotic resistance genes (ARGs) reduction were investigated during anaerobic digestion (AD) of swine manure. FeCl₂ could both improve the accumulative methane production and reduce the abundance of total ARGs, i.e., the maximum increase of CH₄ production of 21.5% at FC5, and the maximum ARGs reduction of 33.3% at FC25. The reduction of pathogenic bacteria and metal resistance genes (MRGs) was enhanced. Acetate and propionate utilization were intensified by enhancing H₂ utilization and direct interspecies electron transfer (DIET), where DIET was further enhanced by the reaction of the FeCl₂ and acetic acid. The bacterial community played important role in the evolution of ARGs (68.26%), which were also affected by MRGs, mobile genetic elements (MGEs), and environmental factors. Therefore, FeCl₂-based AD is a feasible and attractive way to improve methane production and ARG reduction.

How did the evolution of oxygenic photosynthesis influence the temporal and spatial development of the microbial iron cycle on ancient Earth?

Iron is the most abundant redox active metal on Earth and thus provides one of the most important records of the redox state of Earth's ancient atmosphere, oceans and landmasses over geological time. The most dramatic shifts in the Earth's iron cycle occurred during the oxidation of Earth's atmosphere. However, tracking the spatial and temporal development of the iron cycle is complicated by uncertainties about both the timing and location of the evolution of oxygenic photosynthesis, and by the myriad of microbial processes that act to cycle iron between redox states. In this review, we piece together the geological evidence to assess where and when oxygenic photosynthesis likely evolved, and attempt to evaluate the influence of this innovation on the microbial iron cycle.

Response and mechanisms of the performance and fate of antibiotic resistance genes to nano-magnetite during anaerobic digestion of swine manure

Swine manure is an important reservoir of environmental antibiotic resistance genes (ARGs), and anaerobic digestion (AD) is a commonly used method for swine manure treatment. In this study, the optimized dosage of nano-magnetite to enhance methane production was figured out, the changes of the fate of ARGs response to nano-magnetite were investigated, and the microbial mechanisms were deciphered through the microbial community analysis and key functional genes quantification. Results showed that nano-magnetite could improve the methane production by maximum 6.0%, the maximum daily methane production could be increased by 47.8%, and the AD time could be shortened by above 20.0% at the addition of 75 mmol. The improved performance could be associated with the enhancement of direct interspecies electron transfer (DIET) and the inhibition release due to the formation of Fe-S precipitation not the nutrition elements role of nano-magnetite, and nano-magnetite did not significantly influence the dynamics of microbial community. Nano-magnetite could enhance the methanogenesis instead of the acetogenesis reflected by the functional genes analysis, and the limited effects of nano-magnetite on the fate of ARGs could be associated with its limited influence on the microbial community which determined the fate of ARGs during AD of swine manure.

Effects of thymol and carvacrol, alone or in combination, on fermentation and microbial diversity during in vitro culture of bovine rumen microbes

Two essential oils (EO), thymol and carvacrol, were used in six ratio (100:00, 80:20, 60:40, 40:60, 20:80 and 00:100) combinations of both EO and in a dose of 0.2 g L^-1 in bovine ruminal culture medium, 24-h cultures, to evaluate effects on total gas production (TGP), methane production, in vitro dry matter digestibility (IVDMD) and in vitro culture population dynamics of methanogenic and total bacteria. Total DNA extracted from ruminal microorganisms was subjected to denaturing gradient gel electrophoresis (DGGE)-polymerase chain reaction (PCR) to examine effects on bacterial populations. The effect of EO on TGP and IVDMD were assessed by comparison to untreated control cultures. In general, methane production by the microbial populations appeared to be higher with treatments containing the highest concentration of thymol than with treatments containing more carvacrol resulting in a tendency for greater methane-inhibiting activity achieved as the thymol concentration in the thymol:carvacrol mixtures decreased linearly. The population of total bacteria with a 74.5% Dice similarity coefficient for comparison of DGGE band patterns indicating shifts in bacterial constituents as EO ratios changed. No effects on TGP, IVDMD while only slight shifts in the methanogenic populations were seen with an overall 91.5% Dice similarity coefficient.

Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H2 and CO2 under different temperature conditions

The growth of all methanogens is limited to a specific temperature range. However, Methanothermobacter thermautotrophicus can be found in a variety of natural and artificial environments, the temperatures of which sometimes even exceed the temperature growth ranges of thermophiles. As a result, the extent to which methane production and survival are affected by temperature remains unclear. To investigate the mechanisms of methanogenesis that Archaea have evolved to cope with drastic temperature shifts, the responses of Methanothermobacter thermautotrophicus to temperature were investigated under a high temperature growth (71°C) and cold shock (4°C) using Isobaric tags for relative and absolute quantitation (iTRAQ). The results showed that methane formation is decreased and that protein folding and degradation are increased in both high‐ and low‐temperature treatments. In addition, proteins predicted to be involved in processing environmental information processing and in cell membrane/wall/envelope biogenesis may play key roles in affecting methane formation and enhancing the response of M. thermautotrophicus to temperature stress. Analysis of the genomic locations of the genes corresponding to these temperature‐dependent proteins predicted that 77 of the genes likely to form 32 gene clusters. Here, we assess the response of M. thermautotrophicus to different temperatures and provide a new level of understanding of methane formation and cellular putative adaptive responses.

The effects and mechanism of action of methane on ileal motor function

BACKGROUND

Methane has been associated with constipation-predominant irritable bowel syndrome, slowing intestinal transit time by augmenting contractile activity. However, the precise mechanism underlying this effect remains unclear. Therefore, we investigated the mechanisms underlying the effect of methane on contractile activity, and whether such effects are mediated by nerve impulses or muscular contraction.

METHODS

We connected guinea pig ileal muscle strips to a force/tension transducer and measured amplitudes of contraction in response to electrical field stimulation (EFS; 1, 2, 8, 16 Hz) following methane infusion in the presence of tetradotoxin (TTX), atropine, guanethidine, or GR 113808. We then performed calcium imaging using Oregon Green 488 BAPTA-1 AM in order to visualize changes in calcium fluorescence in response to EFS following methane infusion in the presence of TTX, atropine, or a high K⁺ solution.

KEY RESULTS

Methane significantly increased amplitudes of contraction (P<.05), while treatment with TTX abolished such contraction. Methane-induced increases in amplitude were inhibited when lower-frequency (1, 2 Hz) EFS was applied following atropine infusion (P<.05). Neither guanethidine nor GR 113808 significantly altered contraction amplitudes. Methane significantly increased calcium fluorescence, while this increase was attenuated following atropine infusion (P<.05). Although calcium fluorescence was increased by the high K⁺ solution under pretreatment with TTX, the intensity of fluorescence remained unchanged after methane infusion.

CONCLUSIONS AND INFERENCES

The actions of methane on the intestine are influenced by the cholinergic pathway of the enteric nervous system. Our findings support the classification of methane as a gasotransmitter.

Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

BACKGROUND

The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications.

RESULTS

Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis of the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi.

CONCLUSIONS

Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO₂ metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO₂ and formate are common electron carriers in microbial communities.

Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms

The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea.

Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT

Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by 'ancient' CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of ≥1.3 × 10-8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations.

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.

The Pyromaniac Inside You: Salmonella Metabolism in the Host Gut

A metabolically diverse microbial community occupies all available nutrient-niches in the lumen of the mammalian intestine, making it difficult for pathogens to establish themselves in this highly competitive environment. Salmonella serovars sidestep the competition by using their virulence factors to coerce the host into creating a novel nutrient-niche. Inflammation-derived nutrients available in this new niche support a bloom of Salmonella serovars, thereby ensuring transmission of the pathogen to the next susceptible host by the fecal-oral route. Here we review the anaerobic food chain that characterizes resident gut-associated microbial communities along with the winning metabolic strategy Salmonella serovars use to edge out competing microbes in the inflamed intestine.

Methanogens, methane and gastrointestinal motility

Anaerobic fermentation of the undigested polysaccharide fraction of carbohydrates produces hydrogen in the intestine which is the substrate for methane production by intestinal methanogens. Hydrogen and methane are excreted in the flatus and in breath giving the opportunity to indirectly measure their production using breath testing. Although methane is detected in 30%-50% of the healthy adult population worldwide, its production has been epidemiologically and clinically associated with constipation related diseases, like constipation predominant irritable bowel syndrome and chronic constipation. While a causative relation is not proven yet, there is strong evidence from animal studies that methane delays intestinal transit, possibly acting as a neuromuscular transmitter. This evidence is further supported by the universal finding that methane production (measured by breath test) is associated with delayed transit time in clinical studies. There is also preliminary evidence that antibiotic reduction of methanogens (as evidenced by reduced methane production) predicts the clinical response in terms of symptomatic improvement in patients with constipation predominant irritable bowel syndrome. However, we have not identified yet the mechanism of action of methane on intestinal motility, and since methane production does not account for all constipation associated cases, there is need for high quality clinical trials to examine methane as a biomarker for the diagnosis or as a biomarker that predicts antibiotic treatment response in patients with constipation related disorders.

Stable operation during pilot-scale anaerobic digestion of nutrient-supplemented maize/sugar beet silage

Biogas production from maize/sugar beet silage was studied under mesophilic conditions in a continuous stirred tank reactor pilot-scale process. While energy crop mono-digestion is often performed with very long hydraulic retention times (HRTs), the present study demonstrated an efficient process operating with a 50-day HRT and a corrected total solids (TS(corr)) based organic loading rate of 3.4 kg/m(3)d. The good performance was attributed to supplementation with both macro- and micronutrients and was evidenced by good methane yields (318 m(3)/ton TS(corr)), which were comparable to laboratory maximum expected yields, plus low total volatile fatty acid concentrations (<0.8 g/L). A viscoplastic and thixotropic digester fluid behaviour was observed, and the viscosity problems common in crop mono-digestion were not seen in this study. The effluent also complied with Swedish certification standards for bio-fertilizer for farmland application. Nutrient addition thus rendered a stable biogas process, while the effluent was a good quality bio-fertilizer.

Molecular hydrogen and radiation protection

Molecular hydrogen (dihydrogen, H(2)) acts as a therapeutic antioxidant by selectively reducing hydroxyl radicals (•OH) and peroxynitrite (ONOO-). It has been well-known that ionising radiation (IR) causes oxidative damage and consequent apoptosis mainly due to the production of •OH that follows radiolysis of H(2)O. Our department reported the protective effect of H(2) in irradiated cells and mice for the first time, and this effect is well repeated by us and another laboratory in different experimental animal models. A randomised, placebo-controlled investigation also showed consumption of H(2) can improve the quality of life of patients treated with radiotherapy for liver tumours. These encouraging results suggested that H(2) has a potential as a radioprotective agent with efficacy and non-toxicity.

The emergence and early evolution of biological carbon-fixation

The fixation of CO₂ into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of CO₂ reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a "phylometabolic" tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.

Hemoproteins in dissimilatory sulfate- and sulfur-reducing prokaryotes

Dissimilatory sulfate and sulfur reduction evolved billions of years ago and while the bacteria and archaea that use this unique metabolism employ a variety of electron donors, H(2) is most commonly used as the energy source. These prokaryotes use multiheme c-type proteins to shuttle electrons from electron donors, and electron transport complexes presumed to contain b-type hemoproteins contribute to proton charging of the membrane. Numerous sulfate and sulfur reducers use an alternate pathway for heme synthesis and, frequently, uniquely specific axial ligands are used to secure c-type heme to the protein. This review presents some of the types and functional activities of hemoproteins involved in these two dissimilatory reduction pathways.

Inflammation and microflora

Irritable bowel syndrome (IBS) is the most common gastrointestinal condition, affecting 10% to 20% of adults in developed countries. Over the last few years, growing evidence has supported a new hypothesis for IBS based on alterations in intestinal bacterial composition. This article reviews the evidence for a bacterial concept in IBS and begins to formulate a hypothesis of how these bacterial systems could integrate in a new pathophysiologic mechanism in the development of IBS. Data suggesting an interaction between this gut flora and inflammation in the context of IBS is also presented.

Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing

Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation.

Recent advances in hydrogen research as a therapeutic medical gas

Recent basic and clinical research has revealed that hydrogen is an important physiological regulatory factor with antioxidant, anti-inflammatory and anti-apoptotic protective effects on cells and organs. Therapeutic hydrogen has been applied by different delivery methods including straightforward inhalation, drinking hydrogen dissolved in water and injection with hydrogen-saturated saline. This review summarizes currently available data regarding the protective role of hydrogen, provides an outline of recent advances in research on the use of hydrogen as a therapeutic medical gas in diverse models of disease and discusses the feasibility of hydrogen as a therapeutic strategy. It is not an overstatement to say that hydrogen's impact on therapeutic and preventive medicine could be enormous in the future.

Methane and the gastrointestinal tract

INTRODUCTION

Several gases are produced through enteric fermentation in the intestinal tract. Carbon dioxide, hydrogen, hydrogen sulfide, and methane are thought to be the most common of these. Recent evidence suggests that methane may not be inert. In this review article, we summarize the findings with methane.

METHODS

This is a review article discussing the various component gases in the gastrointestinal tract and their relevance to health and disease. Specific attention was paid to understanding methane.

RESULTS

The majority of these gases are eliminated via flatus or absorbed into systemic circulation and expelled from the lungs. Excessive gas evacuation or retention causes gastrointestinal functional symptoms such as belching, flatulence, bloating, and pain. Between 30 and 62% of healthy subjects produce methane. Methane is produced exclusively through anaerobic fermentation of both endogenous and exogenous carbohydrates by enteric microflora in humans. Methane is not utilized by humans, and analysis of respiratory methane can serve as an indirect measure of methane production. Recent literature suggests that gases such as hydrogen sulfide and methane may have active effects on gut function. In the case of hydrogen sulfide, evidence demonstrates that this gaseous product may be produced by human eukaryotic cells. However, in the case of methane, there is increasing evidence that this gas has both physical and biological effects on gut function. It is now often associated with functional constipation and may have an active role here.

CONCLUSION

This review of the literature discusses the significance of enteric flora, the biogenesis of methane, and its clinical associations. Furthermore, we examine the evidence for an active role of methane in gastrointestinal motility and the potential applications to future therapeutics.

Intermediary ecosystem metabolism as a main driver of methanogenesis in acidic wetland soil

Methanogens have a very limited substrate range, and their in situ activities are thus linked to 'intermediary ecosystem metabolism', i.e. complex trophic interactions with other microorganisms catalysing essential intermediary processes that ultimately drive methanogenesis. However, information on intermediary ecosystem metabolism and associated biota is fragmented and often conceptualized rather than resolved. The main objective of this review is to evaluate the concept of intermediary ecosystem metabolism in context with recent work aimed at resolving the complex trophic interactions of a methane-emitting peatland.

Trophic links between fermenters and methanogens in a moderately acidic fen soil

Trophic links between fermentation and methanogenesis of soil derived from a methane-emitting, moderately acidic temperate fen (pH 4.5) were investigated. Initial CO(2):CH(4) production ratios in anoxic microcosms indicated that methanogenesis was concomitant to other terminal anaerobic processes. Methane production in anoxic microcosms at in situ pH was stimulated by supplemental H(2)-CO(2), formate or methanol; supplemental acetate did not stimulate methanogenesis. Supplemental H(2)-CO(2), formate or methanol also stimulated the formation of acetate, indicating that the fen harbours moderately acid-tolerant acetogens. Supplemental monosaccharides (glucose, N-acetylglucosamine and xylose) stimulated the production of CO(2), H(2), acetate and other fermentation products when methanogenesis was inhibited with 2-bromoethane sulfonate 20 mM. Glucose stimulated methanogenesis in the absence of BES. Upper soil depths yielded higher anaerobic activities and also higher numbers of cells. Detected archaeal 16S rRNA genes were indicative of H(2)-CO(2)- and formate-consuming methanogens (Methanomicrobiaceae), obligate acetoclastic methanogens (Methanosaetaceae) and crenarchaeotes (groups I.1a, I.1c and I.3). Molecular analyses of partial sequences of 16S rRNA genes revealed the presence of Acidobacteria, Nitrospirales, Clamydiales, Clostridiales, Alpha-, Gamma-, Deltaproteobacteria and Cyanobacteria. These collective results suggest that this moderately acidic fen harbours phylogenetically diverse, moderately acid tolerant fermenters (both facultative aerobes and obligate anaerobes) that are trophically linked to methanogenesis.

The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

Composition and gene content of a biogas-producing microbial community from a production-scale biogas plant fed with renewable primary products was analysed by means of a metagenomic approach applying the ultrafast 454-pyrosequencing technology. Sequencing of isolated total community DNA on a Genome Sequencer FLX System resulted in 616,072 reads with an average read length of 230 bases accounting for 141,664,289 bases sequence information. Assignment of obtained single reads to COG (Clusters of Orthologous Groups of proteins) categories revealed a genetic profile characteristic for an anaerobic microbial consortium conducting fermentative metabolic pathways. Assembly of single reads resulted in the formation of 8752 contigs larger than 500 bases in size. Contigs longer than 10kb mainly encode house-keeping proteins, e.g. DNA polymerase, recombinase, DNA ligase, sigma factor RpoD and genes involved in sugar and amino acid metabolism. A significant portion of contigs was allocated to the genome sequence of the archaeal methanogen Methanoculleus marisnigri JR1. Mapping of single reads to the M. marisnigri JR1 genome revealed that approximately 64% of the reference genome including methanogenesis gene regions are deeply covered. These results suggest that species related to those of the genus Methanoculleus play a dominant role in methanogenesis in the analysed fermentation sample. Moreover, assignment of numerous contig sequences to clostridial genomes including gene regions for cellulolytic functions indicates that clostridia are important for hydrolysis of cellulosic plant biomass in the biogas fermenter under study. Metagenome sequence data from a biogas-producing microbial community residing in a fermenter of a biogas plant provide the basis for a rational approach to improve the biotechnological process of biogas production.

Genome of Geobacter sulfurreducens: metal reduction in subsurface environments

The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.

Selective optimization in thermophilic acidogenesis of cheese-whey wastewater to acetic and butyric acids: partial acidification and methanation

For partial acidogenesis of cheese-whey wastewater, a set of experiments were carried out to produce short-chain volatile fatty acids (VFA) in laboratory-scale continuously stirred tank reactors (CSTR). The maximum rate of acetic and butyric acid production associated with simultaneous changes in hydraulic retention time (HRT), pH, and temperature was investigated, in which the degree of acidification of the whey to the short-chain VFAs was less than 20% of the influent chemical oxygen demand (COD) concentration. Response surface methodology was successfully applied to determine the optimum physiological conditions where the maximum rates of acetic and butyric acid production occurred. These were 0.40-day HRT, pH 6.0 at 54.1 degrees C and 0.22-day HRT, pH 6.5 at 51.9 degrees C, respectively. The optimum conditions for acetic acid production were selected for partial acidification of cheese-whey wastewater because of a higher rate in combined productions of acetic and butyric acids than that at optimum conditions for butyric acid production. A thermophilic two-phase process with the partial acidification followed by a methanation step was operated. Performance of the two-phase process was compared to the single-phase anaerobic system. The two-phase process clearly showed a better performance in management of cheese-whey wastewater over the single-phase system. Maximum rate of COD removal and the rate of methane production in the two-phase process were, respectively, 116% and 43% higher than those of the single-phase system.

Metabolic characteristics of an aerobe isolated from a methylotrophic methanogenic enrichment culture

An anaerobic methylotrophic methanogenic enrichment culture, with sustained metabolic characteristics, including that of methanation for over a decade, was the choice of the present study on interspecies interactions. Growth and methanation by the enrichment were suppressed in the presence of antibiotics, and no methanogen grown on methanol could be isolated using stringent techniques. The present study confirmed syntrophic metabolic interactions in this enrichment with the isolation of a strain of Pseudomonas sp. The organism had characteristic metabolic versatility in metabolizing a variety of substrates including alcohols, aliphatic acids, amino acids, and sugars. Anaerobic growth was favoured with nitrate in the growth medium. Cells grown anaerobically with methanol, revealed maximal nitrate reductase activity. Constitutive oxidative activity of the membrane system emerged from the high-specific oxygen uptake and nitrate reductase activities of the aerobically and anerobically grown cells respectively. Cells grown anaerobically on various alcohols effectively oxidized methanol in the presence of flavins, cofactor FAD and the methanogenic cofactor F420, suggesting a constitutive alcohol oxidizing capacity. In cells grown anaerobically on methanol, the rate of methanol oxidation with F420 was three times that of FAD. Efficient utilization of alcohols in the presence of F420 is a novel feature of the present study. The results suggest that utilization of methanol by the mixed culture would involve metabolic interactions between the Pseudomonas sp. and the methanogen(s). Methylotrophic, methanogenic partnership involving an aerobe is a novel feature hitherto unreported among anaerobic syntrophic associations and is of ecological significance

The unique biochemistry of methanogenesis

Methanogenic archaea have an unusual type of metabolism because they use H2 + CO2, formate, methylated C1 compounds, or acetate as energy and carbon sources for growth. The methanogens produce methane as the major end product of their metabolism in a unique energy-generating process. The organisms received much attention because they catalyze the terminal step in the anaerobic breakdown of organic matter under sulfate-limiting conditions and are essential for both the recycling of carbon compounds and the maintenance of the global carbon flux on Earth. Furthermore, methane is an important greenhouse gas that directly contributes to climate changes and global warming. Hence, the understanding of the biochemical processes leading to methane formation are of major interest. This review focuses on the metabolic pathways of methanogenesis that are rather unique and involve a number of unusual enzymes and coenzymes. It will be shown how the previously mentioned substrates are converted to CH4 via the CO2-reducing, methylotrophic, or aceticlastic pathway. All catabolic processes finally lead to the formation of a mixed disulfide from coenzyme M and coenzyme B that functions as an electron acceptor of certain anaerobic respiratory chains. Molecular hydrogen, reduced coenzyme F420, or reduced ferredoxin are used as electron donors. The redox reactions as catalyzed by the membrane-bound electron transport chains are coupled to proton translocation across the cytoplasmic membrane. The resulting electrochemical proton gradient is the driving force for ATP synthesis as catalyzed by an A1A0-type ATP synthase. Other energy-transducing enzymes involved in methanogenesis are the membrane-integral methyltransferase and the formylmethanofuran dehydrogenase complex. The former enzyme is a unique, reversible sodium ion pump that couples methyl-group transfer with the transport of Na+ across the membrane. The formylmethanofuran dehydrogenase is a reversible ion pump that catalyzes formylation and deformylation of methanofuran. Furthermore, the review addresses questions related to the biochemical and genetic characteristics of the energy-transducing enzymes and to the mechanisms of ion translocation.

Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates

Although there is significant interest in the potential interactions of microbes with gas hydrate, no direct physical association between them has been demonstrated. We examined several intact samples of naturally occurring gas hydrate from the Gulf of Mexico for evidence of microbes. All samples were collected from anaerobic hemipelagic mud within the gas hydrate stability zone, at water depths in the ca. 540- to 2,000-m range. The delta(13)C of hydrate-bound methane varied from -45.1 per thousand Peedee belemnite (PDB) to -74.7 per thousand PDB, reflecting different gas origins. Stable isotope composition data indicated microbial consumption of methane or propane in some of the samples. Evidence of the presence of microbes was initially determined by 4,6-diamidino 2-phenylindole dihydrochloride (DAPI) total direct counts of hydrate-associated sediments (mean = 1.5 x 10(9) cells g(-1)) and gas hydrate (mean = 1.0 x 10(6) cells ml(-1)). Small-subunit rRNA phylogenetic characterization was performed to assess the composition of the microbial community in one gas hydrate sample (AT425) that had no detectable associated sediment and showed evidence of microbial methane consumption. Bacteria were moderately diverse within AT425 and were dominated by gene sequences related to several groups of Proteobacteria, as well as Actinobacteria and low-G + C Firmicutes. In contrast, there was low diversity of Archaea, nearly all of which were related to methanogenic Archaea, with the majority specifically related to Methanosaeta spp. The results of this study suggest that there is a direct association between microbes and gas hydrate, a finding that may have significance for hydrocarbon flux into the Gulf of Mexico and for life in extreme environments.