Methanogenic Community Composition Research Articles

Microbial methanogenesis in aerobic water: A key driver of surface methane enrichment in a deep reservoir

Significant amounts of the greenhouse gas methane (CH4) are released into the atmosphere worldwide via freshwater sources. The surface methane maximum (SMM), where methane is supersaturated in surface water, has been observed in aquatic systems and contributes significantly to emissions. However, little is known about the temporal and spatial variability of SMM or the mechanisms underlying its development in artificial reservoirs. Here, the community composition of methanogens as major methane producers in the water column and the mcrA gene was investigated, and the cause of surface methane supersaturation was analyzed. In accordance with the findings, elevated methane concentration of SMM in the transition zone, with an annually methane emission flux 2.47 times higher than the reservoir average on a large and deep reservoir. In the transition zone, methanogens with mcrA gene abundances ranging from 0.5 × 103–1.45 × 104 copies/L were found. Methanobacterium, Methanoseata and Methanosarcina were the three dominate methanogens, using both acetic acid and H2/CO2 pathways. In summary, this study contributes to our comprehension of CH4 fluxes and their role in the atmospheric methane budget. Moreover, it offers biological proof of methane generation, which could aid in understanding the role of microbial methanogenesis in aerobic water.

Stochastic processes drive the diversity and composition of methanogenic community in a natural mangrove ecosystem

Methanogens are considered to be crucial components of mangrove ecosystems with ecological significance. However, understanding the assembly processes of methanogenic communities in mangrove ecosystems is relatively insufficient. In the current study, a natural mangrove in a protection zone was employed to investigate the diversity and assembly processes of methanogenic community by using amplicon high-throughput sequencing, a null model as well as a neutral community model. The results showed that methanogenic community in mangrove sediments were highly diverse, with the predominance of methylotrophic Methanolobus, and hydrogenotrophic Methanogenium, Methanospirillum. The diversity, composition, and gene abundance varied obviously across the mangrove sampling sites, whereas the measured environmental variables exhibited a negligible effect. Null model showed that the values of beta nearest-taxon index were mostly between −2 and 2, indicating that stochastic processes contributed more than deterministic processes driving the methanogenic community assembly in mangrove sediments. Neutral community model revealed a high estimated migration rate of methanogenic community, further substantiating the significance of stochastic processes. Among the keystone species identified in network analysis, methanogens affiliated to hydrogenotrophic Methanospirillum may have a crucial role in maintaining the structure and function of methanogenic community. Notably, these keystone species were almost unaffected by measured environmental factors, indicating that the methanogenic community in mangrove sediments is more likely to be affected by stochastic processes. This study deepens the understanding of the diversity and assembly of methanogenic community in mangrove sediments, and provides clues to maintain mangrove ecosystem functioning.

Methanogenic and methanotrophic communities determine lower CH4 fluxes in a subtropical paddy field under long-term elevated CO2

Clarifying the effects of elevated CO2 concentration (e[CO2]) on CH4 emissions from paddy fields and its mechanisms is a crucial part of the research on agricultural systems in response to global climate change. However, the response of CH4 fluxes from rice fields to long-term e[CO2] (e[CO2] duration >10 years) and its microbial mechanism is still lacking. In this study, we used a long-term free-air CO2 enrichment experiment to examine the relationship between CH4 fluxes and the methanogenic and methanotrophic consortia under long- and short-term e[CO2]. We demonstrated that contrary to the effect of short-term e[CO2], long-term e[CO2] decreased CH4 fluxes. This may be associated with the reduction of methanogenic abundance and the increase of methanotrophic abundance under long-term e[CO2]. In addition, long-term e[CO2] also changed the community structure and composition of methanogens and methanotrophs compared with short-term e[CO2]. Partial least squares path modeling analysis showed that long-term e[CO2] also could affect the abundance and composition of methanogens and methanotrophs indirectly by influencing soil physical and chemical properties, thereby ultimately altering CH4 fluxes in paddy soils. These findings suggest that current estimates of short-term e[CO2]-induced CH4 fluxes from paddy fields may be overestimated. Therefore, a comprehensive assessment of climate‑carbon cycle feedbacks may need to consider the microbial regulation of CH4 production and oxidation processes in paddy ecosystems under long-term e[CO2].

Regulation of the methanogenesis pathways by hydrogen at transcriptomic level in time

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.

Climatic effect from oyster reef restoration in Spartina alterniflora invaded intertidal mudflat: From the perspective of CH4 and N2O production

Spartina alterniflora is a dominant invasive species along the coast of China. A surprising phenomenon that the oyster reef formation is substituting the S. alterniflora invasion, was recently observed in the west coast of Bohai Bay, North China. As the intertidal mudflat ecosystem is critical for coastal blue carbon, this paper aims to evaluate the climatic effect of the alternation from the perspective of potential CH4 and N2O production. The sediment geochemical properties and potential CH4 and N2O productions were therefore measured in sediments dominated by Spartina alterniflora (SA), oyster reef (OR), mixture of S. alterniflora and oyster reef (SA-OR) and bare mudflat (BM) at an intertidal mudflat. Meanwhile, sediment microbial community structure and function genes were also determined utilizing metagenome high-throughput sequencing technology. Our results indicated that the formation of oyster reef in S. alterniflora invaded intertidal mudflat might slightly reduce the sediment potential CH4 production and enhance the sediment potential N2O production. The oyster reef formation could alter the community composition of methanogens and the abundance of functional genes in methanogenesis, and transform the main pathway from methylotrophic to hydrogenotrophic methanogenesis in surface sediments. Metagenome sequencing revealed that the oyster reef formation may promote nitrification, inhibit dissimilatory nitrate reduction (DNRA) and nitrate assimilation functions, and reduce the abundance of nosZ genes. Mantel analysis showed that pH, soluble salt and dissolved carbon (DC) were the most important factors influencing the composition of microbial community. In general, our results imply that the growth of oyster reef in the S. alterniflora invaded area has opposing effects from the prospective of the potential CH4 and N2O production.

Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave

Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogenic community composition and their interaction with MOBs in the Heshang Cave to comprehensively understand methane cycling in subsurface biosphere. MOBs in karst cave were dominated by high-affinity MOB, upland soil cluster (USC), with USCγ pmoA gene abundance within the range of 1.34 × 104 to 1.8 × 107 copies·g−1 DW. In contrast, methanogens were dominated by Methanoregula and cluster ZC-I. The mcrA numbers were 7.21 × 103 to 8.31 × 104 copies·g−1 DW, 1–3 orders of magnitude lower than those of MOB. The inter-domain network analysis indicated that MOBs and methanogens cooperated more in the interior of the cave. Despite of the higher number of methanogenic nodes in the network, MOB dominated the keystone taxa, suggesting a leading functional role of MOB. MOB in caves showed a comparable with or higher potential methane oxidizing rate (PMOR, 0.63 ng CH4·g−1 DW·h−1 in sediment versus 11.02 ng CH4·g−1 DW·h−1 in weathered rock) than those in soils, whereas methane produced by methanogens was undetected. Collectively, high absolute abundances of MOB, high PMORs, the dominance of methanotrophic keystone taxa in the inter-domain network confirmed the superiority of MOBs over methanogens in the oligotrophic karst cave, mounting new evidence on caves as an important methane sink in terms of the interaction between methanogens and MOBs.

Decreased CH4 emissions associated with methanogenic and methanotrophic communities and their interactions following Fe(III) fertiliser application in rice paddies

Rice paddies are important sources of atmospheric methane (CH4), where CH4 fluxes are determined by the balance of production and oxidation. While the application of Fe(III) fertilizer is a proven effective strategy for mitigating CH4 emissions from rice paddies, little is known about the role of methanogen and methanotroph communities and their interactions. In this study, we measured the CH4 flux in a rice paddy field experiment, where the responses of methanogenic and methanotrophic activities to Fe(III) fertiliser applied at medium (Fe-M) and high (Fe-H) levels were examined using real-time quantitative PCR coupled with co-occurrence network analysis after Illumina MiSeq sequencing of the mcrA and pmoA genes. Relative to the control without Fe(III) fertiliser application, in the Fe-M and Fe-H treatments, seasonal CH4 emissions were significantly decreased by 65% and 62%, respectively. Fe(III) fertilisation significantly decreased the copy numbers and potential activity of methanogens, and had an opposite effect on methanotrophs. We found Methanothrix was the predominant genus more adaptive to grow in Fe-rich environments. Fe(III) fertilisation caused a shift in the methanotrophic community towards a predominance of Type II methanotrophs. Soil total Fe concentration, soil electrical conductivity, and different valences of iron were key factors in the composition of methanogenic and methanotrophic communities. Fe(III) fertilisation led to a less complex community taxonomic structure mostly attributed to fewer nodes and edges in both the co-occurrence and mutual exclusion networks of methanogen and methanotrophs. Our findings suggest that adding Fe(III) fertiliser in rice paddies could mitigate CH4 emissions by regulating both methanogens and methanotrophs.

Acetoclastic methanogenesis pathway stability despite the high microbial taxonomic variability in the transition from acidogenesis to methanogenesis during food waste anaerobic digestion

Anaerobic digestion (AD) is a microbial-mediated biogeochemical process that includes hydrolysis, acidogenesis, acetogenesis and methanogenesis. AD instability usually occurs in the transition from the acidogenesis phase (AP) to the methanogenesis phase (MP) due to over acidification. However, the underlying microbial mechanism of this transition has not been well characterized. In the present study, the transition of bacterial and methanogenic community composition, methanogenesis functional gene expression and metabolic pathways from AP to MP during food waste (FW) AD were investigated in a bioreactor using metagenomics and reverse transcription PCR technology. AP and MP were identified by changes in methane production, gas accumulation, pH and volatile fatty acids (VFAs). Concomitant with the changes in these physiochemical parameters, the bacterial and methanogenic community composition showed succession patterns. The bacterial composition transformed from acidogenic bacteria (Propionispira and Bacteroides) to hydrolytic bacteria (Smithella, Syntrophus and Syntrophorhabdus), and the methanogen composition transformed from the domination of acetoclastic methanogens (Methanosaeta) to the codomination of hydrogenotrophic methanogens (Methanoculleus, Methanolinea and Methanobacterium) and acetoclastic methanogens (Methanosaeta). The expression level of the methanogenesis functional gene mcrA significantly (p < 0.05) increased in response to the increasing methane production. In contrast, acetoclastic methanogenesis as the main methanogenesis metabolic pathway remained stable. These results showed that FWAD key physiochemical parameters drive the variation in microbial community composition and functional genes expression but not the methanogenesis metabolic pathway. The finding suggests that FWAD process may be better predicted by methanogenic functional characteristics than by microbial community composition.

Effects of brackish water inflow on methane-cycling microbial communities in a freshwater rewetted coastal fen

Abstract. Rewetted peatlands can be a significant source of methane (CH4), but in coastal ecosystems, input of sulfate-rich seawater could potentially mitigate these emissions. The presence of sulfate as an electron acceptor during organic matter decomposition is known to suppress methanogenesis by favoring the growth of sulfate reducers, which outcompete methanogens for substrate. We investigated the effects of a brackish water inflow on the microbial communities relative to CH4 production–consumption dynamics in a freshwater rewetted fen at the southern Baltic Sea coast after a storm surge in January 2019 and analyzed our data in context with the previous freshwater rewetted state (2014 serves as our baseline) and the conditions after a severe drought in 2018 (Fig. 1). We took peat cores at four previously sampled locations along a brackishness gradient to compare soil and pore water geochemistry as well as the microbial methane- and sulfate-cycling communities with the previous conditions. We used high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to characterize pools of DNA and RNA targeting total and putatively active bacteria and archaea. Furthermore, we measured CH4 fluxes along the gradient and determined the concentrations and isotopic signatures of trace gases in the peat. We found that both the inflow effect of brackish water and the preceding drought increased the sulfate availability in the surface and pore water. Nevertheless, peat soil CH4 concentrations and the 13C compositions of CH4 and total dissolved inorganic carbon (DIC) indicated ongoing methanogenesis and little methane oxidation. Accordingly, we did not observe a decrease in absolute methanogenic archaea abundance or a substantial change in methanogenic community composition following the inflow but found that the methanogenic community had mainly changed during the preceding drought. In contrast, absolute abundances of aerobic methanotrophic bacteria decreased back to their pre-drought level after the inflow, while they had increased during the drought year. In line with the higher sulfate concentrations, the absolute abundances of sulfate-reducing bacteria (SRB) increased – as expected – by almost 3 orders of magnitude compared to the freshwater state and also exceeded abundances recorded during the drought by over 2 orders of magnitude. Against our expectations, methanotrophic archaea (ANME), capable of sulfate-mediated anaerobic methane oxidation, did not increase in abundance after the brackish water inflow. Altogether, we could find no microbial evidence for hampered methane production or increased methane consumption in the peat soil after the brackish water inflow. Because Koebsch et al. (2020) reported a new minimum in CH4 fluxes at this site since rewetting of the site in 2009, methane oxidation may, however, take place in the water column above the peat soil or in the loose organic litter on the ground. This highlights the importance of considering all compartments across the peat–water–atmosphere continuum to develop an in-depth understanding of inflow events in rewetted peatlands. We propose that the changes in microbial communities and greenhouse gas (GHG) fluxes relative to the previous freshwater rewetting state cannot be explained with the brackish water inflow alone but were potentially reinforced by a biogeochemical legacy effect of the preceding drought.

Phosphorus control and dredging decrease methane emissions from shallow lakes

Freshwater ecosystems are an important source of the greenhouse gas methane (CH4), and their emissions are expected to increase due to eutrophication. Two commonly applied management techniques to reduce eutrophication are the addition of phosphate-binding lanthanum modified bentonite (LMB, trademark Phoslock©) and dredging, but their effect on CH4 emissions is still poorly understood. Here, this study researched how LMB and dredging affected CH4 emissions using a full-factorial mesocosm design monitored for 18 months. The effect was tested by measuring diffusive and ebullitive CH4 fluxes, plant community composition, methanogen and methanotroph activity and community composition, and a range of physicochemical water and sediment variables. LMB addition decreased total CH4 emissions, while dredging showed a trend towards decreasing CH4 emissions. Total CH4 emissions in all mesocosms were much higher in the summer of the second year, likely because of higher algal decomposition and organic matter availability. First, LMB addition lowered CH4 emissions by decreasing P-availability, which reduced coverage of the floating fern Azolla filiculoides, and thereby prevented anoxia and decreased surface water NH4+ concentrations, lowering CH4 production rates. Second, dredging decreased CH4 emissions in the first summer, possibly it removed the methanogenic community, and in the second year by preventing autumn and winter die-off of the rooted macrophyte Potamogeton cripsus. Finally, methanogen community composition was related to surface water NH4+ and O2, and porewater total phosphorus, while methanotroph community composition was related to organic matter content. To conclude, LMB addition and dredging not only improve water quality, but also decrease CH4 emissions, mitigating climate change.

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea.

The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann-Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfate-reducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

Changes in sediment methanogenic archaea community structure and methane production potential following conversion of coastal marsh to aquaculture ponds

Widespread conversion of coastal wetlands into aquaculture ponds in coastal region often results in degradation of the wetland ecosystems, but its effects on sediment's potential to produce greenhouse gases remain unclear. Using field sampling, incubation experiments and molecular analysis, we studied the sediment CH4 production potential and the relevant microbial communities in a brackish marsh and the nearby aquaculture ponds in the Min River Estuary in southeastern China. Sediment CH4 production potential was higher in the summer and autumn months than in spring and winter months, and it was significantly correlated with sediment carbon content among all environmental variables. The mean sediment CH4 production potential in the aquaculture ponds (20.1 ng g−1 d−1) was significantly lower than that in the marsh (45.2 ng g−1 d−1). While Methanobacterium dominated in both habitats (41–59%), the overall composition of sediment methanogenic archaea communities differed significantly between the two habitats (p < 0.05) and methanogenic archaea alpha diversity was lower in the aquaculture ponds (p < 0.01). Network analysis revealed that interactions between sediment methanogenic archaea were much weaker in the ponds than in the marsh. Overall, these findings suggest that conversion of marsh land to aquaculture ponds significantly altered the sediment methanogenic archaea community structure and diversity and lowered the sediment's capacity to produce CH4.

Effects of Pig Manure and Its Organic Fertilizer Application on Archaea and Methane Emission in Paddy Fields

Paddy fields account for 10% of global CH4 emissions, and the application of manure may increase CH4 emissions. In this study, high-throughput sequencing technology was used to investigate the effects of manure application on CH4 emissions and methanogens in paddy soil. Three treatments were studied: a controlled treatment (CK), pig manure (PM), and organic fertilizer (OF). The results showed that the contents of Zn, Cr and Ni in paddy soil increased with the application of manure, but the contents of heavy metals gradually decreased with the growth of rice. The Shannon index and Ace index showed that the application of pig manure and organic fertilizer less affected the diversity and richness of soil Archaea. The results of community composition analysis showed that Methanobacterium, Methanobrevibacter, Methanosphaera, Methanosarcina and Rice_Cluster_I were the main methanogens in paddy soil after manure and organic fertilizer application. Soil environmental factors were changed after applied manure, among which total potassium (TK) and total nitrogen (TN) were the main environmental factors affecting methanogens in paddy soil. The changes of soil environmental factors affected the community composition of methanogens, and the increase of the relative abundance of methanogens maybe the main reason for the increase of CH4 emission flux. The relative abundance of methanogens and CH4 emission flux in paddy soil were increased by both pig manure and organic fertilizer application, and pig manure had a bigger impact than organic manure.

Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.

Microbe-mediated reduction of methane emission in rice-frog crop ecosystem

Rice–frog crop ecosystem (RFCE) can significantly reduce CH4 emission from paddy soils to mitigate global warming. However, information on the correlation of soil microbial communities with paddy soil CH4 emission in RFCEs remains limited. This study evaluated the influence of frogs on CH4 flux, paddy soil/water properties, and abundance/community composition of methanogens and methanotrophs in an RFCE between 2018 and 2019. The study parameters were compared between “with frogs” (RFCE; 15,000 frogs ha−1) and “without frogs” (control check [CK]) conditions. Frogs in paddies significantly decreased the CH4 flux during the rice-growing seasons (p < 0.05) but increased the paddy water/soil dissolved oxygen (DO) concentration, redox potential (Eh), and soil organic carbon (SOC) content. Compared with the CK, the RFCE significantly decreased the relative abundance of the soil methanogen species Candidatus Methanoperedens nitroreducens and Methanocella arvoryzae, genera Candidatus Methanoperedens and Methanocella, and families Methanoperedenaceae and Methanocellaceae (p < 0.05); however, it significantly increased the abundance of the soil methanotroph species Methylosinus sp. LW2, Methylocystis sp. KS3, and Methylocystis sp. KS30; genera Methylosinus and Methylocystis; and family Methylocystaceae (p < 0.05). Furthermore, variation partitioning analysis revealed that oxygen (DO and Eh) explained 41.2% of the variation in the abundance of soil methanogens, which was greater than the effects of C/N (38.2%) and SOC content (38.1%). For soil methanotrophs, oxygen (DO and Eh) explained 45.6% of the variation, which was more than the effects of C/N or pH. Oxygen concentration in the paddy soil/water was the driving factor for the change in the composition of soil methanogenic and methanotrophic microbial communities. Bioturbation due to the frogs increased oxygen availability in the paddy soil, decreased CH4 production by soil methanogens, and increased CH4 oxidation by type II methanotrophs, all of which reduced CH4 emission. Thus, this study provides strong evidence for the microbial mechanisms underlying the reduction of CH4 emission from RFCE.

Beyond the usual suspects: methanogenic communities in eastern North American peatlands are also influenced by nickel and copper concentrations.

Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here, we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analysed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.

Methanogen Community Dynamics and Methanogenic Function Response to Solid Waste Decomposition.

Methane production during solid waste decomposition is a typical methanogen-mediated and enzyme-catalyzed anaerobic digestion (AD). Methanogen community dynamics and metabolic diversity during the decomposition are not known. In this study, we investigated methanogen community dynamics and methanogenic pathways during solid waste decomposition in a bioreactor using high-throughput Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt), respectively. We also related the methanogen community differences with solid waste and leachate physiochemical parameters. Results showed that the percentage of biodegradable matter (BDM) in solid waste decreased from 55 ± 5% in aerobic phase (AP) to 30 ± 2% in anaerobic acid phase (ACP), and to 13 ± 11% in methanogenic phase (MP), resulting in 76% BDM consumption by microbes. Methanogen community structure varied in AP, ACP, and MP, showing that Methanomicrobiales and Methanosarcinales were dominant in AP and MP and archaea E2 was abundant in ACP. Each phase had abundant core methanogen orders, genera, and species with significant difference (p < 0.05). Redundancy analysis showed that biochemical oxygen demand (BOD5) and nitrate significantly influenced methanogen community composition, suggesting that methanogen community structure is nutrient-dependent. Two methanogenic pathways including acetoclastic and hydrogenotrophic pathways with associated functional genes differed at three phases. ACP had the lowest abundance of these genes, indicating that methanogenesis was inhibited in acidogenesis. Abundant hydrogenotrophic and acetoclastic methanogenesis functional genes in MP and AP are in response to the abundance of Methanomicrobiales and Methanosarcinales. The findings provide previously unidentified insight into the mechanism of methanogen community structure and function during solid waste bioconversion for methane.

Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China.

Soil methanogenic microorganisms are one of the primary methane‐producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla–Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.

Biogeographic Pattern of Methanogenic Community in Surface Water along the Yangtze River

Methanogenesis from oxic water has been proven to be a significant component of methane source in large and deep freshwater ecosystems. However, the biogeography of methanogenic community in surface water of large rivers remains uncertain. Here, the community ecology and biogeographic pattern of methanogenic community along the Yangtze River (one of the largest rivers in the world) were studied by using high-throughput sequencing, and the relative importance of environmental and spatial variables on the assemblage of methanogenic community was assessed. The results showed a distinct spatial distribution that the Shannon diversity and Shannon evenness of methanogenic community in downstream of the Yangtze River were significantly higher than those in upstream and midstream sections. The most abundant three genera of methanogenic community were Methanobacterium, Methanosarcina and Methanosaeta, which did not exhibit significant difference between different sections. Besides, the composition of methanogenic community also showed a clear spatial variation along the river. Significant distance effects appeared on both methanogenic community and environmental variables. However, no significant relationship was found between methanogenic community and environmental variables. Compared to the limited contributions of spatial and environmental variables, interactions among taxa could be an important driver in structuring the assembly of methanogenic community. In addition, Methanobacteriales, Methanomassiliicoccales and Methanocellales were the key species of methanogenic community in upstream, midstream and downstream sections, respectively. Overall, the methanogenic community exhibited obvious biogeographic pattern along the Yangtze River, which was attributed to a joint effect of abiotic and biotic factors.

Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.