Methanogenic Community Composition Research Articles

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.

The process of methanogenesis in paddy fields under different elevated CO2 concentrations

Understanding the process of methanogenesis in paddy fields under the scenarios of future climate change is of great significance for reducing greenhouse gas emissions and regulating the soil carbon cycle. Methyl Coenzyme M Reductase subunit A (mcrA) of methanogens is a rate-limiting enzyme that catalyzes the final step of CH4 production. However, the mechanism of methanogenesis change in the paddy fields under different elevated CO2 concentrations (e[CO2]) is rarely explored in earlier studies. In this research, we explored how the methanogens affect CH4 flux in paddy fields under various (e[CO2]). CH4 flux and CH4 production potential (MPP), and mcrA gene abundance were quantitatively analyzed under C (ambient CO2 concentration), C1 (C + 160 ppm CO2), and C2 (C + 200 ppm CO2) treatments. Additionally, the community composition and structure of methanogens were also compared with Illumina MiSeq sequencing. The results showed that C2 treatment significantly increased CH4 flux and MPP at the tillering stage. E[CO2] had a positive effect on the abundance of methanogens, but the effect was insignificant. We detected four known dominant orders of methanogenesis in this study, such as Methanosarcinales, Methanobacteriales, Methanocellales, and Methanomicrobiales. Although e[CO2] did not significantly change the overall community structure and diversity of methanogens, C2 treatment significantly reduced the relative abundance of two uncultured genera compared to C treatment. A linear regression model of DOC, methanogenic abundance, and MPP can explain 67.2% of the variation of CH4 flux under e[CO2]. Overall, our results demonstrated that CH4 flux in paddy fields under e[CO2] was mainly controlled by soil unstable C substrate and the abundance and activity of methanogens in rhizosphere soil.

Changes in the diversity and abundance of syntrophic and methanogenic communities in response to rice phenology

Anaerobic methane production from paddy soils plays an important role in global methane emissions. Syntrophic-methanogenic associations have been viewed as a key regulator of methane generation in paddy fields. However, the effects of rice phenology on the diversity and abundance of syntrophic and methanogenic communities remain largely unknown. This study investigated the changes in syntrophic-methanogenic associations at different rice growth by comparing the 16S RNA sequences of total (DNA-based) and active (RNA-based) microbial communities in rhizosphere and bulk soils. Moreover, the concentrations of specific syntrophs and methanogens were quantified using qPCR assay. Statistical significant differences in the alpha and beta diversities were observed between DNA-based and RNA-based syntrophic communities. The relative abundance of syntrophs in rhizosphere soil was significantly higher at RNA level compared to that at DNA level, indicating that syntrophs display considerably high specific activities. Syntrophic bacteria accounted for 6.23–6.81% of the active communities in rhizosphere soil and 6.12–6.71% in bulk soil. Besides, the quantities of methanogens increased over the entire period of rice growth, and peaked at flowering stage. Such changing pattern was consistent with the total number of short-chain fatty acids-degrading syntrophs at flowering stage, suggesting that rice phenology can affect both syntrophic and methanogenic activities. Furthermore, not only environmental factors (e.g., pH and SOC), but also organic acids (e.g., citrate and succinate), shaped the composition and abundance of syntrophic and methanogenic communities in paddy soils.

The thermal response of soil microbial methanogenesis decreases in magnitude with changing temperature

Microbial methanogenesis in anaerobic soils contributes greatly to global methane (CH4) release, and understanding its response to temperature is fundamental to predicting the feedback between this potent greenhouse gas and climate change. A compensatory thermal response in microbial activity over time can reduce the response of respiratory carbon (C) release to temperature change, as shown for carbon dioxide (CO2) in aerobic soils. However, whether microbial methanogenesis also shows a compensatory response to temperature change remains unknown. Here, we used anaerobic wetland soils from the Greater Khingan Range and the Tibetan Plateau to investigate how 160 days of experimental warming (+4°C) and cooling (−4°C) affect the thermal response of microbial CH4 respiration and whether these responses correspond to changes in microbial community dynamics. The mass-specific CH4 respiration rates of methanogens decreased with warming and increased with cooling, suggesting that microbial methanogenesis exhibited compensatory responses to temperature changes. Furthermore, changes in the species composition of methanogenic community under warming and cooling largely explained the compensatory response in the soils. The stimulatory effect of climate warming on soil microbe-driven CH4 emissions may thus be smaller than that currently predicted, with important consequences for atmospheric CH4 concentrations.

Pretreatments of Broussonetia papyrifera: in vitro assessment on gas and methane production, fermentation characteristic, and methanogenic archaea profile.

ObjectiveThe present study was conducted to examine the gas production, fermentation characteristics, nutrient degradation, and methanogenic community composition of a rumen fluid culture with Broussonetia papyrifera (B. papyrifera) subjected to ensiling or steam explosion (SE) pretreatment.MethodsFresh B. papyrifera was collected and pretreated by ensiling or SE, which was then fermented with ruminal fluids as ensiled B. papyrifera group, steam-exploded B. papyrifera group, and untreated B. papyrifera group. The gas and methane production, fermentation characteristics, nutrient degradation, and methanogenic community were determined during the fermentation.ResultsCumulative methane production was significantly improved with SE pretreatment compared with ensiled or untreated biomass accompanied with more volatile fatty acids production. After 72 h incubation, SE and ensiling pretreatments decreased the acid detergent fiber contents by 39.4% and 22.9%, and neutral detergent fiber contents by 10.6% and 47.2%, respectively. Changes of methanogenic diversity and abundance of methanogenic archaea corresponded to the variations in fermentation pattern and methane production.ConclusionCompared with ensiling pretreatment, SE can be a promising technique for the efficient utilization of B. papyrifera, which would contribute to sustainable livestock production systems.

Biochar decreases methanogenic archaea abundance and methane emissions in a flooded paddy soil

Biochar addition can reduce methane (CH4) emissions from paddy soils while the mechanisms involved are not entirely clear. Here, we studied the effect of biochar addition on CH4 emissions, and the abundance and community composition of methanogens and methanotrophs over two rice cultivation seasons. The experiment had the following five treatments: control (CK), chemical fertilizer application only (BC0), and 0.5% (w/w) (BC1), 1% (BC2), and 2% of biochar applied with chemical fertilizers (BC3). The season-wide CH4 emissions were decreased (P < 0.05) by 22.2–95.7% in biochar application compared with BC0 in the two rice seasons (2017 and 2018). In 2017, biochar application decreased methanogenic archaea (mcrA) but increased methanotrophic bacteria (pmoA) abundances, and decreased the ratio of mcrA/pmoA, as compared with BC0 (P < 0.05). In 2018, the abundance of mcrA was lower in BC2 and BC3 than in BC0 (P < 0.05) but was not different between BC0 and BC1, and the abundance of pmoA was lower in BC1, BC2 and BC3 than in BC0 (P < 0.05). The CH4 emissions were positively related to abundances of the mcrA gene (P < 0.01) but not to that of the pmoA gene in two rice seasons. Rice grain yield was increased by 62.2–94.1% in biochar addition treatments compared with BC0 in the first year (P < 0.01) and by 29.9–37.6% in BC2 and BC3 compared with BC0 in the second year (P < 0.05). Biochar application decreased CH4 emissions by reducing methanogenic archaea abundance in the studied flooded paddy soil.

Recovery of methanogenic community and its activity in long-term drained peatlands after rewetting

Peatland rewetting is a widely used restoration technique, yet the recovery of anaerobic processes is poorly characterized. Microbes involved in anaerobic processes, especially methanogens, could reflect the stabilization of anaerobic conditions, vegetation succession and overall restoration success.We investigated the effect of long-term drainage and hydrological rewetting on methanogenic abundance, community composition and CH4 production potential in bogs and spruce swamp forests. Additionally, the substrate limitation of methanogens was tested with a focus on original peatland plant species and their spreading after rewetting by addition of natural substrates.Drainage strongly reduced the abundance and diversity of the methanogenic community. After rewetting, methanogenic abundance and community composition reached almost a pristine-like state, however their CH4 production remained as low as in the drained sites. Substrate addition confirmed the substrate limitation of methanogens due to strongly decomposed peat and the slow spreading of original peatland vegetation. The addition of natural substrates supported methanogenesis close to a pristine-like level.The limited CH4 production reflected not fully recovered anaerobic microbial community composition and vegetation structure 7–16 years after rewetting, although anaerobic conditions seemed to stabilize. Thus, the re-establishment of peatland vegetation structure is crucial for the recovery of methanogenic activity and microbial processes in rewetted peatlands. Moreover, methanogenic community composition, abundance and activity could be used as indicators of restoration success. Originality significant statementPeatland drainage is increasingly recognized as a major problem affecting the status of valuable natural habitats, water quality and global carbon balance. Rewetting projects are set up to combat and mitigate the losses; yet not enough is known about the recovery of anaerobic processes, especially methanogenesis, which are assumed to reflect stabilization of anaerobic conditions and overall restoration success. Forestry-drained spruce swamp forests and bogs, common in northern Europe, are currently rewetted for both nature conservation purposes and for their anticipated function as hydrological buffers, but information on the recovery of anaerobic microbial communities and especially methanogens are only partly known.Our study concerns the effect of long-term drainage and hydrological rewetting on methanogenic abundance, community composition and activity (CH4 production potential) in undrained, drained and rewetted bogs and spruce swamp forests in the Bohemian Forest, Central Europe. We searched for a reason of limited methanogenic activity in rewetted sites by addition of natural substrates simulating the spreading of original peatland plants (Sphagnum, sedges). This paper contributes to scientific understanding on how long it takes for rewetted peatlands to recover anaerobic microbial communities, anaerobic processes and what are the crucial factors in this process. These results provides a basis for further studies on the trophic relations between anaerobic microbes and recovery of the drained peatlands after rewetting. This study can also extend a set of indicators which should be use for restoration progress evaluation.

Spatial and seasonal variation of methanogenic community in a river-bay system in South China.

River-bay system is a transitional zone connecting land and ocean and an important natural source for methane emission. Methanogens play important roles in the global greenhouse gas budget and carbon cycle since they produce methane. The abundance and community assemblage of methanogens in such a dynamic system are not well understood. Here, we used quantitative PCR and high-throughput sequencing of the mcrA gene to investigate the abundance and community composition of methanogens in the Shenzhen River-Bay system, a typical subtropical river-bay system in Southern of China, during the wet and dry seasons. Results showed that mcrA gene abundance was significantly higher in the sediments of river than those of estuary, and was higher in wet season than dry season. Sequences of mcrA gene were mostly assigned to three orders, including Methanosarcinales, Methanomicrobiales, and Methanobacteriales. Specifically, Methanosarcina, Methanosaeta, and Methanobacterium were the most abundant and ubiquitous genera. Methanogenic communities generally clustered according to habitat (river vs. estuary), and salinity was the major factor driving the methanogenic community assemblage. Furthermore, the indicator groups for two habitats were identified. For example, Methanococcoides, Methanoculleus, and Methanogenium preferentially existed in estuarine sediments, whereas Methanomethylovorans, Methanolinea, Methanoregula, and Methanomassiliicoccales were more abundant in riverine sediments, indicating distinct ecological niches. Overall, these findings reveal the distribution patterns of methanogens and expand our understanding of methanogenic community assemblage in the river-bay system. Key Points • Abundance of methanogens was relatively higher in riverine sediments. • Methanogenic community in estuarine habitat separated from that in riverine habitat. • Salinity played a vital role in regulating methanogenic community assemblage.

Effect of phosphorus amendments on rice rhizospheric methanogens and methanotrophs in a phosphorus deficient soil

Methane emission can be affected by soil fertility, but little is known about the influence of soil phosphorus (P) nutrition on methane production and oxidation processes. In this study, a pot experiment was conducted to explore the effects of P amendments on activity, abundance and community composition of soil methanogens and methanotrophs using P deficient paddy soil. The abundance and community composition of methanogens and methanotrophs, methane production and oxidation potentials were investigated by real-time quantitative PCR, Miseq high-throughput sequencing and biochemical assays, respectively. The results showed that although P amendments induced increases of both methanogenic and methanotrophic abundances and potential activities within bulk soils, the increases were relatively small. In contrast, P applications resulted in large and significant increases in the copy numbers and potential activity of methanogens within rhizosphere soils, whereas, this phenomenon was not detected for methanotrophs. Moreover, the methanogenic community structure remained similar amongst the P amendment treatments for both rhizosphere and bulk soils. For methanotrophs, P application induced clear shifts in the community composition within rhizosphere soils but not in bulk soils, where the relative abundance of type I methanotrophs increased whilst type II decreased. Our data indicate that the application of phosphate to P deficient paddy soils could preferentially stimulate the abundance and activity of methanogens over methanotrophs within the rice rhizosphere. Ultimately, improving plant growth by P input may accelerate methane emissions through stimulating rhizosphere methanogenic populations without a concomitant increase in the methanotrophic compartment.

Methanogenic response to long-term permafrost thaw is determined by paleoenvironment.

ABSTRACTMethane production in thawing permafrost can be substantial, yet often evolves after long lag phases or is even lacking. A central question is to which extent the production of methane after permafrost thaw is determined by the initial methanogenic community. We quantified the production of methane relative to carbon dioxide (CO2) and enumerated methanogenic (mcrA) gene copies in long-term (2–7 years) anoxic incubations at 4 °C using interglacial and glacial permafrost samples of Holocene and Pleistocene, including Eemian, origin. Changes in archaeal community composition were determined by sequencing of the archaeal 16S rRNA gene. Long-term thaw stimulated methanogenesis where methanogens initially dominated the archaeal community. Deposits of interstadial and interglacial (Eemian) origin, formed under higher temperatures and precipitation, displayed the greatest response to thaw. At the end of the incubations, a substantial shift in methanogenic community composition and a relative increase in hydrogenotrophic methanogens had occurred except for Eemian deposits in which a high abundance of potential acetoclastic methanogens were present. This study shows that only anaerobic CO2 production but not methane production correlates significantly with carbon and nitrogen content and that the methanogenic response to permafrost thaw is mainly constrained by the paleoenvironmental conditions during soil formation.

Population dynamics of methanogens and methanotrophs along the salinity gradient in Pearl River Estuary: implications for methane metabolism.

Methane, a major greenhouse gas, plays an important role in global carbon cycling and climate change. Methanogenesis is identified as an important process for methane formation in estuarine sediments. However, the metabolism of methane in the water columns of estuaries is not well understood. The goal of this research was to examine the dynamics in abundance and community composition of methanogens and methanotrophs, and to examine whether and how they take part in methane metabolism in the water columns from the lower Pearl River (freshwater) to the coastal South China Sea (seawater). Quantitative PCR (qPCR) and high-throughput sequencing results showed that the abundance of methanogens decreased with increasing salinity, suggesting that growth of these methanogens in the Pearl River Estuary may be influenced by high salinity. Also, the methane concentration in surface waters was lower than that in near-bottom waters at most sites, suggesting sediment methanogens are a likely source of methane. In the estuarine mixing zone, significantly high methane concentrations existed with the presence of salt-tolerant methanogens (e.g., Methanomicrobiaceae, Methanocella, Methanosaeta and Methanobacterium) and methanotrophs (e.g., Methylocystis and Methylococcaceae), which were found in brackish habitats. Furthermore, a number of methanotrophic OTUs (from pmoA gene sequence data) had specific positive correlations with methanogenic OTUs (from mcrA gene sequence data), and some of these methanogenic OTUs were correlated with concentrations of particulate organic carbon (POC). The results indicate that methanotrophs and methanogens may be intimately linked in methane metabolism attached with particles in estuarine waters.

Spatial variability of sediment methane production and methanogen communities within a eutrophic reservoir: Importance of organic matter source and quantity.

Freshwater reservoirs are an important source of the greenhouse gas methane (CH4) to the atmosphere, but global emission estimates are poorly constrained (13.3-52.5 Tg C yr-1), partially due to extreme spatial variability in emission rates within and among reservoirs. Spatial heterogeneity in the availability of organic matter (OM) for biological CH4 production by methanogenic archaea may be an important contributor to this variation. To investigate this, we measured sediment CH4 potential production rates, OM source and quantity, and methanogen community composition at 15 sites within a eutrophic reservoir in Ohio, USA. CH4 production rates were highest in the shallow riverine inlet zone of the reservoir, even when rates were normalized to OM quantity, indicating that OM was more readily utilized by methanogens in the riverine zone than in the transitional or lacustrine zones. Sediment stable isotopes and C:N indicated a greater proportion of terrestrial OM in the particulate sediment of this zone. Methanogens were present at all sites, but the riverine zone contained a higher relative abundance of methanogens capable of acetoclastic and methylotrophic methanogenesis, likely reflecting differences in decomposition processes or OM quality. While we found that methane potential production rates were negatively correlated with autochthonous carbon in particulate sediment OM, rates were positively correlated with indicators of autochthonous carbon in the porewater dissolved OM. It is likely that both dissolved and particulate sediment OM affect CH4 production rates, and that both terrestrial and aquatic OM sources are important in the riverine methane production hot spot.

Stable isotopes of C and H in methane fermentation of agriculture substrates at different temperature conditions

AbstractAgricultural substrates (maize silage and cattle manure) were used to carry out methane fermentation process in bioreactors under laboratory conditions. Identical mixtures of these substrates were incubated for 43 days at 20, 30 and 40ºC to determine how different temperature conditions affect the δ13C(CH4), δH(CH4), and δ13C(CO2) values. To ensure correct anaerobic digestion, the following parameters of the organic substrates and fermentation solutions were monitored: total organic carbon (TOC), volatile solids (VS), volatile fatty acids (VFA), chemical oxygen demand (COD) and carbon to nitrogen ratio (C/N). The variants with higher incubation temperature yielded higher amounts of biogas (20ºC=84.5, 30ºC=101.8 and 40ºC=133.3 dm3/kg VS). In the case of gas products of methane fermentation, it was observed that the higher temperature of incubation affects the depletion in heavy isotopes. At 20ºC, 30ºC, and 40ºC mean values of δ13C(CH4) reached −26.4, −29.7, and −35.4‰, respectively. Mean values of δ2H(CH4) were −311.6, −354.0, and −398.5permil, and of δ13C(CO2) +8.9, +3.7, and −2.3‰, respectively. Moreover, the apparent fractionation coefficient α13C(CO2-CH4) were calculated, which decreased when the temperature increased. This isotopic tool was used to identify acetoclastic reaction as a dominant methanogenesis pathway. Observed changes in the isotopic composition of gaseous products obtained at different incubation temperatures may indicate decomposition of different carbon sources (e.g. lactate, propionate) to acetate and its fermentation by acetoclastic methanogens. It is possible that this was also related to the observation of the various metabolic models due to the varied methanogenic community composition.

Organic matter supply and bacterial community composition predict methanogenesis rates in temperate lake sediments

AbstractThe objective of our study was to identify environmental conditions that structure lake sediment microbial communities and determine whether community composition explained inter‐lake variation in potential methanogenesis rates. We performed a comparative analysis of microbial communities and methanogenesis rates in 14 lake sediments along gradients of pH and primary productivity. Variation in methanogen community composition and non‐methanogen microbial community composition was best explained by pH and sediment organic matter content. However, these regulators of methanogen community structure were not associated with differences in methanogenesis rates. Instead, variation in lake methanogenesis rates was best explained by proxies for organic matter supplied to sediments (lake chlorophyll a concentration and sediment pore‐water total phosphorus) and the composition of the non‐methanogen microbial community. Our results suggest a role for sediment bacterial community in influencing methanogenesis via the supply of growth substrates.

Spartina alterniflora invasion drastically increases methane production potential by shifting methanogenesis from hydrogenotrophic to methylotrophic pathway in a coastal marsh

Abstract 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. 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. 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 methylamine‐utilising Methanosarcinaceaein 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. Synthesis. Our results suggest that invasive Spartina alternifloraplants 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.

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents

The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, CH4, and metagenome methanogen concentration estimates in 20–40 °C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29–33 h. Only 1011 methanogenic cells occupying 1.8–18 m3 of ocean crust per m2 of vent seafloor area were needed to produce the observed CH4 anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities.

Effect of temperature on the microbial community responsible for methane production in alkaline NamCo wetland soil

The Tibetan plateau is a cold environment at high altitude and is very sensitive to global climate change. Wetlands on this plateau are among the major sources of the important greenhouse gas methane, and temperature is an important factor in controlling CH4 production. However, it remains unknown how CH4 production and microbial processes in such wetlands respond to climate warming. Therefore, we anaerobically incubated soil slurries at 10, 20, 30 and 45 °C for 100 days to investigate the effects of temperature on CH4 production and microbial community structure in the wetland soil next to NamCo, an alkaline lake on the Tibetan plateau. Rates and pathways of CH4 production were determined by measuring accumulation of CH4 and stable isotope fractionation, respectively. The microbial community structures were investigated by Illumina sequencing of bacterial and archaeal 16S rRNA and methanogenic mcrA genes and/or transcripts. Increasing the temperature from 10 to 30 °C enhanced CH4 production, but at 45 °C it almost ceased and the methanogenic precursor acetate accumulated. At lower temperatures, acetate accumulated only if acetoclastic CH4 production was inhibited with methyl fluoride. The abundance of bacterial and archaeal 16S rRNA genes and mcrA genes were generally around 108 g−1 dry weight soil or higher. Alphaproteobacteria became increasingly abundant with time of incubation (up to 100 days) and temperature increasing from 10 to 30 °C. At 45 °C, however, Firmicutes became the dominant bacterial phylum. While about >70% of CH4 was produced from acetoclastic methanogenesis at 10–30 °C, hydrogenotrophic methanogenesis was the dominant (>82%) pathway at 45 °C. The acetoclastic genus Methanoseata was the main methanogen at low (10 °C) and moderate (20 °C and 30 °C) temperatures, but the hydrogenotrophic genera Methanoregula and Methanomassiliicoccus dominated at high temperature (45 °C). Bathyarchaeota, with unknown function, dominated next to methanogenic Euryarchaeota the archaeal community, especially on DNA level. The methanogenic archaeal community composition of NamCo soil resembled that of alkaline lake sediments from the Tibetan Plateau. Structure and function of the methanogenic microbial community in alkaline wetlands and their temperature response seem to be different from those found in neutral paddy soil or acidic peatland soil.