Methanotrophic Community Structure Research Articles

Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin.

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.

Variations of activity and community structure of nitrite-driven anaerobic methanotrophs in soils between native and invasive species in China's coastal wetlands

Nitrite-driven anaerobic oxidation of methane (nitrite-driven AOM), mediated by ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera)-related bacteria, is a newly-discovered CH4 consumption process in coastal wetlands. Although Spartina alterniflora invasion significantly affects CH4 emissions from coastal wetlands, its impact on the nitrite-driven AOM process and the underlying mechanisms remain unknown. Here, we examined nitrite-driven AOM activity and M. oxyfera-related bacterial community in four coastal wetlands along the southeastern coast of China, under invasive Spartina alterniflora and native plants, including Kandelia candel, Avicennia marina or Phragmites australis. Linear mixed-effects models indicated that the Spartina alterniflora invasion stimulated the overall nitrite-driven AOM activity by an average of 61.5% in coastal wetlands (p < 0.05), but had no impact on the M. oxyfera-related bacterial abundance (p > 0.05). The nitrite-driven AOM activity was 7.1 times higher under Spartina alterniflora than under native species in Yueqing Bay (p < 0.05), and was 34.7%, 8.9% and 15.1% higher under Spartina alterniflora than under native species in Hengsha Island, Jiulong River and Zhanjiang, respectively (p > 0.05). Spartina alterniflora invasion increased the bacterial abundance in Yueqing Bay and Jiulong River Estuary by 6.8 and 7.6 times, respectively, while decreased the abundance by 34.4% and 51.4%, respectively, in Hengsha Island and Zhanjiang (p > 0.05). The partial least squares path model indicated an indirect impact of Spartina alterniflora invasion on the nitrite-driven AOM activity through its effect on soil properties, primarily including dissolved organic carbon content and nitrate content. The Spartina alterniflora invasion did not greatly alter M. oxyfera-related bacterial community. Overall, we shed new light on the potential impact of Spartina alterniflora invasion on CH4 cycling in coastal wetlands.

Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta.

Biogas digestive effluent (BDE) has been applied to rice fields in the Vietnamese Mekong Delta (VMD). However, limited information is available on the community composition and isolation of methanotrophs in these fields. Therefore, the present study aimed (i) to clarify the responses of the methanotrophic community in paddy fields fertilized with BDE or synthetic fertilizer (SF) and (ii) to isolate methanotrophs from these fields. Methanotrophic communities were detected in rhizospheric soil at the rice ripening stage throughout 2 cropping seasons, winter-spring (dry) and summer-autumn (wet). Methanotrophs were isolated from dry-season soil samples. Although the continued application of BDE markedly reduced net methane oxidation potential and the copy number of pmoA genes, a dissimilarity ordination ana-lysis revealed no significant difference in the methanotrophic community between BDE and SF fields (P=0.167). Eleven methanotrophic genera were identified in the methanotrophic community, and Methylosinus and Methylomicrobium were the most abundant, accounting for 32.3-36.7 and 45.7-47.3%, respectively. Type-I methanotrophs (69.4-73.7%) were more abundant than type-II methanotrophs (26.3-30.6%). Six methanotrophic strains belonging to 3 genera were successfully isolated, which included type I (Methylococcus sp. strain BE1 and Methylococcus sp. strain SF3) and type II (Methylocystis sp. strain BE2, Methylosinus sp. strain SF1, Methylosinus sp. strain SF2, and Methylosinus sp. strain SF4). This is the first study to examine the methanotrophic community structure in and isolate several methanotrophic strains from BDE-fertilized fields in VMD.

Temporal and environmental factors drive community structure and function of methanotrophs in volcanic forest soils

Temporal and environmental factors drive community structure and function of methanotrophs in volcanic forest soils

Water table level controls methanogenic and methanotrophic communities and methane emissions in a Sphagnum-dominated peatland.

Peatlands are important sources of the greenhouse gas methane emissions equipoised by methanogens and methanotrophs. However, knowledge about how microbial functional groups associated with methane production and oxidation respond to water table fluctuations has been limited to date. Here, methane-related microbial communities and the potentials of methane production and oxidation were determined along sectioned peat layers in a subalpine peatland across four Sphagnum-dominated sites with different water table levels. Methane fluxes were also monitored at these sites. The results showed that mcrA gene copies for methanogens were the highest in the 10- to 15-cm peat layer, which was also characterized by the maximum potential methane production (24.53 ± 1.83 nmol/g/h). Copy numbers of the pmoA gene for type Ia and Ib methanotrophs were enriched in the 0-5 cm peat layer with the highest potential methane oxidation (43.09 ± 3.44 nmol/g/h). For the type II methanotrophs, the pmoA gene copies were higher in the 10- to 15-cm peat layer. Hydrogenotrophic methanogens and type II methanotrophs dominated the methane functional groups. Deterministic process contributed more to methanogenic and methanotrophic community assemblages in comparison with stochastic process. The level of water table significantly shaped methanogenic and methanotrophic community structures and regulated methane fluxes. Compared with vascular plants, Sphagnum mosses significantly reduced the methane emissions in peatlands. Collectively, these findings enhance a comprehensive understanding of the effect of the water table level on methane functional groups, with consequential implications for reducing methane emissions within peatland ecosystems.IMPORTANCEThe water table level is recognized as a critical factor in regulating methane emissions, which are largely dependent on the balance of methanogens and methanotrophs. Previous studies on peat methane emissions have been mostly focused on spatial-temporal variations and the relationship with meteorological conditions. However, the role of the water table level in methane emissions remains unknown. In this work, four representative microhabitats along a water table gradient in a Sphagnum-dominated peatland were sampled to gain an insight into methane functional communities and methane emissions as affected by the water table level. The changes in methane-related microbial community structure and assembly were used to characterize the response to the water table level. This study improves the understanding of the changes in methane-related microbial communities and methane emissions with water table levels in peatlands.

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].

Effects of deglaciation on the succession of methanotrophic communities in inland and tidewater glaciers in the high Arctic, Svalbard

The high Arctic region of Svalbard has undergone significant landscape transformations due to accelerated deglaciation driven by climate warming. The expansion of exposed soil surfaces during rapid deglaciation provides new habitats for plants and microorganisms and contributes to ecosystem succession. The primary succession process has the potential to impact methane flux by influencing the activities of methanotrophs and methanogens. While the primary succession of plant communities following glacier retreat has been extensively studied, microbial succession, in particular that of methanotrophs and methanogens, is still poorly understood. Moreover, previous investigations have focused on the forelands of inland or mountainous glaciers, neglecting those of tidewater glaciers that extend to the coastal line. In this study, we investigated the abundance of methanotrophs and methanogens, as well as methanotrophic communities along a 100-year soil chronosequence in the forelands of inland and tidewater glaciers in Svalbard. The abundance of methanotrophs showed a gradual increase with soil age in both glacier types, while the abundance of methanogens exhibited significant differences only in tidewater glaciers. Our results revealed clear trends in the structure of methanotrophic communities with an increase in their diversity during the deglaciation process in both glacier types. These trends were mediated by changes in soil physicochemical properties such as soil organic carbon and total nitrogen. Our findings indicate that methane oxidation may be enhanced by the increase in the abundance and diversity of methanotrophs in both glacier types throughout the successional stages, and that carbon and nitrogen contents play a crucial role in structuring the community at different stages of succession in the glacier forefield. These insights significantly contribute to our understanding of microbial dynamics during deglaciation and their implications for methane dynamics in the high Arctic.

The diversity of plant communities in different habitats can lead to distinct methanotrophic communities

Methanotrophic communities are susceptible to environmental interference in natural ecosystems. However, little is known about methanotrophs and their drivers in the riparian zone ecosystem. Therefore, the soil methanotrophic community structure, assembly process, and their driving factors were examined in five habitats in the riparian zone ecosystem of Three Gorges Reservoir in China. Soil samples were collected from the woody plant community, perennial plant community, annual plant community, perennial mixed annual plant community, and bare land in the riparian zone areas. We assessed plant community diversity, analyzed soil physiochemical properties, and measured enzyme activities to find the driving factors for the methanotrophic community. The findings revealed that Methylosarcina, Methylocystis, and rice paddy clusters dominated habitats. They preferred different pH levels and plant diversity. The diversity of the soil methanotrophic community was greater in vegetation-covered areas than on bare land. Likewise, the co-occurrence network of soil methanotrophs was more complex in vegetation-covered areas than in bare land, indicating a more stable community structure. Soil nitrogen, catalase, and plant diversity influence stability and diversity. During the transformation from bare land to plant community, the assembly process of the soil methanotrophic community converted from stochastic to deterministic processes, in which dispersal limitation and homogenous selection played prominent roles and were primarily influenced by soil pH and plant diversity. This research helps us understand the evolution of methanotrophs during vegetation restoration. It can also help us find plant communities that can effectively sequester carbon pools and plant them in riparian zones around reservoir systems to maintain soil and water quality.

Characterization of methanotrophic community and activity in landfill cover soils under dimethyl sulfide stress

Landfill cover soil is the environmental interface between landfills and the atmosphere and plays an important role in mitigating CH4 emission from landfills. Here, stable isotope probing microcosms with CH4 or CH4 and dimethyl sulfide (DMS) were carried out to characterize activity and community structure of methanotrophs in landfill cover soils under DMS stress. The CH4 oxidation activity in the landfill cover soils was not obviously influenced at the DMS concentration of 0.05%, while it was inhibited at the DMS concentrations of 0.1% and 0.2%. DMS-S was mainly oxidized to sulfate (SO42-) in the landfill cover soils. In the landfill cover soils, DMS could inhibit the expression of bacteria and decrease the abundances of pmoA and mmoX genes, while it could prompt the expression of pmoA and mmoX genes. γ-Proteobacteria methanotrophs including Methylocaldum, Methylobacter, Crenothrix and unclassified Methylococcaceae and α-Proteobacteria methanotrophs Methylocystis dominated in assimilating CH4 in the landfill cover soils. Of them, Methylobacter and Crenothrix had strong tolerance to DMS or DMS could promote the growth and activity of Methylobacter and Crenothrix, while Methylocaldum had weak tolerance to DMS and showed an inhibitory effect. Metagenomic analyses showed that methanotrophs had the genes of methanethiol oxidation and could metabolize CH4 and methanethiol simultaneously in the landfill cover soils. These findings suggested that methanotrophs might metabolize sulfur compounds in the landfill cover soils, which may provide the potential application in engineering for co-removal of CH4 and sulfur compounds.

Salinity significantly affects methane oxidation and methanotrophic community in Inner Mongolia lake sediments.

Methanotrophs oxidize methane (CH4) and greatly help in mitigating greenhouse effect. Increased temperatures due to global climate change can facilitate lake salinization, particularly in the regions with cold semiarid climate. However, the effects of salinity on the CH4 oxidation activity and diversity and composition of methanotrophic community in the sediment of natural lakes at a regional scale are still unclear. Therefore, we collected lake sediment samples from 13 sites in Mongolian Plateau; CH4 oxidation activities of methanotrophs were investigated, and the diversity and abundance of methanotrophs were analyzed using real-time quantitative polymerase chain reaction and high throughput sequencing approach. The results revealed that the diversity of methanotrophic community decreased with increasing salinity, and community structure of methanotrophs was clearly different between the hypersaline sediment samples (HRS; salinity > 0.69%) and hyposaline sediment samples (HOS; salinity < 0.69%). Types II and I methanotrophs were predominant in HRS and HOS, respectively. Salinity was significantly positively correlated with the relative abundance of Methylosinus and negatively correlated with that of Methylococcus. In addition, CH4 oxidation rate and pmoA gene abundance decreased with increasing salinity, and salinity directly and indirectly affected CH4 oxidation rate via regulating the community diversity. Moreover, high salinity decreased cooperative association among methanotrophs and number of key methanotrophic species (Methylosinus and Methylococcus, e.g). These results suggested that salinity is a major driver of CH4 oxidation in lake sediments and acts by regulating the diversity of methanotrophic community and accociation among the methanotrophic species.

Long-Term Inorganic and Organic Fertilizations Affect CH4 Oxidation Potential and Methanotrophic Community Structure in Paddy Soils

Long-Term Inorganic and Organic Fertilizations Affect CH4 Oxidation Potential and Methanotrophic Community Structure in Paddy Soils

Spatial variations of activity and community structure of nitrite-dependent anaerobic methanotrophs in river sediment

Rivers are an important site for methane emissions and reactive nitrogen removal. The process of nitrite-dependent anaerobic methane oxidation (n-damo) links the global carbon cycle and the nitrogen cycle, but its role in methane mitigation and nitrogen removal in rivers is poorly known. In the present study, we investigated the activity, abundance, and community composition of n-damo bacteria in sediment of the upper, middle, and lower reaches of Wuxijiang River (Zhejiang Province, China). The 13CH4 stable isotope experiments showed that the methane oxidation activity of n-damo was 0.11–1.88 nmol CO2 g−1 (dry sediment) d−1, and the activity measured from the middle reaches was significantly higher than that from the remaining regions. It was estimated that 3.27 g CH4 m−2 year−1 and 8.72 g N m−2 year−1 could be consumed via n-damo. Quantitative PCR confirmed the presence of n-damo bacteria, and their 16S rRNA gene abundance varied between 5.45 × 105 and 5.86 × 106 copies g−1 dry sediment. Similarly, the abundance of n-damo bacteria was significantly higher in the middle reaches. High-throughput sequencing showed a high n-damo bacterial diversity, with totally 152 operational taxonomic units being detected at 97 % sequence similarity cut-off. In addition, the n-damo bacterial community composition also varied spatially. The inorganic nitrogen (NH4+, NO2−, NO3−) level was found to be the key environmental factor controlling the n-damo activity and bacterial community composition. Overall, our results showed the spatial variations and environmental regulation of the activity and community structure of n-damo bacteria in river sediment, which expanded our understanding of the quantitative importance of n-damo in both methane oxidation and reactive nitrogen removal in riverine systems.

Diversity and Composition of Methanotroph Communities in Caves.

ABSTRACTMethane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98%) of the samples, including cave sites where CH4 concentrations were at or below detection limits (≤0.3 ppmv). We identified a core methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations, suggesting these microorganisms contribute to CH4 flux in subterranean ecosystems.IMPORTANCE Recent observations have shown the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14% of Earth’s land surface area, and therefore may represent a potentially important, but overlooked, CH4 sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air.

The community characteristics and functions of methanotrophs in karst Lake Caohai, Guizhou Plateau

草海是由喀斯特盆地积水发育而形成的一个完整的、典型的高原湖泊湿地生态系统，同时也是中国面积最大的岩溶构造湖.甲烷氧化菌作为一类能够将甲烷氧化为CO₂和水的独特微生物，其活动与生态系统中能量流动和元素循环的关键步骤密不可分.为了解贵州草海喀斯特高原湖泊湿地中甲烷氧化菌的群落结构特征及功能，利用宏基因组技术对浅水沼泽、莎草湿地、深水沉积物进行研究.结果表明，草海湿地中主要的好氧甲烷氧化菌为Methylobacter和Methylomonas，主要的厌氧甲烷氧化菌为Candidatus_Methylomirabilis_oxyfera，属于NC10门的反硝化型厌氧甲烷氧化菌.所研究的4种代谢功能基因种类多样性表现为碳代谢＞氮代谢＞硫代谢＞甲烷代谢；基于KEGG数据库共注释到6大类功能和18条与碳、甲烷、氮、硫相关的完整代谢路径.PCoA分析表明浅水沼泽和莎草湿地中甲烷氧化菌的种类和功能相似，且与深水沉积物存在差异.物种与功能相关性网络分析结果显示Methylacidiphilum_fumariolicum和Methylacidiphilum_kamchatkense与草海湖泊湿地中的各个代谢功能均具有较强的相关性.显著影响草海湿地中大多数甲烷氧化菌的群落结构的环境因素是硝酸盐、电导率、总磷和有机质.;Lake Caohai is a complete and typical plateau lake wetland ecosystem formed by the accumulation of water in the karst basin. It is also the largest karst structural lake in China. Methanotrophs is a kind of unique microorganisms that can oxidize methane to CO₂ and water. Their activities are inseparable from the key steps of energy flow and element cycle in the ecosystem. In order to understand the community structure and function of methanotrophs in the wetland of karst Lake Caohai, Guizhou Plateau, we used metagenomics technology to study shallow-water marshes, sedge wetlands, and deep-water sediments. The results showed that the main aerobic methanotrophs in the Lake Caohai wetland were Methylobacter and Methylomonas, and the main anaerobic methanotrophs were Candidatus_Methylomirabilis_oxyfera, which belonged to the NC10 denitrifying anaerobic methanotrophs. The diversity of the four metabolic function genes studied is carbon metabolism>nitrogen metabolism>sulfur metabolism>methane metabolism; based on the KEGG database, a total of 6 categories of functions and 18 complete metabolisms related to carbon, methane, nitrogen, and sulfur are annotated path. PCoA analysis showed that the types and functions of methanotrophs in shallow-water marshes and sedge wetlands are similar and different from those in deep-water sediments. Species and function correlation network analysis results show that Methylacidiphilum_fumariolicum and Methylacidiphilum_kamchatkense have strong correlations with the various metabolic functions in the Lake Caohai wetland. The environmental factors that significantly affect the community structure of methanotrophs in Lake Caohai wetland are nitrate, electrical conductivity, total phosphorous and soil organic matter.

Biogeographical distribution and regulation of methanotrophs in Chinese paddy soils

AbstractMethanotrophs contribute significantly to methane consumption in paddy ecosystems. Currently, the biogeographical distribution and regulation of methanotrophs in Chinese paddy soils remain poorly understood. Here, we investigated the activity, abundance and community structure of methanotrophs in paddy soils from different geographical regions and three climate zones across China, with a total of 20 sampling sites. The results showed that the methanotrophic activity and pmoA gene abundance varied from 0.67 to 2.23 μmol CH4 g−1 (dry soil) h−1 and 1.39 × 105 to 1.03 × 107 copies g−1 dry soil, respectively, and the methanotrophic communities were dominated by Methylocystis (type II). Heterogeneously distributed methanotrophic communities were observed among different climate zones characterised by a significant variation of the relative abundance of Methylococcus (type I). Furthermore, high and intermediate rates of nitrogen (N) fertilisation showed a significantly lower methanotrophic activity than the low rates of N fertilisation. However, no significant variation of methanotrophic abundance or community composition was observed among different N fertilisation levels. In addition, the soil ammonium content, water content, clay content, salinity, pH, mean annual precipitation and mean annual temperature was identified as the key factors affecting the activity, abundance and community composition of methanotrophs. Overall, our results showed the biogeographical distribution of methanotrophs in Chinese paddy soils, which can be largely influenced by climate conditions, N fertilisation rates and soil physiochemical properties.Highlights Activity and abundance of methanotrophs varied greatly across Chinese paddy fields. Methanotrophic community varied substantially across different climate zones. Higher rates of N fertilization could decrease methanotrophic activity. Soil properties (like NH4+, pH and moisture) significantly affected methanotrophs.

Active Methanotrophs and Their Response to Temperature in Marine Environments: An Experimental Study

Aerobic methane (CH4) oxidation plays a significant role in marine CH4 consumption. Temperature changes resulting from, for example, global warming, have been suggested to be able to influence methanotrophic communities and their CH4 oxidation capacity. However, exact knowledge regarding temperature controls on marine aerobic methane oxidation is still missing. In this study, CH4 consumption and the methanotrophic community structure were investigated by incubating sediments from shallow (Bohai Bay) and deep marine environments (East China Sea) at 4, 15, and 28 °C for up to 250 days. The results show that the abundance of the methanotrophic population, dominated by the family Methylococcaceae (type I methanotrophs), was significantly elevated after all incubations and that aerobic methane oxidation for both areas had a strong temperature sensitivity. A positive correlation between the CH4 oxidation rate and temperature was witnessed in the Bohai Bay incubations, whereas for the East China Sea incubations, the optimum temperature was 15 °C. The systematic variations of pmoA OTUs between the Bohai Bay and East China Sea incubations indicated that the exact behaviors of CH4 oxidation rates with temperature are related to the different methanotrophic community structures in shallow and deep seas. These results are of great significance for quantitatively evaluating the biodegradability of CH4 in different marine environments.

Response of methanotrophic activity and community structure to plant invasion in China’s coastal wetlands

Coastal wetlands are critical in the global carbon budget while vulnerable to plant invasion. Spartina alterniflora (S. alterniflora), a typical invasive plant species, has rapidly expanded in China’s coastal area since 1979, which disturbed the carbon cycle of the coastal wetland ecosystems. However, until now, the effect and underlying mechanisms of S. alterniflora invasion on methanotrophs are poorly known in coastal wetlands. Here, a large-scale investigation of the activity, abundance and community structure of methanotrophs was conducted in seven wetlands under both native (dominated by Phragmites australis, Kandelia candel or Avicennia marina) and invasive plants (dominated by S. alterniflora) across the southeast coast of China. Compared with the native community, S. alterniflora invasion led to a significant (p < 0.05) increase in activity and abundance of methanotrophs, which increased by 62.1% and 64.0% in average, respectively. The invasion of S. alterniflora did not greatly alter the methanotrophic community structure in most of the examined wetlands. However, the relative abundance of type I methanotrophs decreased under P. australis community, while type II methanotrophs (Methylocystis) increased after S. alterniflora invasion. In addition, the soil organic carbon content, ammonium content and salinity were identified as important environmental factors affecting the activity and community structure of methanotrophs. Overall, our results demonstrated that the activity and abundance of methanotrophs responded positively to S. alterniflora invasion, suggesting the important role of methanotrophs in reducing methane emissions from China’s coastal wetlands.

Effect of elevated atmospheric CO2 concentration on the activity, abundance and community composition of aerobic methanotrophs in paddy soils

The elevated atmospheric CO2 concentration (eCO2) has a great impact on soil microbial communities and their functions; however, how the activity and communities of methanotrophs respond to eCO2 in paddy ecosystem is poorly known. Here, we examined the effects of a 4-year exposure to eCO2 (EC; ambient + 200 ppm) in open top chambers on the potential activity, abundance and community composition of methanotrophs in paddy fields in Nanjing City, China. The potential activity was measured in a slurry incubation under aerobic condition, and the community composition and abundance of methanotrophs were analyzed through Illumina Miseq sequencing and quantitative PCR of pmoA genes. The results demonstrated that EC significantly increased (p < 0.05) the methane oxidation potential and pmoA gene abundance of methanotrophs by 52.9%–56.7% and 83.5%–213.6%, respectively, during late rice growth stages as compared with ambient condition (CK). Further, the community composition of methanotrophs in soil changed significantly (p < 0.05), with the dominant methanotrophs shifting from type II under CK to type I under EC. The variation of soil dissolved organic carbon and inorganic nitrogen levels caused by eCO2 had an important impact on the methane oxidation potential and methanotrophic community structure. Taken together, our results indicate that eCO2 can have an important impact on the activity, abundance and community composition of methanotrophs, adding new insights into the effects of rising CO2 on methane cycling in paddy ecosystems.

Microbial Community Structure of Soil Methanogens and Methanotrophs During Degradation and Restoration of Reed Wetlands in the Songnen Plain

Wetlands are an important global source and sink of methane. However, human activities and climatic conditions are causing serious degradation of wetlands in China. In response to this, the relevant departments have progressively carried out wetland restoration projects over the past few years. To investigate the response of microbial communities of bacteria, methanogens, and methanotrophs during degradation and restoration of wetlands, soil samples were collected from undegraded reed wetlands, degraded reed wetlands, and restored reed wetlands in the Songnen Plain. Microbial diversity and community composition were studied by high-throughput sequencing based on the 16S rRNA gene of bacteria, the mcrA gene of methanogens, and the pmoA gene of methanotrophs. The results indicate that the degradation of reed wetlands results in a decrease in bacterial and methanogenic α-diversity and an increase in methanotrophic α-diversity. Bacterial α-diversity and methanogenic α-diversity were both significantly positively correlated with soil water content. At different taxonomic levels, higher relative abundances of Rhizobiales and Methanobacteriaceae were detected in the undegraded wetland soils. Wetland degradation decreased the relative abundance of Rhizobiales but increased that of the pathogenic bacteria Burkholderiaceae and microorganisms resistant to harsh and extreme environments including Sphingomonas, Rubrobacter, Methylobacter, Methylomonas, and Methylococcus. In the restored wetland soils, the relative abundances of Bacillus, Methanosarcinaceae, Methanomicrobiaceae, and the type Ⅱ methanotroph Methylocystis were higher. Therefore, different wetland conditions can indirectly change soil properties and, consequently, change the community structure of methanogens and methanotrophs.

Methanotroph community structure and processes in an inland river affected by natural gas macro-seeps.

Methane availability in freshwaters is usually associated with spatial-temporal variation in methanogenesis. Unusually, however, natural gas macro-seeps occur along the Condamine River in eastern Australia which elevate ambient water-column methane concentrations more than 3,000 times. We quantified the spatial-temporal variation in methane oxidation rates and the total microbial and methanotroph community composition (through the amplification and sequencing of 16S rRNA and particulate methane monooxygenase (pmoA) genes), and the factors mediating this variation, in reaches with and without macro-seeps. Sediment methane oxidation rates were, on average, 29 times greater, and the abundance of methanotrophs significantly higher, in the vicinity of methane macro-seeps compared to non-seep sites. Methylocystis was the most abundant methanotroph group at all sites, but type Ib methanotrophs showed the steepest increase in abundance at seep sites. pmoA gene analysis identified these as clade 501, while 16S rRNA gene analysis identified these as the closely related genus Methylocaldum. Sediment methane oxidation rates and the relative abundance and composition of benthic microbial communities were primarily influenced by methane availability which was in turn related to variation in river discharge. Methane-derived carbon may be an important energy source for the aquatic food webs in reaches affected by natural gas macro-seeps.