Abundance Of Methanotrophs Research Articles

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.

Liming modifies greenhouse gas fluxes from soils: A meta-analysis of biological drivers

Acidic soils cover about 30% of the world’s land. Liming is a management practice applied worldwide to reduce the negative effects of acidification on soil fertility and plant growth. Liming also affects the biotic and abiotic soil properties controlling the production and consumption of the greenhouse gases (GHGs) carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4). Although our understanding of how liming regulates net GHG emissions is increasing, the impact of liming on soil biological drivers of GHG emissions has not been quantitatively synthesized. Here we conducted a global meta-analysis using 1474 paired observations from 124 studies to explore the responses of GHG emissions to liming, with a focus on soil biological factors. We show that the N2O mitigation capacity of liming could be linked to (i) increases in bacterial abundance of N2O reductase genes (NosZ) and decreases in fungi:bacteria ratio, both contributing to a lower N2O:N2 product ratio of denitrification; and (ii) reductions in soil mineral nitrogen (N) via stimulation of plant N uptake. The limited evidence available indicates that liming reduced CH4 emissions and the abundance of methanogens, but it had no effect on CH4 uptake and abundance of methanotrophs. Liming-induced increases in soil CO2 emissions can be explained by higher heterotrophic and/or autotrophic respiration. The strong coupling between liming effects on GHG emissions and on soil microbial communities involved in GHG production and consumption can be used to identify strategies to reduce GHGs in response to liming, and to improve process-based models for better predictions of soil GHG emissions.

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.

Characterization of anaerobic oxidation of methane and microbial community in landfills with aeration

Landfills are the third largest source of anthropogenic CH4 emissions. Anaerobic oxidation of methane (AOM) activity and communities of methane-oxidizing bacteria were investigated in three informal landfills in this study, namely, BJ, CH and SZ landfills, among which BJ and CH represent traditional anaerobic landfills, while the SZ landfill was subjected to aeration to accelerate waste stabilization. The AOM rates of the investigated landfilled wastes ranged from 3.66 to 23.91 nmol g−1 h−1. Among the three landfills, the AOM rate was highest in the SZ-1-Top sample, which was closest to the aeration pipe. Among the possible electron acceptors for AOM, including NO3−, NO2−, SO42− and Fe3+, the NO2−-N content was the only variable that was positively correlated with the AOM rate. Compared with α-Proteobacteria methanotrophs, γ-Proteobacteria methanotrophs were more abundant in the landfilled waste, especially Methylobacter, which was detected in nearly all samples. Members of the family Methylomirabilaceae, including Candidatus Methylomirabilis, were also detected in the SZ-1 and SZ-2-Bot samples. The relative abundance of the main methanotrophs in the families Methylomonadaceae, Methylococcaceae, Rokubacteriales and Methylomirabilaceae, the genus Methylocystis and the phylum NC10 were all positive correlations with the contents of NO2−-N in the landfilled waste samples. Additionally, significantly positive correlations were observed between the AOM rates and the relative abundance of the main methanotrophs except for the family Methylococcaceae. This indicated that aeration could enhance the conversion of nitrogen compounds in the landfilled waste, in which the high contents of NO2−-N could stimulate the growth of methanotrophs and increase AOM rate. These findings are helpful for understanding the mechanisms of CH4 oxidation in landfills and for taking effective measures to mitigate CH4 emissions from landfills.

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.

Microtopography Matters: Belowground CH4 Cycling Regulated by Differing Microbial Processes in Peatland Hummocks and Lawns

AbstractWater table depth and vegetation are key controls of methane (CH4) emissions from peatlands. Microtopography integrates these factors into features called microforms. Microforms often differ in CH4 emissions, but microform‐dependent patterns of belowground CH4 cycling remain less clearly resolved. To investigate the impact of microtopography on belowground CH4 cycling, we characterized depth profiles of the community composition and activity of CH4‐cycling microbes using 16S rRNA amplicon sequencing, incubations, and measurements of porewater CH4 concentration and isotopic composition from hummocks and lawns at Sallie's Fen in NH, USA. Geochemical proxies of methanogenesis and methanotrophy indicated that microforms differ in dominant microbial CH4 cycling processes. Hummocks, where water table depth is lower, had higher porewater redox potential (Eh) and higher porewater δ13C‐CH4 values in the upper 30 cm than lawns, where water table depth is closer to the peat surface. Porewater δ13C‐CH4 and δD‐CH3D values were highest at the surface of hummocks where the ratio of methanotrophs to methanogens was also greatest. These results suggest that belowground CH4 cycling in hummocks is more strongly regulated by methanotrophy, while in lawns methanogenesis is more dominant. We also investigated controls of porewater CH4 chemistry. The ratio of the relative abundance of methanotrophs to methanogens was the strongest predictor of porewater CH4 concentration and δ13C‐CH4, while vegetation composition had minimal influence. As microbial community composition was strongly influenced by redox conditions but not vegetation, we conclude that water table depth is a stronger control of belowground CH4 cycling across microforms than vegetation.

Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils.

The process of nitrite-dependent anaerobic methane oxidation (n-damo) catalysed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a novel pathway in regulating methane (CH4 ) emissions from paddy fields. Nitrogen fertilization is essential to improve rice yields and soil fertility; however, its effect on the n-damo process is largely unknown. Here, the potential n-damo activity, abundance and community composition of M. oxyfera-like bacteria were investigated in paddy fields under three long-term (32 years) fertilization treatments, i.e. unfertilized control (CK), chemical fertilization (NPK) and straw incorporation with chemical fertilization (SNPK). Relative to the CK, both NPK and SNPK treatments significantly (p < 0.05) increased the potential n-damo activity (88%-110%) and the abundance (52%-105%) of M. oxyfera-like bacteria. The variation of soil organic carbon (OrgC) content and inorganic nitrogen content caused by the input of chemical fertilizers and straw returning were identified as the key factors affecting the potential n-damo activity and the abundance of M. oxyfera-like bacteria. However, the community composition and diversity of M. oxyfera-like bacteria did not change significantly by the input of fertilizers. Overall, our results provide the first evidence that long-term fertilization greatly stimulates the n-damo process, indicating its active role in controlling CH4 emissions from paddy fields.

Biochar Amendments Facilitate Methane Production by Regulating the Abundances of Methanogens and Methanotrophs in Flooded Paddy Soil

The application of biochar in conjunction with fertilizer in agricultural production is one of the most promising types of management to improve soil quality. However, the effects on the soil microbial community and methane (CH4) emissions from the interactive mechanisms of biochar combined with fertilizer are unclear. In this study, soil column trial was conducted to monitor the surface water nitrogen, dissolved organic carbon (DOC) and CH4 emission dynamics during the process of leaching. Additionally, bacterial and archaeal communities of the soil (0-10 cm) amended with biochar derived from different pyrolysis temperatures (300°C, 500°C, and 700°C) were also analyzed. High-throughput sequencing revealed that the soil archaeal and bacterial community diversities increased under the biochar amendments. The CH4 emission flux of all the treatments in the whole leaching period ranged from 0.0001 to 2.04 μg m-2 h-1, and the DOC ranged from 1.86 to 24.4 mg L-1. Our results showed that biochar amendments significantly increase the soil pH, total nitrogen (TN), and DOC contents, while inhibiting the loss of NO3− N during leaching. In addition, biochar addition increased the paddy soil CH4 emissions, which ascribed to the increasing ratio of the abundances of methanogens to methanotrophs. Consequently, the higher CH4 emissions were probably caused by the stimulation of methanogenic archaea under the biochar amendments. Thus, the results obtained in this study can be applied to guide the application of biochar on greenhouse gas emissions in paddy soil.

Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil

Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.

Methane emission, methanogenic and methanotrophic communities during rice-growing seasons differ in diversified rice rotation systems

Appropriate crop rotation in rice field is an important measure to maintain soil fertility and rice productivity. However, the effects of different rice rotation systems on methane (CH4) emission and the underlying mechanisms, as well as rice grain yields have not been well assessed. Here, a 2-year field study involving three rice rotation systems (Wh-PR: wheat-flooded rice rotation, Ra-PR: rapeseed-flooded rice rotation, Ra-UR: rapeseed-aerobic rice rotation) was conducted. CH4 emissions, methanogenic and methanotrophic communities and rice grain yields were measured during rice growing seasons to determine which rice rotation pattern can reduce CH4 emissions and improve rice grain yields. The average cumulative CH4 emission was 136.19 kg C ha−1 in Ra-PR system, which was significantly higher than that in Wh-PR and Ra-UR systems by 60.6 % and 14.6-fold, respectively. These results were mainly attributed to the low soil dissolved organic carbon in Wh-PR system and the well aerated soil condition in Ra-UR system, as compared with Ra-PR system. Rice grain yields exhibited no significant differences among the three rotation systems in 2019 and 2020. The abundances of methanogens in Ra-PR system were obviously higher than those in Wh-PR and Ra-UR systems. While the abundances of methanotrophs were comparable between Ra-PR and Wh-PR systems, which exhibited significantly lower abundances than that in Ra-UR system. CH4 fluxes showed markedly positive relations to the abundances of methanogens, while exhibited no relationship with the abundances of methanotrophs. Both methanogenic and methanotrophic community compositions differed considerably in Wh-PR and Ra-UR systems in comparison with Ra-PR system. Specifically, the relative low abundances of Methanothrix and Type I methanotrophs occurred in Wh-PR and Ra-UR systems, whereas Methanosarcina, Methanocella, Methanomassiliicoccus and type II methanotrophs (Methylocystis and Methylosinus) were found in higher relative abundances in Wh-PR and Ra-UR systems. Overall, changing the preceding upland crop types or introducing aerobic rice to substitute flooded rice in rice-based rotation systems could diminish CH4 emissions, mainly by regulating soil properties and eventually changing soil methanogenic and methanotrophic communities.

Eutrophic levels and algae growth increase emissions of methane and volatile sulfur compounds from lakes

Eutrophic lakes are hot spots of CH4 and volatile sulfur compound (VSC) emissions, especially during algal blooms and decay. However, the response of CH4 and VSC emissions to lake eutrophication and algae growth as well as the underlying mechanisms remain unclear. In this study, the emissions of CH4 and VSCs from four regions of Lake Taihu with different eutrophic levels were investigated in four months (i.e., March, May, August and December). The CH4 emissions ranged from 20.4 to 126.9 mg m−2 d−1 in the investigated sites and increased with eutrophic levels and temperature. H2S and CS2 were the dominant volatile sulfur compounds (VSCs) emitted from the lake. The CH4 oxidation potential of water ranged from 2.1 to 14.9 μg h−1 L−1, which had positive correlations with trophic level index and the environmental variables except for the NH4+-N concentration. Eutrophic levels could increase the abundances of bacteria and methanotrophs in lake water. α-Proteobacteria methanotroph Methylocystis was more abundant than γ-Proteobacteria methanotrophs in March and May, while the latter was more abundant in August and November. The relative abundance of Cyanobacteria, including Microcystis, A. granulata var. angustissima and Cyanobium had significantly positive correlations with temperature, turbidity, SO42--S, and total sulfur. Partial least squares path modelling revealed that the algal growth could promote VSC emissions, which had a positive correlation with CH4 oxidation potential, likely due to the positive correlation between the CH4 and VSC emissions from lakes. These findings indicate that water eutrophication and algae growth could increase the emissions of CH4 and VSCs from lakes. Controlling algae growth might be an effective way to mitigate the emissions of CH4 and VSCs from freshwater lakes.

Unexpected Parabolic Temperature Dependency of CH4 Emissions from Rice Paddies.

Global warming is expected to affect methane (CH4) emissions from rice paddies, one of the largest human-induced sources of this potent greenhouse gas. However, the large variability in warming impacts on CH4 emissions makes it difficult to extrapolate the experimental results over large regions. Here, we show, through meta-analysis and multi-site warming experiments using the free air temperature increase facility, that warming stimulates CH4 emissions most strongly at background air temperatures during the flooded stage of ∼26 °C, with smaller responses of CH4 emissions to warming at lower and higher temperatures. This pattern can be explained by divergent warming responses of plant growth, methanogens, and methanotrophs. The effects of warming on rice biomass decreased with the background air temperature. Warming increased the abundance of methanogens more strongly at the medium air temperature site than the low and high air temperature sites. In contrast, the effects of warming on the abundance of methanotrophs were similar across the three temperature sites. We estimate that 1 °C warming will increase CH4 emissions from paddies in China by 12.6%─substantially higher than the estimates obtained from leading ecosystem models. Our findings challenge model assumptions and suggest that the estimates of future paddy CH4 emissions need to consider both plant and microbial responses to warming.

Soil greenhouse gas fluxes following conversion of tropical forests to fertilizer-based sugarcane systems in northwestern Uganda

Tropical deforestation for fertilizer-based agriculture has greatly increased in the last decades resulting in significant greenhouse gas (GHG; carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O)) emissions. Unfortunately, empirical studies on soil GHG fluxes from African deforestation hotspots are still limited, creating uncertainties in global GHG budgets. Therefore, we assessed how soil GHG fluxes along with their auxiliary controls (water filled pore space (WFPS), temperature, and mineral nitrogen (N)) differed between the forest and sugarcane plantations. This assessment was based on monthly (forest) and intensive (sugarcane) GHG and auxiliary measurements between May 2019 and June 2020. Measurements were conducted in four reference forest plots and 12 sugarcane plots randomly assigned to three fertilization treatment groups (low, standard, and high), representing the fertilization gradient used by sugarcane farmers in Uganda. Despite the use of different fertilization rates as treatments for the sugarcane experiment, neither auxiliary controls nor soil GHG fluxes significantly differed among the treatments. Soil CO2 effluxes were higher under sugarcane (17.6 ± 0.0 Mg C ha-1 yr-1) compared to forest (14.5 ± 0.1 Mg C ha-1 yr-1; p < 0.001) because of the higher autotrophic respiration from the sugarcane’s fine root biomass and the microbial decomposition of the sugarcane’s larger soil organic carbon (SOC) stocks. Conversely, soil CH4 uptake under sugarcane (−1.1 ± 0.0 kg C ha-1 yr-1) was three times lower than under forest (−3.1 ± 0.0 kg C ha-1 yr-1; p < 0.001), owing to the likely alteration of methanotroph abundance upon conversion. Likewise, soil N2O emissions were smaller under sugarcane (1.3 ± 0.0 kg N ha-1 yr-1) compared to forest (1.8 ± 0.0 kg N ha-1 yr-1; p < 0.001) because excess N from fertilizer addition in the sugarcane was either lost through leaching or taken up by the sugarcane crop. Only seasonal variability in WFPS, among the auxiliary controls, affected CH4 uptake at both sites (p < 0.001) and soil CO2 effluxes under sugarcane (p = 0.018). Noteworthy, soil N2O fluxes from both sites were unaltered by the seasonality-mediated changes in auxiliary controls. We conclude that even with the increased SOC sequestration and the lower N2O emissions under sugarcane compared to forest, the forest-sugarcane conversion resulted in a yearly net C loss of 2.8 Mg CO2-eq ha-1 from soils to atmosphere, largely arising from the higher soil CO2 effluxes and to a smaller extent from a reduced CH4 uptake under sugarcane.

Reduced methane emissions in former permafrost soils driven by vegetation and microbial changes following drainage.

In Arctic regions, thawing permafrost soils are projected to release 50 to 250 Gt of carbon by 2100. This data is mostly derived from carbon‐rich wetlands, although 71% of this carbon pool is stored in faster‐thawing mineral soils, where ecosystems close to the outer boundaries of permafrost regions are especially vulnerable. Although extensive data exists from currently thawing sites and short‐term thawing experiments, investigations of the long‐term changes following final thaw and co‐occurring drainage are scarce. Here we show ecosystem changes at two comparable tussock tundra sites with distinct permafrost thaw histories, representing 15 and 25 years of natural drainage, that resulted in a 10‐fold decrease in CH4 emissions (3.2 ± 2.2 vs. 0.3 ± 0.4 mg C‐CH4 m−2 day−1), while CO2 emissions were comparable. These data extend the time perspective from earlier studies based on short‐term experimental drainage. The overall microbial community structures did not differ significantly between sites, although the drier top soils at the most advanced site led to a loss of methanogens and their syntrophic partners in surface layers while the abundance of methanotrophs remained unchanged. The resulting deeper aeration zones likely increased CH4 oxidation due to the longer residence time of CH4 in the oxidation zone, while the observed loss of aerenchyma plants reduced CH4 diffusion from deeper soil layers directly to the atmosphere. Our findings highlight the importance of including hydrological, vegetation and microbial specific responses when studying long‐term effects of climate change on CH4 emissions and underscores the need for data from different soil types and thaw histories.

Redox Zone and Trophic State as Drivers of Methane-Oxidizing Bacterial Abundance and Community Structure in Lake Sediments

Eutrophication is expected to increase methane production in freshwater sediments worldwide over the coming decades. Methane-oxidizing bacteria (MOB) consume a significant fraction of this sedimentary methane, but the factors that control their distributions and activities are not understood. By combining genetic approaches (pmoA, 16S rRNA gene, metagenomics) with geochemical and sedimentological analyses, we investigate the role of trophic state, electron acceptors, oxygen (O2) and methane fluxes, and potential methylotrophic partner organisms in driving the distributions, abundances, and community compositions of MOB across five lakes in central Switzerland. Although methane fluxes were highest in the eutrophic lakes, methanotrophic abundances peaked in oxic and anoxic sediments of an oligotrophic lake. In all lakes, Type I gammaproteobacterial Methylococcaceae dominated oxic and suboxic bottom water and surface sediments, showing strong correlations with abundances of putatively methylotrophic Methylophilaceae, whereas Type II alphaproteobacterial Methylocystaceae increased in deeper, anoxic sediment layers. Methanotrophic bacteria belonging to the NC10 phylum were predominantly detected within denitrifying sediment of the oligotrophic lake, matching their presumed nitrite-dependent lifestyle. While dominant MOB taxa at the genus-level follow vertical distributions of different aerobic and anaerobic respiration reactions, trophic state at the time of sediment deposition was the best predictor of MOB community structure at the operational taxonomic unit (OTU) level. Elevated methane fluxes combined with low MOB abundances in surface sediments of eutrophic lakes, moreover, support the notion that in eutrophic lakes a major portion of sedimentary methane bypasses the biological methane filter and escapes to overlying water.

Sheep grazing impacts on soil methanotrophs and their activity in typical steppe in the Loess Plateau China

Soil methanotrophs are the only biological sink for atmospheric methane (CH4). The activity and the diversity of methanotrophic communities in grassland soils can be impacted by animal grazing. In this study, soils were collected from a 17-year running grazing intensity trial in a typical steppe in the Loess Plateau, China to examine the responses of CH4 oxidation rate and active methanotroph composition and abundance to different levels of sheep grazing. Soils were collected from summer grazed pastures at no (0 sheep ha−1), low (2.67 sheep ha−1), moderate (5.33 sheep ha−1) and high (8.67 sheep ha−1) levels of grazing. We found that all soils were able to oxidize atmospheric and high concentration (10%) CH4 through soil methanotrophs. Compared to ungrazed soils, the atmospheric CH4 oxidation rate and methanotroph abundance were higher in low and high grazed soils but lower in moderately grazed soils. Across all soils, the in-situ methanotroph community was dominated by upland soil cluster gamma methanotrophs and potentially contributed to the atmospheric concentration CH4 oxidation. Soil methanotroph community responses to the high 13CH4 concentration revealed an increase in methanotroph abundance and a transition of the active methanotroph community to traditional Type I (Methylocaldum and Methylobacter) and Type II (Methylocystis) methanotrophs. Methylocaldum responses to the high CH4 concentration were greater in highly grazed soil than in ungrazed soil. The activity of Methylobacter and Methylocystis under high CH4 concentrations was reduced by high grazing intensity. This study provides evidence that recent intensifications of animal grazing can result in particular community assembly of microbial methane oxidizers responsible for CH4 sink capabilities of grassland soils.

Muskoxen homogenise soil microbial communities and affect the abundance of methanogens and methanotrophs

Grazing herbivores may affect soil microbial communities indirectly by impacting soil structure and vegetation composition. In high arctic environments, this impact is poorly elucidated, while having potentially wide-reaching effects on the ecosystem.This study examines how a key arctic herbivore, the muskox Ovibos moschatus, affects the soil microbial community in a high arctic fen. Environmental DNA was extracted from soil samples taken from grazed control plots and from muskox exclosures established 5 years prior. We sequenced amplicons of the 16S rRNA gene to provide insight into the microbial communities. We found that in the grazed control plots, microbial communities exhibited high evenness and displayed highly similar overall diversity. In plots where muskoxen had been excluded, microbial diversity was significantly reduced, and had more uneven intra-sample populations and overall lower ecological richness and evenness. We observed that the composition of microbial communities in grazed soils were significantly affected by the presence of muskoxen, as seen by elevated relative abundances of Bacteroides and Firmicutes, two major phyla found in muskox faeces. Furthermore, an increase in relative abundance of bacteria involved in degradation of recalcitrant carbohydrates and cycling of nitrogen was observed in grazed soil. Ungrazed soils displayed increased abundances of bacteria potentially involved in anaerobic oxidation of methane, whereas some methanogens were more abundant in grazed soils. This corroborates a previous finding that methane emissions are higher in arctic fens under muskox grazing. Our results show that the presence of large herbivores stimulates soil microbial diversity and has a homogenizing influence on the inter-species dynamics in soil microbial communities. The findings of this study, thus, improve our understanding of the effect of herbivore grazing on arctic ecosystems and the derived methane cycling.

Increased annual methane uptake driven by warmer winters in an alpine meadow

Pronounced nongrowing season warming and changes in soil freeze-thaw (F-T) cycles can dramatically alter net methane (CH4 ) exchange rates between soils and the atmosphere. However, the magnitudes and drivers of warming impacts on CH4 uptake in different stages of the F-T cycle are poorly understood in cold alpine ecosystems, which have been found to be a net sink of atmospheric CH4 . Here, we reported a year-round ecosystem daily CH4 uptake in an alpine meadow on the Qinghai-Tibetan Plateau after a 5-year warming experiment that included a control, a low-level warming treatment (+2.4℃ at 5cm soil depth), and a high-level warming treatment (+4.5℃ at 5cm soil depth). We found that warming shortened the F-T cycle under the low-level warming and soils did not freeze under the high-level warming. Although both warming treatments increased the mean CH4 uptake rate, only the high-level warming significantly increased annual CH4 uptake compared to the control. The warming-induced stimulation of CH4 uptake mainly occurred in the cold season, which was mostly during spring thaw under low-level warming and during the frozen winter under high-level warming due to a longer period with thawed soil. We also found that warming significantly stimulated daily CH4 uptake mainly by reducing near-surface soil water content in the warm season, whereas both soil water content and temperature controlled daily CH4 uptake in different ways during the autumn freeze, frozen winter, and spring thaw periods of the control. Our study revealed a strong warming effect on CH4 uptake during the entire F-T cycle in the alpine meadow, especially the unfrozen winter. Our results also suggested the important roles of soil pH, available phosphorus, and methanotroph abundance in regulating annual CH4 uptake in response to warming, which should be incorporated into biogeochemical models for accurately forecasting CH4 fluxes under future climate scenarios.