Methanotrophic Community Research Articles

Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems

Riparian buffer systems (RBS) are a common agroforestry practice that involves maintaining a forested boundary adjacent to water bodies to protect the aquatic ecosystems in agricultural landscapes. While RBS have potential for carbon sequestration, they also can be sources of methane emissions. Our study site at Washington Creek in Southern Ontario, includes a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR). The objective of this study was to assess the diversity and activity of CH4 cycling microbial communities in soils sampled during hot moments of methane fluxes (July 04 and August 15). We used qPCR and high-throughput amplicon sequencing from both DNA and cDNA to target methanogen and methanotroph communities. Methanogens, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus, and Methanoreggula, were abundant in all RBSs, but they were significantly more active in UNF soils, where CH4 emissions were highest. Methylocystis was the most prevalent taxon among methanotrophs in all the riparian sites, except for AGR soils where the methanotrophs community was composed primarily of members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USCα). The main factors influencing the composition and assembly of methane-cycling microbiomes were soil carbon and moisture content. We concluded that the differences in CH4 fluxes observed between RBSs were primarily caused by differences in the presence and activity of methanogens, which were influenced by total soil carbon and water content. Overall, this study emphasizes the importance of understanding the microbial drivers of CH4 fluxes in RBSs in order to maximize RBS environmental benefits.

Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils.

CH4 emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH4 oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH4 produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH4 oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH4 oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH4 emissions via the reduction of CH4 oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO3- is responsible for the decrease in CH4 oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH4 oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH4 emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH4 dynamics in Arctic regions.

Thermal acclimation of methanotrophs from the genus Methylobacter

Methanotrophs oxidize most of the methane (CH4) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH4 oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH4 oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH4 is consumed to support growth at different CH4 concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH4 uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH4 oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH4 consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH4 uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH4 emissions.

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.

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

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

Distribution of methanogenic and methanotrophic consortia at soil-water interfaces in rice paddies across climate zones

Periphytic biofilms (PB) at the soil-water interface contributes 7-38% of the methane emission from rice paddies, yet the biogeographical mechanism underlying and affecting the process remain elusive. In this study, rice fields along an edapho-vclimatic gradient were sampled, and the environmental drivers affecting distribution of methanogenic and methanotrophic communities were evaluated. The methanogenic and methanotrophic communities at soil-water interface showed less complex inter/intra-generic interactions than those in soil, and their relative abundances were weakly driven by spatial distance, soil organic carbon, soil total nitrogen and pH. The nutrient supply and buffering capacity of extracellular polymeric substance released by PB reduced their interaction and enhanced the resilience on edaphic environment changes. Climate affected soil metal content, extracellular polymeric substance content, and thus the methane-related communities, and caused geographical variation in the impacts of PB on methane emissions from rice paddies. This study facilitates our understanding of geographical differences in the contribution of PB to methane emission.

Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column.

The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.

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

Prolonged Effect of Forest Soil Compaction on Methanogen and Methanotroph Seasonal Dynamics.

Methane (CH4) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH4 uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH4 uptake by forest soils, subjected to compaction by heavy machinery 7years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH4 microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10cm depth interval and in summer in the 10-20cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH4 fluxes and the potential effect of physical disturbances.

Effects of enhanced-efficiency nitrogen fertilizers on CH4 and CO2 emissions in a global perspective

It is widely recommended that enhanced efficiency nitrogen fertilizers (EENFs; urease inhibitors, nitrification inhibitors, urease and nitrification inhibitors combined, coated controlled-release urea) be applied to croplands to improve N use efficiency and crop yield via regulating N transformations. However, EENFs may inevitably affect soil C dynamics for the coupled relationship between soil carbon (C) and N biogeochemical cycles. Yet, a comprehensive assessment of the effects of EENFs on soil C dynamics is lacking. Here, we conducted a global meta-analysis using 67 publications to assess the overall effects of EENFs on soil CH 4 production, CO 2 emission, organic C (SOC) content, dissolved organic C (DOC) content, microbial biomass C (MBC) content under different environmental and management conditions (climate conditions, soil properties and fertilizer management practices). Our results showed that on average, compared to conventional N fertilizer, EENFs with the same amount of N fertilizer have a non-significant impact on CH 4 emission, which further depended on environmental and management conditions. Best scenarios for CH 4 reduction included: paddy field (25.8%), urease inhibitor (26.9%) and medium N application rate (150–300 kgN ha −1 ; 23.6%), mainly due to the decreased stimulation of NH 4 + on CH 4 production; acid soil (33.7%), which was attributed to the enhanced methanotrophic communities' activities. The positive effect was also amplified by the increased mean annual precipitation and soil clay content that facilitated CH 4 production. Contrarily, EENFs significantly reduced CO 2 emission by 9.3%. The greater reduction was observed for the conditions producing more CO 2 after fertilization, i.e. field experiment, alkaline soils, low soil inorganic N content and high N application rate (≥300 kgN ha −1 ). Nitrification inhibitors and coated N fertilizer were the best available options as they can reduce inorganic C dissolution in calcareous soil and SOC mineralization, respectively. Besides, EENFs application did not significantly alter SOC, DOC and MBC contents. Our findings highlighted the role of EENFs played in decreasing soil C emission in agroecosystems. • Global use of EENFs did not significantly affect SOC, DOC, MBC contents. • EENFs succeed in reducing CO 2 emission (9.3%) rather than CH 4 emission. • EENFs provide a viable solution for decreasing soil C emissions in global agroecosystems.

Exploring methane cycling in an arctic lake in Kangerlussuaq Greenland using stable isotopes and 16S rRNA gene sequencing

Lakes are currently responsible for a significant amount of total natural methane emission. Microbial oxidation of methane plays a central role in Arctic carbon cycling, potentially reducing methane emissions from lakes, though little is known about methane cycling in the water column of Arctic lakes. We previously detected surprisingly large enrichments of heavy carbon and hydrogen isotopes of methane in three small lakes in Greenland suggesting unusually efficient methanotrophic communities in these Arctic lakes. Using stable isotope and 16S rRNA gene sequencing we determined carbon and hydrogen isotopes and microbial community composition down the water column of Teardrop lake, under open-water conditions. We found that isotopic values of methane in Teardrop lake were again highly enriched 13C and 2H at 4 m depth with −13.2‰ and −27.1‰ values for carbon and hydrogen isotopes, respectively. Methane concentrations slightly increased at the depth interval with isotope enrichment, not typical of classic methanotrophy. Consistent with isotopic enrichment of the heavy isotopes we detected the highest relative abundance of putative methanotrophs, in particular Methylovulum at 4 m. The highest relative abundance of putative methanogens was detected at 3 m as well as at 5 m. At the same depth interval, temperature and oxidation reduction potential also increase, supporting increased microbial activity within the water column. Based on geochemical and microbial observations, we suggest that the methane cycling in Teardrop lake is decoupled from a traditional depth dependent model where the dominant source of methane is in the anoxic sediments. Instead, methane in the water column is likely from a combination of anoxic sediment, littoral transport and oxic methanogenesis in the mid-water column, and recycling of carbon within the water column is leading to extreme isotope enrichments. Thus, understanding linkages between depth-dependent microbial dynamics and methane biogeochemistry are necessary to constrain the sensitivity of the methane cycle to future climate change.

The Effect of Lanthanum on the Composition of Methanotrophic Community of Sod-Podzolic Soil

The Effect of Lanthanum on the Composition of Methanotrophic Community of Sod-Podzolic Soil

Seasonality of water column methane oxidation and deoxygenation in a dynamic marine environment

Most of the methane input to the world’s oceans is intercepted by microorganisms in sediment and the overlying water column and oxidized before it has an opportunity to reach the atmosphere, where it acts as a greenhouse gas. The factors controlling methane consumption in the ocean are not well established and its biogeochemistry in dynamic marine environments is understudied in-part because of challenges in capturing spatial and temporal variability. Our study focused on the factors that structure methane’s biogeochemistry in a dynamic marine environment, the Santa Barbara Basin. The deep-water column of the Santa Barbara Basin experiences seasonal oxygen loss and episodic replenishment which we found to be major factors in structuring the accumulation of methane and the rate at which microorganisms consumed that methane. We found the gradual decline in oxygen that commonly occurs through the summer culminated with a pronounced accumulation of methane in the water column during the fall. Rates of methane oxidation remained low in summer, increased with the buildup of methane in fall, and remained elevated into spring, even after methane concentration had declined. However, results from methane oxidation kinetics experiments revealed a zero-order kinetic dependence on oxygen concentration, indicating that oxygen’s effect on methanotrophy at the ecosystem scale is likely indirect. We also captured an apparent mixing event during fall that drove spatial and temporal variability in oxygen, nitrate and methane concentrations in the Santa Barbara Basin, with stark variations at the investigated timescale of 8 days and along isobaths at a spatial scale of 7 km. Collectively, these results indicate the seasonal development and attenuation of a methanotrophic community associated with restricted circulation, but also of a spatiotemporal variability not previously appreciated for this environment.

Spatial and temporal variation in δ13C values of methane emitted from a hemiboreal mire: methanogenesis, methanotrophy, and hysteresis

Abstract. The reasons for spatial and temporal variation in methane emission from mire ecosystems are not fully understood. Stable isotope signatures of the emitted methane can offer clues to the causes of these variations. We measured the methane emission (FCH4) and 13C signature (δ13C) of emitted methane by automated chambers at a hemiboreal mire for two growing seasons. In addition, we used ambient methane mixing ratios and δ13C to calculate a mire-scale 13C signature using a nocturnal boundary-layer accumulation approach. Microbial methanogenic and methanotrophic communities were determined by a captured metagenomics analysis. The chamber measurements showed large and systematic spatial variations in δ13C-CH4 of up to 15 ‰ but smaller and less systematic temporal variation. According to the spatial δ13C–FCH4 relations, methanotrophy was unlikely to be the dominating cause for the spatial variation. Instead, these were an indication of the substrate availability of methanogenesis being a major factor in explaining the spatial variation. Genetic analysis indicated that methanogenic communities at all sample locations were able to utilize both hydrogenotrophic and acetoclastic pathways and could thus adapt to changes in the available substrate. The temporal variation in FCH4 and δ13C over the growing seasons showed hysteresis-like behavior at high-emission locations, indicative of time-lagged responses to temperature and substrate availability. The upscaled chamber measurements and nocturnal boundary-layer accumulation measurements showed similar average δ13C values of −81.3 ‰ and −79.3 ‰, respectively, indicative of hydrogenotrophic methanogenesis at the mire. The close correspondence of the δ13C values obtained by the two methods lends confidence to the obtained mire-scale isotopic signature. This and other recently published data on δ13C values of CH4 emitted from northern mires are considerably lower than the values used in atmospheric inversion studies on methane sources, suggesting a need for revision of the model input.

Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm

In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50–60 cm) and, active process of aerobic denitrification in the top soil (0–10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.

Propagule limitation affects the response of soil methane oxidizer community to increased salinity

The extent to which propagule limitation can govern the responses of microbially-mediated processes (such as methane oxidation) to sudden environmental changes, is poorly understood. Here, we compared the ability of the methanotroph community in lakeshore soils of two lakes to respond to an experimental increase in salinity. One set of samples was taken from lakeshore soils of a freshwater lake (Yang Lake), the other from a slightly brackish lake (Qinghai Lake), both on the Tibetan Plateau. Samples were incubated in microcosms by adding ∼ 5 % 13CH4 or 12CH4 and different concentrations of NaCl solution. DNA stable-isotope probing (DNA-SIP) followed by high-throughput sequencing was used to determine how the active methanotrophic populations differed in lakeshore soils with different salinity levels. Samples from saline and freshwater lake initially showed much-reduced methane oxidation ability and methanotrophic activity at increased salinity. For the freshwater samples with the salinity of 25 to 50 g/L after NaCl addition, there was no adaptation and increase in methanotrophy after 7 days. By contrast, samples from the brackish lake showed an initial depression of methane oxidation, followed by greatly increased rates after several days. Sequencing revealed that this recovery of methanotrophy in the brackish lake samples was associated with a major switchover in composition of active methanotroph community. In particular, the relative abundance of Type Ⅰa methanotrophs became more abundant at increased salinity. It appears that in this freshwater lake environment, isolation from any nearby high-salinity-tolerant bacterial sources has prevented the possibility of full adaptation to a high salinity change in the environment, and only a moderate salinity adaptation is possible by species-sorting from within the existing community. By contrast, in the higher-salinity environment, the highly salinity-tolerant Methylomicrobium was able to break the establishment limitation in the high salinity environment and become the dominant methanotroph. Our study provides an instance of propagule limitation preventing adaptation to changed conditions.

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.

Atmospheric methane oxidation is affected by grassland type and grazing and negatively correlated to total soil respiration in arid and semiarid grasslands in Inner Mongolia

Methane (CH4) is an important trace greenhouse gas and atmospheric CH4 uptake by high-affinity methanotrophs in grassland soil accounts for an important proportion of the terrestrial CH4 sink. However, our understanding of the comprehensive effects of grassland type and grazing treatment on active soil methanotrophs and atmospheric CH4 uptake is still under debate. This study investigates the impact of grazing on CH4 oxidation rate and active atmospheric CH4 oxidizing methanotroph communities in two arid and semiarid grassland ecosystems (meadow and desert) by detecting transcripts of methane monooxygenase (pmoA) genes. Atmospheric CH4 oxidation rates differed according to grassland type and grazing treatment. The highest activity was found in desert grasslands with moderate grazing and the lowest activity in meadow grasslands with exclosures. The differences in activities were linked with changes in abundance, composition and co-occurrence network patterns of active methanotrophs and CO2 production rate. Redundancy, correlation and random forest analyses indicated that pmoA transcripts, available phosphorus (AP), NO3−-N, and CO2 production rate were the most important factors predicting active methanotroph community composition and atmospheric CH4 oxidation activity in these grassland ecosystems. A glucose amendment incubation experiment showed that addition of glucose increased heterotrophic microbial respiration and inhibited atmospheric CH4 oxidation. This study provides evidence that CO2 production rate is an important factor associated with atmospheric CH4 oxidation activity in arid and semiarid grassland ecosystems and suggests that interactions between methanotrophs and other heterotrophs influence methanotroph activity in grassland ecosystems.

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.

Trait-Based Model Reproduces Patterns of Population Structure and Diversity of Methane Oxidizing Bacteria in a Stratified Lake

In stratified lakes, methane oxidizing bacteria are critical methane converters that significantly reduce emissions of this greenhouse gas to the atmosphere. Efforts to better understand their ecology uncovered a surprising diversity, vertical structure, and seasonal succession. It is an open question how this diversity has to be considered in models of microbial methane oxidation. Likewise, it is unclear to what extent simple microbial traits related to the kinetics of the oxidation process and temperature optimum, suggested by previous studies, suffice to understand the observed ecology of methane oxidizing bacteria. Here we incorporate niche partitioning in a mechanistic model of seasonal lake mixing and microbial methane oxidation in a stratified lake. Can we model MOB diversity and niche partitioning based on differences in methane oxidation kinetics and temperature adaptation? We found that our model approach can closely reproduce diversity and niche preference patterns of methanotrophs that were observed in seasonally stratified lakes. We show that the combination of trait values resulting in coexisting methanotroph communities is limited to very confined regions within the parameter space of potential trait combinations. However, our model also indicates that the sequence of community assembly, and variations in the stratification and mixing behavior of the lake result in different stable combinations. A scenario analysis introducing variable mixing conditions showed that annual weather conditions and the pre-existing species also affect the developing stable methanotrophic species composition of the lake. Both, effect of pre-existing species and the environmental impact suggest that the MOB community in lakes may differ from year to year, and a stable community may never truly occur. The model further shows that there are always better-adapted species in the trait parameter space that would destabilize and replace an existing stable community. Thus, natural selection may drive trait values into the specific configurations observed in nature based on physiological limits and tradeoffs between traits.