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Recent evidence suggests that the microbial community in the human intestine may play an important role in the pathogenesis of obesity. We examined 184,094 sequences of microbial 16S rRNA genes from PCR amplicons by using the 454 pyrosequencing technology to compare the microbial community structures of 9 individuals, 3 in each of the categories of normal weight, morbidly obese, and post-gastric-bypass surgery. Phylogenetic analysis demonstrated that although the Bacteria in the human intestinal community were highly diverse, they fell mainly into 6 bacterial divisions that had distinct differences in the 3 study groups. Specifically, Firmicutes were dominant in normal-weight and obese individuals but significantly decreased in post-gastric-bypass individuals, who had a proportional increase of GAMMAPROTEOBACTERIA: Numbers of the H₂-producing Prevotellaceae were highly enriched in the obese individuals. Unlike the highly diverse Bacteria, the Archaea comprised mainly members of the order Methanobacteriales, which are H₂-oxidizing methanogens. Using real-time PCR, we detected significantly higher numbers of H₂-utilizing methanogenic Archaea in obese individuals than in normal-weight or post-gastric-bypass individuals. The coexistence of H₂-producing bacteria with relatively high numbers of H₂-utilizing methanogenic Archaea in the gastrointestinal tract of obese individuals leads to the hypothesis that interspecies H₂ transfer between bacterial and archaeal species is an important mechanism for increasing energy uptake by the human large intestine in obese persons. The large bacterial population shift seen in the post-gastric-bypass individuals may reflect the double impact of the gut alteration caused by the surgical procedure and the consequent changes in food ingestion and digestion.

Abstract To investigate the differences in microbial community structure between mesophilic and thermophilic in situ biogas-upgrading systems by H2 addition, two reactors (35 °C and 55 °C) were run for four stages according to different H2 addition rates (H2/CO2 of 0:1, 1:1, and 4:1) and mixing mode (intermittent and continuous). 16S rRNA gene-sequencing technology was applied to analyze microbial community structure. The results showed that the temperature is a crucial factor in impacting succession of microbial community structure and the H2 utilization pathway. For mesophilic digestion, most of added H2 was consumed indirectly by the combination of homoacetogens and strict aceticlastic methanogens. In the thermophilic system, most of added H2 may be used for microbial cell growth, and part of H2 was utilized directly by strict hydrogenotrophic methanogens and facultative aceticlastic methanogens. Continuous stirring was harmful to the stabilization of mesophilic system, but not to the thermophilic one.

Methanogenic archaea reside primarily in the rumen and the lower segments of the intestines of ruminants, where they utilize the reducing equivalents derived from rumen fermentation to reduce carbon dioxide, formic acid, or methylamines to methane（CH_4）. Research on methanogens in the rumen has attracted great interest in the last decade because CH_4 emission from ruminants contributes to global greenhouse gas emission and represents a loss of feed energy. Some DNA-based phylogenetic studies have depicted a diverse and dynamic community of methanogens in the rumen. In the past decade, researchers have focused on elucidating the underpinning that determines and affects the diversity, composition, structure, and dynamics of methanogen community of the rumen. Concurrently, many researchers have attempted to develop and evaluate interventions to mitigate enteric CH_4 emission. Although much work has been done using plant secondary metabolites, other approaches such as using nitrate and 3-nitrooxy propanol have also yielded promising results. Most of these antimethanogenic compounds or substances often show inconsistent results among studies and also lead to adverse effects on feed intake and digestion and other aspects of rumen fermentation when fed at doses high enough to achieve effective mitigation. This review provides a brief overview of the rumen methanogens and then an appraisal of most of the antimethanogenic compounds and substances that have been evaluated both in vitro and in vivo. Knowledge gaps and future research needs are also discussed with a focus on methanogens and methane mitigation.

1. Plant invasion can strongly influence carbon (C) cycling processes, thus it may affect climate change by altering C sequestration and greenhouse gas emissions in the invaded ecosystem. Since 1979, the exotic Spartina alterniflora has rapidly expanded in China's coastal areas, where significant increase in methane (CH₄) emissions has been documented from post-invaded sites. However, a mechanistic understanding of the structural and functional changes of associated methanogens accompanying this invasion remains elusive. 2. Here we conducted integrated biogeochemical investigations on methanogenic substrates, activity, and diversity to identify implications of S. alterniflora invasion for methanogenesis in coastal wetlands. To do this, we collected and analysed 0-50 cm soil profiles from an uncolonised tidal flat (TF) and salt marshes that S. alterniflora has invaded for 1 year (SA-1) and 12 years (SA-12) in Jiangsu, China. Methanogenic community composition was characterised by massive parallel sequencing. The rates and pathways of methanogenesis were determined by adding trace concentrations of ¹³C-labelled substrates to anaerobic incubated samples. 3. Our results revealed that 12-year invasion of S. alterniflora drastically increased CH₄ production potential by one order of magnitude over that of TF. This substantial increase was primarily attributed to methanogenesis from trimethylamine; its rates increased by two orders of magnitude over TF whereas those from acetate and H₂/CO₂ increased far less. Hydrogenotrophic methanogenesis was the dominant pathway operating in the TF, but methanotrophic pathway contributed most to CH₄ production in the surface layer of SA-1 and uppermost 40-cm layers of SA-12. Consistent with these observations, the dominant methanogens shifted from obligate hydrogenotrophic Methanococcales in TF to potential methylamineutilising Methanosarcinaceae in SA-12. Our Mantel analysis indicated that 'non-competitive' trimethylamine, derived from cytoplasmic osmolytes of S. alterniflora, was the major driver of this change in methanogenic community composition. 4. Synthesis. Our results suggest that invasive Spartino alterniflora plants gradually facilitated the local dominance of methylotrophic Methanosarcinaceae by changing the key type of methanogenic substrate in coastal marshes. Shifts in methanogen communities and enhanced availability of trimethylamine elevated the rates and importance of methylotrophic methanogenesis, thereby markedly increasing CH₄ production potential and emission rates in this type of ecosystem.

This study investigated the effects of placement of N at different soil depths on CH4 emissions and related microbial communities in no-tillage paddy soil. Five fertilizing treatments, including no N fertilizer, N surface broadcasting, and N deep placement at the soil depths of 5 cm, 10 cm, and 20 cm were applied in the paddy field. The composition of main microbial groups were determined using phospholipid fatty acid (PLFA) analysis. The absolute real-time quantitative PCR was applied to determine the abundance of the methanogenic and methanotrophic populations with mcrA, pmoA, mmoX, and mxaF as the functional gene markers. Compared with N surface broadcasting, the deep placement of N (i) significantly increased the microbial biomass carbon (C) and dissolved organic C by 7–90% and 6–75%, respectively; (ii) significantly enhanced the amount of the total PLFAs by 12–70% and the bacterial PLFAs by 15–82%; (iii) significantly mitigated the CH4 emissions by 6–39%; and (iv) significantly enhanced the abundance of the methanogenic and methanotrophic populations by 16–55% and 13–210%, respectively. The percent changes varied over a wide range due to different N placement depths as well as the seasonal variations. Moreover, structural equation modeling revealed that N deep placement directly or indirectly affected the CH4-related microbial communities through the increased labile soil organic C fractions by activating plant growth and soil microbial abundance, thereby mitigating the CH4 emissions in no-tillage paddy soil.

Methanogens are members of anaerobe microbiota of the digestive tract of mammals, including humans. However, the sources, modes of acquisition, and dynamics of digestive tract methanogens remain poorly investigated. In this study, we aimed to expand the spectrum of animals that could be sources of methanogens for humans by exploring methanogen carriage in animals. We used real-time PCR, PCR-sequencing, and multispacer sequence typing to investigate the presence of methanogens in 407 fecal specimens collected from nine different mammalian species investigated here. While all the negative controls remained negative, we obtained by PCR-sequencing seven different species of methanogens, of which three (Methanobrevibacter smithii, Methanobrevibacter millerae and Methanomassiliicoccus luminyensis) are known to be part of the methanogens present in the human digestive tract. M. smithii was found in 24 cases, including 12/24 (50%) in pigs, 6/24 (25%) in dogs, 4/24 (16.66%) in cats, and 1/24 (4.16%) in both sheep and horses. Genotyping these 24 M. smithii revealed five different genotypes, all known in humans. Our results are fairly representative of the methanogen community present in the digestive tract of certain animals domesticated by humans, and other future studies must be done to try to cultivate methanogens here detected by molecular biology to better understand the dynamics of methanogens in animals and also the likely acquisition of methanogens in humans through direct contact with these animals or through consumption of the meat and/or milk of certain animals, in particular cows.

The biomethane formation from 4 H2 + CO2 by pure cultures of two methanogens, Methanocaldococcus fervens and Methanobacterium thermophilum, has been studied. The goal of the study was to understand the regulation of the enzymatic steps associated with biomethane biosynthesis by H2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily “switched off” and “switched on” by H2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H2/CO2 trigger although this methanogen also converted H2/CO2 to CH4. From practical points of view, the regulatory function of H2/CO2 suggests that in the power-to-gas (P2G) renewable excess electricity conversion and storage systems, the composition of the biomethane-generating methanogenic community is essential for sustainable operation. In addition to managing the specific hydrogenotrophic methanogenesis biochemistry, H2/CO2 affected several, apparently unrelated, metabolic pathways. The redox-regulated overall biochemistry and symbiotic relationships in the methanogenic communities should be explored in order to make the P2G technology more efficient.Key points • Hydrogenotrophic methanogens may respond distinctly to H2/CO2 in bio-CH4 formation.• H2/CO2 can also activate metabolic routes, which are apparently unrelated to methanogenesis.• Sustainable conversion of the fluctuating renewable electricity to bio-CH4 is an option.

The unprecedented population and anthropogenic activity rise have challenged the future look up for shifts in global temperature and climate patterns. Anthropogenic activities such as land fillings, building dams, wetlands converting to lands, combustion of biomass, deforestation, mining, and the gas and coal industries have directly or indirectly increased catastrophic methane (CH 4 ) emissions at an alarming rate. Methane is 25 times more potent trapping heat when compared to carbon dioxide (CO 2 ) in the atmosphere. A rise in atmospheric methane, on a 20-year time scale, has an impact of 80 times greater than that of CO 2 . With increased population growth, waste generation is rising and is predicted to reach 6 Mt by 2025. CH 4 emitted from landfills is a significant source that accounts for 40% of overall global methane emissions. Various mitigation and emissions reduction strategies could significantly reduce the global CH 4  burden at a cost comparable to the parallel and necessary CO 2  reduction measures, reversing the CH 4  burden to pathways that achieve the goals of the Paris Agreement. CH 4  mitigation directly benefits climate change, has collateral impacts on the economy, human health, and agriculture, and considerably supports CO 2  mitigation. Utilizing the CO 2  from the environment, methanogens produce methane and lower their carbon footprint. NGOs and the general public should act on time to overcome atmospheric methane emissions by utilizing the raw source for producing carbon–neutral fuel. However, more research potential is required for green energy production and to consider investigating the untapped potential of methanogens for dependable energy generation.

Nanosized conductive carbon materials have been reported to stimulate methanogenesis by anaerobic microbiomes, while other studies have shown their antimicrobial activities. The present study examined effects of conductive carbon nanoparticles (carbon black Vulcan, CB) on methanogenesis from glucose by anaerobic sludge. We found that a relatively high concentration (e.g., 2% w / v ) of CB entirely inhibited the methanogenesis, where a substantial amount of acetate was accumulated after degradation of glucose. Quantitative real-time PCR assays and metabarcoding of 16S rRNA amplicons revealed that, while bacteria were stably present irrespective of the presence and absence of CB, archaea, in particular methanogens, were largely decreased in the presence of CB. Pure-culture experiments showed that methanogenic archaea were more seriously damaged by CB than fermentative bacteria. These results demonstrate that CB specifically inhibits methanogens in anaerobic sludge. We attempted to supplement cathode chambers of microbial electrolysis cells with CB for inhibiting methanogenesis from hydrogen, demonstrating that hydrogen is stably produced in the presence of CB.

Background As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. Results Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems. Conclusions The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.