Methanotrophic community structure and activity under warming and grazing of alpine meadow on the Tibetan Plateau

More enhanced non-growing season methane exchanges under warming on the Qinghai-Tibetan Plateau

Uncertainty in methane (CH4) exchanges across wetlands and grasslands in the Qinghai-Tibetan Plateau (QTP) is projected to increase due to continuous permafrost degradation and asymmetrical seasonal warming. Temperature plays a vital role in regulating CH4 exchange, yet the seasonal patterns of temperature dependencies for CH4 fluxes over the wetlands and grasslands on the QTP remain poorly understood. Here, we demonstrated a stronger warming response of CH4 exchanges during the non-growing season compared to the growing season on the QTP. Analyzing 9745 daily observations and employing four methods -regression fitting of temperature-CH4 flux, temperature dependence calculations, field-based and model-based control experiments-we found that warming intensified CH4 emissions in wetlands and uptakes in grasslands. Specifically, the average reaction intensity in the non-growing season surpasses that in the growing season by 1.89 and 4.80 times, respectively. This stronger warming response of CH4 exchanges during the non-growing season significantly increases the regional CH4 exchange on the QTP. Our research reveals that CH4 exchanges in the QTP have a higher warming sensitivity in non-growing seasons, which meanwhile are dominated by a larger warming rate than the annual average. The combined effects of these two factors will significantly alter the CH4 source/sink on the QTP. Neglecting these impacts would lead to inaccurate estimations of CH4 source/sink over the QTP under climate warming.

Effects of warming and isolation from precipitation on the soil carbon, nitrogen, and phosphorus, and their stoichiometries in an alpine meadow in the Qinghai–Tibet Plateau: A greenhouse warming study

Introduction

In the Qinghai–Tibet Plateau (QTP), alpine meadows are among the most noticeable reflection of global climate change. However, effects of global warming on soils hosting alpine meadows in the QTP, such as reduced moisture because of low precipitation, remain unclear.

Methods

Here, the soil moisture content (SMC), pH, dissolved organic carbon (DOC), ammonium nitrogen (NH4+–N), nitrate nitrogen (NO3−–N) and available phosphorus (AP) contents in the QTP were analyzed. The changes in and stoichiometries of total carbon, nitrogen, and phosphorus (TC, TN, and TP), microbial biomass carbon, nitrogen, and phosphorus (MBC, MBN, and MBP), β-1,4-glucosidase (BG), β-1,4-N-acetylglucoaminosidase (NAG), leucine aminopeptidase (LAP), and acid phosphatase (ACP) in the 0–30 cm layer of soils associated with warming in a greenhouse in the QTP from 2015 to 2020 were characterized.

Results

We found that warming in the greenhouse significantly decreased the SMC, NO3−–N, MBC, MBN, MBP, BG, LAP, ACP, and enzymatic C:N ratio. The warming increased the DOC, NH4+–N, AP, MBC:MBN, and enzymatic N:P ratios noticeably. The pH, TC, TN, TP, C:N, C:P, N:P, MBC:MBP, MBN:MBP, and enzymatic C:P ratios were minimally affected.

Conclusion

The results showed that warming and isolation from precipitation promoted mineralization of N and P in the soil but did not significantly alter the cycling of elements in soils in an alpine meadow.

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

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

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 5 cm soil depth), and a high-level warming treatment (+4.5℃ at 5 cm 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.

Effects of Different Grazing Disturbances on the Plant Diversity and Ecological Functions of Alpine Grassland Ecosystem on the Qinghai-Tibetan Plateau

Grazing is one of the main human disturbance factors in alpine grassland on the Qinghai-Tibet Plateau (QTP), which can directly or indirectly influence the community structures and ecological functions of grassland ecosystems. However, despite extensive field grazing experiments, there is currently no consensus on how different grazing management approaches affect alpine grassland diversity, soil carbon (C), and nitrogen (N). Here, we conducted a meta-analysis of 70 peer-reviewed publications to evaluate the general response of 11 variables related to alpine grassland ecosystems plant diversity and ecological functions to grazing. Overall, the results showed that grazing significantly increased the species richness, Shannon-Wiener index, and Pielou evenness index values by 9.89% (95% CI: 2.75-17.09%), 7.28% (95% CI: 1.68-13.62%), and 3.74% (95% CI: 1.40-6.52%), respectively. Aboveground biomass (AGB) and belowground biomass (BGB) decreased, respectively, by 41.91% (95% CI: -50.91 to -32.88%) and 17.68% (95% CI: -26.94 to -8.52%). Soil organic carbon (SOC), soil total nitrogen (TN), soil C:N ratio, and soil moisture decreased by 13.06% (95% CI: -15.88 to -10.15%), 12.62% (95% CI: -13.35 to -8.61%), 3.27% (95% CI: -4.25 to -2.09%), and 20.75% (95% CI: -27.89 to -13.61%), respectively, whereas, soil bulk density and soil pH increased by 17.46% (95% CI: 11.88-24.53%) and 2.24% (95% CI: 1.01-3.64%), respectively. Specifically, moderate grazing, long-durations (>5 years), and winter grazing contributed to increases in the species richness, Shannon-Wiener index, and Pielou evenness index. However, AGB, BGB, SOC, TN, and soil C:N ratios showed a decrease with enhanced grazing intensity. The response ratio of SOC was positively associated with AGB and BGB but was negatively related to the Shannon-Wiener index and Pielou evenness index. Furthermore, the effects of grazing on plant diversity, AGB, BGB, SOC, and TN in alpine grassland varied with grazing duration, grazing season, livestock type, and grassland type. The findings suggest that grazing should synthesize other appropriate grazing patterns, such as seasonal and rotation grazing, and, furthermore, additional research on grazing management of alpine grassland on the QTP is needed in the future.

The Effect of Multi-Years Reclaimed Water Irrigation on Dryland Carbon Sequestration in the North China Plain

Reclaimed water is an alternative water source which could alleviate the shortage of water resources in agricultural systems. Many researchers have studied the effect of reclaimed water on soil environment, crop yield, etc. However, carbon sequestration in reclaimed water irrigated agricultural systems is less studied. This study investigates methane uptake and photosynthesis in reclaimed water irrigation systems contributing to carbon sequestration estimation and analyzes the important factors impacting them. The results show that CH4 uptake is related to soil water-filled pore space (WFPS) with a quadratic and it has the highest uptake when WFPS is between 40 and 50%. Long-term reclaimed water irrigation could significantly decrease (p < 0.05) CH4 uptake and macroaggregate stability in the topsoil. However, reclaimed water had no significant impact on photosynthesis in comparison. The type of fertilizer is an important factor which impacts CH4 emission from soil; urea had a lower CH4 uptake and a higher CO2 emission than slow-released fertilizer. Overall, reclaimed water irrigation could effectively decrease soil carbon sequestration. A soil wetted proportion level of 40–50% was recommended in this study for favorable methane oxidation. Slow-released fertilizer in reclaimed water irrigated agriculture could better control soil carbon emission and soil carbon absorption.

Soil Bacterial Community Responses to N Application and Warming in a Qinghai-Tibetan Plateau Alpine Steppe

Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&amp;N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.

Increased CO2 emissions surpass reductions of non-CO2 emissions more under higher experimental warming in an alpine meadow

It is well documented that warming can accelerate greenhouse gas (GHG) emissions, further inducing a positive feedback and reinforcing future climate warming. However, how different kinds of GHGs respond to various warming magnitudes remains largely unclear, especially in the cold regions that are more sensitive to climate warming. Here, we concurrently measured carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) fluxes and their total balance in an alpine meadow in response to three levels of warming (ambient, +1.5 °C, +3.0 °C). We found warming-induced increases in CH₄ uptake, decreases in N₂O emissions and increases in CO₂ emissions at the annual basis. Expressed as CO₂-equivalents with a global warming potential of 100 years (GWP100), the enhancement of CH₄ uptake and reduction of N₂O emissions offset only 9% of the warming-induced increase in CO₂ emissions for 1.5 °C warming, and only 7% for 3.0 °C warming. CO₂ emissions were strongly stimulated, leading to a significantly positive feedback to climate system, for 3.0 °C warming but less for 1.5 °C warming. The warming with 3.0 °C altered the total GHG balance mainly by stimulating CO₂ emissions in the non-growing season due to warmer soil temperatures, longer unfrozen period, and increased soil water content. The findings provide an empirical evidence that warming beyond global 2 °C target can trigger a positive GHG-climate feedback and highlight the contribution from non-growing season to this positive feedback loop in cold ecosystems.

Rainfall increasing offsets the negative effects of nighttime warming on GHGs and wheat yield in North China Plain

The effects of nighttime warming and rainfall increasing on crop productivity and soil greenhouse gas emissions are few studied. This study was conducted with a field experiment to investigate the effects of nighttime warming, rainfall increasing and their interaction on wheat grain yield, methane (CH₄) and nitrous oxide (N₂O) emissions during a winter wheat growing season in the North China Plain (NCP). The results showed that nighttime warming and rainfall increasing significantly altered soil temperature and moisture, and thus the CH₄ and N₂O emissions from the soil. Nighttime warming significantly promoted soil CH₄ uptake by 21.2% and increased soil N₂O emissions by 22.4%. Rainfall increasing stimulated soil N₂O emissions by 15.7% but decreased soil CH₄ uptake by 18.6%. Nighttime warming significantly decreased wheat yield by 5.5%, while rainfall increasing enhanced wheat yield by 4.0%. The results indicate that the positive effect of nighttime warming on CH₄ uptake and negative effect on wheat yield can be offset by rainfall increasing in the NCP. Generally, rainfall increasing significantly raised the global warming potential and greenhouse gas intensity induced by CH₄ and N₂O emissions. Overall, this study improves our understanding of agroecosystem C and N cycling in response to nighttime warming and rainfall increasing under future climate change.

Variation in the Soil Prokaryotic Community Under Simulated Warming and Rainfall Reduction in Different Water Table Peatlands of the Zoige Plateau

Climate change and water table drawdown impact the community structure and diversity of peatland soil prokaryotes. Nonetheless, how soil prokaryotes of different water tables respond to climate change remains largely unknown. This study used 16S rRNA gene sequencing to evaluate the variation in soil prokaryotes under scenarios of warming, rainfall reduction, and their combination in different water table peatlands on the Zoige Plateau in China. Stimulated climate change affected some of the diversity indexes and relative abundances of soil prokaryotes in three water table peatlands. Additionally, those from the dry-rewetting event peatland had the most dominant phyla (genera) that showed significant changes in a relative abundance due to the simulated climate change treatments. Regarding functional microbial groups of carbon and nitrogen cycling, simulated climate change did not affect the abundances of the Euryarchaeota, Proteobacteria, Verrucomicrobia, and Methanobacterium in three water table peatlands, except NC10 and Nitrospirae. Redundancy analysis showed that the prokaryotic community variation was primary impacted by site properties of the different water table peatlands rather than the simulated climate change treatments. Moreover, the water table, total carbon, total nitrogen, and soil pH were the primary factors for the overall variation in the soil prokaryotic structure. This study provides a theoretical guidance for management strategies in the Zoige peatland, under climate change scenarios. More attention should be given to the interactive effects of peatland water table drawdown and simulated climate changes for better restorative efforts in water table drawdown, rather than simply adapting to climate change.

Effects of increased precipitation combined with nitrogen addition and increased temperature on methane fluxes in alpine meadows of the Tibetan Plateau

Climate change and anthropogenic activities have resulted in increased atmospheric methane (CH₄) concentration. Increased nitrogen deposition and precipitation accompanies climate warming and can change soil carbon and nitrogen dynamics and microbial processes and alter CH₄ fluxes. To quantify the sink of the vast alpine meadows of the Tibetan Plateau and to examine how precipitation addition (P), warming (W), and nitrogen addition (N) affect CH₄ fluxes in alpine meadows, we conducted continuous 3-growing season experiments in an alpine meadow using the static chamber and gas chromatograph method. Soil CH₄ samples were collected during the early, peak, and late stages of the growing season from 2015 to 2017. Our results suggested that neither P, W, nor N had an interaction effect on soil CH₄ uptake. P significantly increased and decreased the copies number of particulate methane monooxygenase alpha subunit (pmoA) and methyl-coenzyme M reductase alpha subunit (mcrA), respectively. However, P significantly decreased CH₄ uptake, particularly under the combined treatment of P and N. Compared with the control, CH₄ uptake decreased under P, N, PW, and PN by 50.64%, 6.24%, 39.37%, and 75.06%, respectively, whereas under W and WN CH₄ uptake increased by 16.19% and 7.56%, respectively. Soil CH₄ uptake was positively correlated with soil temperature and pmoA and negatively correlated with soil moisture and NH₄⁺-N content. CH₄ uptake was significantly affected by the sampling period. CH₄ uptake was significantly lower rates during peak growing season compared with those during the early and late stages of the growing season. Our results suggest that, (1) CH₄ fluxes of alpine grassland ecosystems are more sensitive to P than W or N, and (2) precipitation controls CH₄ flux response to increasing nitrogen deposition in alpine meadows on the Tibetan Plateau. Therefore, future research should focus on the response and feedback of CH₄ uptake to changes in precipitation.

Upland soil cluster γ dominates the methanotroph communities in the karst Heshang Cave

Microorganisms are thought to play a critical role in methane (CH4) consumption in karst caves and yet the presence and diversity of methane-oxidizing bacteria (MOB) remain a mystery. In Heshang Cave, CH4 concentration decreases from 1.9 ppm at the entrance to 0.65 ppm inside the cave. To explore the presence and diversity of MOB in this cave, weathered rocks and sediment samples were collected from the cave and subjected to molecular analysis. The abundances of MOB were 107-108 copies g-1 dry sample via quantification of the pmoA gene, which are comparable to or even higher than those reported in other terrestrial environments, and account for up to 20% of the total microbial communities. Phylogenetically, MOB communities were dominated by the 'high-affinity' upland soil cluster γ (USCγ), although the predominance of Type Ia MOB was also detected in the permanently waterlogged stream sediment. The estimated CH4 oxidation potential varied dramatically among samples in the range of 0.6-80 CH4 m-3 d-1. Collectively, this study provides compelling evidence that the high-affinity MOB capable of oxidizing CH4 at the atmospheric level are present in Heshang Cave, which may play an important role in the CH4 consumption, and supports karst caves as important atmospheric CH4 sinks.

Upland Soil Cluster Gamma dominates methanotrophic communities in upland grassland soils

Aerobic methanotrophs in upland soils consume atmospheric methane, serving as a critical counterbalance to global warming; however, the biogeographic distribution patterns of their abundance and community composition are poorly understood, especial at a large scale. In this study, soils were sampled from 30 grasslands across >2000 km on the Qinghai-Tibetan Plateau to determine the distribution patterns of methanotrophs and their driving factors at a regional scale. Methanotroph abundance and community composition were analyzed using quantitative PCR and Illumina Miseq sequencing of pmoA genes, respectively. The pmoA gene copies ranged from 8.2 × 10⁵ to 1.1 × 10⁸ per gram dry soil. Among the 30 grassland soil samples, Upland Soil Cluster Gamma (USCγ) dominated the methanotroph communities in 26 samples. Jasper Ridge Cluster (JR3) was the most dominant methanotrophic cluster in two samples; while Methylocystis, cluster FWs, and Methylobacter were abundant in other two wet soil samples. Interestingly, reanalyzing the pmoA genes sequencing data from existing publications suggested that USCγ was also the main methanotrophic cluster in grassland soils in other regions, especially when their mean annual precipitation was <500 mm. Canonical Analysis of Principal Coordinates including all soil samples indicated that the methanotrophic community composition was significantly correlated with local environmental factors, among which mean annual precipitation and pH showed the strongest correlations. Variance partitioning analysis showed that environmental factors and spatial distance were significant factors affecting the community structure of methanotrophs, and environmental properties were more important factors. Collectively, these findings indicate that atmospheric methane may be mainly oxidized by USCγ in upland soils. They also highlight the key role of water availability and pH in determining the abundance and community profiles of grassland soil methanotrophs.

Biogeographic Patterns and Assembly Mechanisms of Bacterial Communities Differ Between Habitat Generalists and Specialists Across Elevational Gradients

A core issue in microbial ecology is the need to elucidate the ecological processes and underlying mechanisms involved in microbial community assembly. However, the extent to which these mechanisms differ in importance based on traits of taxa with different niche breadth is poorly understood. Here, we used high-throughput sequencing to examine the relative importance of environmental selection and stochastic processes in shaping soil bacterial sub-communities with different niche breadth (including habitat generalists, specialists and other taxa) across elevational gradients on the subalpine slope of Mount Wutai, Northern China. Our findings suggested that the composition of soil bacterial communities differed significantly different among elevational gradients. According to the niche breadth index, 10.9% of OTUs were defined as habitat generalists (B-value >8.7) and 10.0% of OTUs were defined as habitat specialists (B-value <1.5). Generalists and specialists differed distinctly in diversity and biogeographic patterns across elevational gradients. Environmental selection (deterministic processes) and spatial factors (stochastic processes) seemed to determine the assembly and biogeography of habitat generalists. However, for specialists, deterministic processes strongly influenced the distribution, while stochastic processes were not at play. Environmental drivers for generalists and specialists differed, as did their importance. Elevation, total nitrogen and pH were the main factors determining habitat generalists, and soil water content, nitrate nitrogen and pH had the strongest impacts on specialists. Moreover, variation partitioning analysis revealed that environmental selection had a much greater impact on both generalists (17.7% of pure variance was explained) and specialists (3.6%) than spatial factors. However, generalists had a much stronger response to spatial factors (2.3%) than specialists (0.3%). More importantly, null models of β-diversity suggested that specialists deviated significantly from non-neutral assembly mechanisms (relative null deviation= 0.64–0.74) relative to generalists (0.16–0.65) (P < 0.05). These results indicate that generalists and specialists are governed by different assembly mechanisms and present distinct biogeographical patterns. The large proportion of unexplained variation in specialists (93.3%) implies that very complex assembly mechanisms exist in the assembly of specialists across elevational gradients on the subalpine slope of Mount Wutai. It is essential to understand the microbial community assembly at a more refined level, and to expand the current understanding of microbial ecological mechanisms.

Alpine soil microbial ecology in a changing world

Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.

Annual N2O emissions from conventionally grazed typical alpine grass meadows in the eastern Qinghai-Tibetan Plateau

Annual nitrous oxide (N₂O) emissions from high-altitude alpine meadow grasslands have not been effectively characterized because of the scarcity of whole-year measurements. The authors performed a year-round measurement of N₂O fluxes from three conventionally grazed alpine meadows that represent the typical meadow landscape in the eastern Qinghai-Tibetan Plateau (QTP). The results showed that annual N₂O emissions averaged 0.123±0.053 (2SD, i.e., the double standard deviation indicating the 95% confidence interval) kgNha^-1yr^-1 across the three meadow sites. N₂O flux pulses during the spring freezing-thawing period (FTP) were observed at only one site, indicating a large spatial variability in association with soil moisture differences. Approximately 34-57% (mean: 46%) of the annual N₂O emissions occurred in the non-growing season, highlighting the substantial importance of accurate flux observations during this period. The simultaneous observations showed conservative, marginal nitric oxide (NO) fluxes of 0.058±0.032 (2SD) kgNha^-1yr^-1. The N₂O fluxes across the three field sites correlated negatively with the soil nitrate concentrations during the entire year-round period (P<0.05). Furthermore, a significant joint regulatory effect of topsoil temperature and moisture on the N₂O and NO fluxes was observed during the relatively warm periods. Based on the results of the present and previous studies, a simple extrapolation roughly estimated the annual total N₂O emission from Chinese grasslands to be 73±15 (2SD) GgNyr^-1 (1Gg=10⁹g). A linear dependence of the annual N₂O fluxes on the aboveground net primary productivity (ANPP) was also found. This result may provide a simple approach for estimating the N₂O emission inventories of frigid alpine or temperate grasslands that are ungrazed either in the summer or year round. However, further confirmation of this relationship with a wider ANPP range is still needed in the future studies.

Grazing alters net ecosystem C fluxes and the global warming potential of a subtropical pasture

The impact of grazing on C fluxes from pastures in subtropical and tropical regions and on the environment is uncertain, although these systems account for a substantial portion of global C storage. We investigated how cattle grazing influences net ecosystem CO₂ and CH₄ exchange in subtropical pastures using the eddy covariance technique. Measurements were made over several wet-dry seasonal cycles in a grazed pasture, and in an adjacent pasture during the first three years of grazer exclusion. Grazing increased soil wetness but did not affect soil temperature. By removing aboveground biomass, grazing decreased ecosystem respiration (R_eco ) and gross primary productivity (GPP). As the decrease in R_eco was larger than the reduction in GPP, grazing consistently increased the net CO₂ sink strength of subtropical pastures (55, 219 and 187 more C/m² in 2013, 2014, and 2015). Enteric ruminant fermentation and increased soil wetness due to grazers, increased total net ecosystem CH₄ emissions in grazed relative to ungrazed pasture (27-80%). Unlike temperate, arid, and semiarid pastures, where differences in CH₄ emissions between grazed and ungrazed pastures are mainly driven by enteric ruminant fermentation, our results showed that the effect of grazing on soil CH₄ emissions can be greater than CH₄ produced by cattle. Thus, our results suggest that the interactions between grazers and soil hydrology affecting soil CH₄ emissions play an important role in determining the environmental impacts of this management practice in a subtropical pasture. Although grazing increased total net ecosystem CH₄ emissions and removed aboveground biomass, it increased the net storage of C and decreased the global warming potential associated with C fluxes of pasture by increasing its net CO₂ sink strength.

High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils

Glacier forefield soils can provide a substantial sink for atmospheric CH₄, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH₄ oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH₄ flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH₄ increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH₄ uptake rates ranging from -3.7 to -0.03 mg CH₄ m^-2 day^-1 Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH₄ emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH₄ flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH₄ sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH₄ inventories.IMPORTANCE Oxidation of methane (CH₄) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH₄ oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH₄ oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH₄ in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH₄ oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH₄ inventories.

A five-year study of the impact of nitrogen addition on methane uptake in alpine grassland

It remains unclear how nitrogen (N) deposition affects soil methane (CH₄) uptake in semiarid and arid zones. An in situ field experiment was conducted from 2010 to 2014 to systematically study the effect of various N application rates (0, 10, 30, and 90 kg N ha⁻¹ yr⁻¹) on CH₄ flux in alpine grassland in the Tianshan Mountains. No significant influence of N addition on CH₄ uptake was found. Initially the CH₄ uptake rate increased with increasing N application rate by up to 11.5% in 2011 and then there was gradual inhibition by 2014. However, the between-year variability in CH₄ uptake was very highly significant with average uptake ranging from 52.9 to 106.6 μg C m⁻² h⁻¹ and the rate depended largely on seasonal variability in precipitation and temperature. CH₄ uptake was positively correlated with soil temperature, air temperature and to a lesser extent with precipitation, and was negatively correlated with soil moisture and NO₃⁻-N content. The results indicate that between-year variability in CH₄ uptake was impacted by precipitation and temperature and was not sensitive to elevated N deposition in alpine grassland.

Evaluation and update of cutoff values for methanotrophic pmoA gene sequences

The functional pmoA gene is frequently used to probe the diversity and phylogeny of methane-oxidizing bacteria (MOB) in various environments. Here, we compared the similarities between the pmoA gene and the corresponding 16S rRNA gene sequences of 77 described species covering gamma- and alphaproteobacterial methanotrophs (type I and type II MOB, respectively) as well as methanotrophs from the phylum Verrucomicrobia. We updated and established the weighted mean pmoA gene cutoff values on the nucleotide level at 86, 82, and 71 % corresponding to the 97, 95, and 90 % similarity of the 16S rRNA gene. Based on these cutoffs, the functional gene fragments can be entirely processed at the nucleotide level throughout software platforms such as Mothur or QIIME which provide a user-friendly and command-based alternative to amino acid-based pipelines. Type II methanotrophs are less divergent than type I both with regard to ribosomal and functional gene sequence similarity and GC content. We suggest that this agrees with the theory of different life strategies proposed for type I and type II MOB.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow

Warming and grazing significantly affect the structure and function of an alpine meadow ecosystem. Yet, the responses of soil microbes to these disturbances are not well understood. Controlled asymmetrical warming (+1.2/1.7°C during daytime/nighttime) with grazing experiments were conducted to study microbial response to warming, grazing and their interactions. Significant interactive effects of warming and grazing were observed on soil bacterial α-diversity and composition. Warming only caused significant increase in bacterial α-diversity under no-grazing conditions. Grazing induced no substantial differences in bacterial α-diversity and composition irrespective of warming. Warming, regardless of grazing, caused a significant increase in soil bacterial community similarity across space, but grazing only induced significant increases under no-warming conditions. The positive effects of warming on bacterial α-diversity and grazing on community similarity were weakened by grazing and warming, respectively. Soil and plant variables explained well the variations in microbial communities, indicating that changes in soil and plant properties may primarily regulate soil microbial responses to warming in this alpine meadow. The results suggest that bacterial communities may become more similar across space in a future, warmed climate and moderate grazing may potentially offset, at least partially, the effects of global warming on the soil microbial diversity.

Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways

Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating the methane emission in soil ecosystems to the atmosphere. However, the impact of plant species and plantation ways on the distribution of MOB remains unclear. The present study investigated MOB abundance and structure in plateau soils with different plant species and plantation ways (natural and managed). Soils were collected from unmanaged wild grassland and naturally forested sites, and managed farmland and afforested sites. A large variation in MOB abundance and structure was found in these studied soils. In addition, both type I MOB (Methylocaldum) and type II MOB (Methylocystis) were detected in these soils, while type II MOB usually outnumbered type I MOB. The distribution of soil MOB community was found to be collectively regulated by plantation way, plant species, the altitude of sampling site, and soil properties.

Considerable methane uptake by alpine grasslands despite the cold climate: in situ measurements on the central Tibetan Plateau, 2008-2013

The uptake of CH4 by aerate soil plays a secondary role in the removal of tropospheric CH4 , but it is still highly uncertain in terms of its magnitude, spatial, and temporal variation. In an attempt to quantify the sink of the vast alpine grasslands (1,400,000 km(2)) of the Tibetan Plateau, we conducted in situ measurements in an alpine steppe (4730 m) and alpine meadow (4900 m) using the static chamber and gas chromatograph method. For the alpine steppe, measurements (2008-2013) suggested that there is large interannual variability in CH4 uptake, ranging from -48.8 to -95.8 μg CH4 m(-2) h(-1) (averaged of -71.5 ± 2.5 μg CH4 m(-2) h(-1)), due to the variability in precipitation seasonality. The seasonal pattern of CH4 uptakes in the form of stronger uptake in the early growing season and weaker uptake in the rainy season closely matched the precipitation seasonality and subsequent soil moisture variation. The relationships between alpine steppe CH4 uptake and soil moisture/temperature are best depicted by a quadratic function and an exponential function (Q10 = 1.67) respectively. Our measurements also showed that the alpine meadow soil (average of -59.2 ± 3.7 μg CH4 m(-2) h(-1)) uptake less CH4 than the alpine steppe and produces a similar seasonal pattern, which is negatively regulated by soil moisture. Our measurements quantified--at values far higher than those estimated by process-based models--that both the alpine steppe and alpine meadow are considerable CH4 sinks, despite the cold weather of this high-altitude area. The consecutive measurements gathered in this study also highlight that precipitation seasonality tends to drive the interannual variation in CH4 uptake, indicating that future study should be done to better characterize how CH4 cycling might feedback to the more extreme climate.

Aerobic and nitrite-dependent methane-oxidizing microorganisms in sediments of freshwater lakes on the Yunnan Plateau

Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) bacteria can play an important role in mitigating the methane emission produced in anoxic sediment layers to the atmosphere. However, the environmental factors regulating the distribution of these methane-oxidizing microorganisms in lacustrine ecosystems remain essentially unclear. The present study investigated the distribution of aerobic MOB and n-damo bacteria in sediments of various freshwater lakes on the Yunnan Plateau (China). Quantitative PCR assay and clone library analysis illustrated the spatial variations in the abundances and structures of aerobic MOB and n-damo bacterial communities. Type I MOB (Methylosoma and Methylobacter) and type II MOB (Methylocystis) were detected, while type I MOB was more abundant than type II MOB. Lake sediments n-damo bacterial communities were composed of novel Methylomirabilis oxyfera-like pmoA genes. Lake sediments in the same geographic region could share a relatively similar aerobic MOB community structure. Moreover, Pearson's correlation analysis indicated that n-damo pmoA gene diversity showed a positive correlation with the ratio of organic matter to total nitrogen in lake sediment.

Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils

Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment ecosystems.

Differential responses of arbuscular mycorrhizal fungi to nitrogen addition in a near pristine Tibetan alpine meadow

Elucidating the responses of soil microbial abundance and community composition to nitrogen (N) addition is important for predicting ecosystem function under increased atmospheric N deposition. We examined the arbuscular mycorrhizal (AM) fungal community under three N forms (NH4(+)-N, NO3(-)-N, and NH4NO3-N) and two N rates (1.5 and 7.5 g N m(-2) year(-1)) in an alpine meadow of the Qinghai-Tibetan Plateau. AM fungal extraradical hyphal density was significantly decreased by NH4(+)-N in May, but was not affected by N form nor N rate in August. N rate, but not N form, significantly affected AM fungal spore density; high N rate decreased spore density. No direct N addition effect was observed on AM fungal community; however, soil available phosphorus, pH, and NO3(-)-N were considered as important factors that influenced AM fungal community composition. Structural equation model results showed that N rate, not N form, strongly affected soil characteristics, which directly influenced community compositions of plants and AM fungi, as well as spore density. Therefore, AM fungal community was influenced by N addition, primarily because of altered soil characteristics, and partially by a modified plant community, but not or just slightly by direct N addition effects in this alpine meadow ecosystem.

Atmospheric methane oxidizers are present and active in Canadian high Arctic soils

The melting of permafrost and the associated potential for methane emissions to the atmosphere are major concerns in the context of global warming. However, soils can also represent a significant sink for methane through the activity of methane-oxidizing bacteria (MOB). In this study, we looked at the activity, diversity, and community structure of MOB at two sampling depths within the active layer in three soils from the Canadian high Arctic. These soils had the capacity to oxidize methane at low (15 ppm) and high (1000 ppm) methane concentrations, but rates differed greatly depending on the sampling date, depth, and site. The pmoA gene sequences related to two genotypes of uncultured MOB involved in atmospheric methane oxidation, the 'upland soil cluster gamma' and the 'upland soil cluster alpha', were detected in soils with near neutral and acidic pH, respectively. Other groups of MOB, including Type I methanotrophs and the 'Cluster 1' genotype, were also detected, indicating a broader diversity of MOB than previously reported for Arctic soils. Overall, the results reported here showed that methane oxidation at both low and high methane concentrations occurs in high Arctic soils and revealed that different groups of atmospheric MOB inhabit these soils.

Characterizing changes in soil bacterial community structure in response to short-term warming

High altitude alpine meadows are experiencing considerably greater than average increases in soil surface temperature, potentially as a result of ongoing climate change. The effects of warming on plant productivity and soil edaphic variables have been established previously, but the influence of warming on soil microbial community structure has not been well characterized. Here, the impact of 15 months of soil warming (both +1 and +2 °C) on bacterial community structure was examined in a field experiment on a Tibetan plateau alpine meadow using bar-coded pyrosequencing. Warming significantly changed (P < 0.05) the structure of the soil bacterial community, but the alpha diversity was not dramatically affected. Changes in the abundance of the Actinobacteria and Alphaproteobacteria were found to contribute the most to differences between ambient (AT) and artificially warmed conditions. A variance partitioning analysis (VPA) showed that warming directly explained 7.15% variation in bacterial community structure, while warming-induced changes in soil edaphic and plant phenotypic properties indirectly accounted for 28.3% and 20.6% of the community variance, respectively. Interestingly, certain taxa showed an inconsistent response to the two warming treatments, for example Deltaproteobacteria showed a decreased relative abundance at +1 °C, but a return to AT control relative abundance at +2 °C. This suggests complex microbial dynamics that could result from conditional dependencies between bacterial taxa.

The impacts of climate change and human activities on biogeochemical cycles on the Qinghai-Tibetan Plateau

With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's 'third pole') has increased by 0.2 °C per decade over the past 50 years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH(4)) emissions from wetlands and increased CH(4) consumption of meadows, but might increase CH(4) emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO(2)) and CH(4). Nitrous oxide (N(2)O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles.

The arbuscular mycorrhizal fungal community response to warming and grazing differs between soil and roots on the Qinghai-Tibetan plateau

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most plant species in terrestrial ecosystems, and are affected by environmental variations. To reveal the impact of disturbance on an AM fungal community under future global warming, we examined the abundance and community composition of AM fungi in both soil and mixed roots in an alpine meadow on the Qinghai-Tibetan Plateau, China. Warming and grazing had no significant effect on AM root colonization, spore density and extraradical hyphal density. A total of 65 operational taxonomic units (OTUs) of AM fungi were identified from soil and roots using molecular techniques. AM fungal OTU richness was higher in soil (54 OTUs) than in roots (34 OTUs), and some AM fungi that differed between soil and roots, showed significantly biased occurrence to warming or grazing. Warming and grazing did not significantly affect AM fungal OTU richness in soil, but warming with grazing significantly increased AM fungal OTU richness in roots compared to the grazing-only treatment. Non-metric multidimensional scaling analysis showed that the AM fungal community composition was significantly different between soil and roots, and was significantly affected by grazing in roots, whereas in soil it was significantly affected by warming and plant species richness. The results suggest that the AM fungal community responds differently to warming and grazing in soil compared with roots. This study provides insights into the role of AM fungi under global environmental change scenarios in alpine meadows of the Qinghai-Tibetan Plateau.

Freeze-coring method for characterization of microbial community structure and function in wetland soils at high spatial resolution

A simple freeze-coring method was developed to obtain structurally intact cores from wetland soils. A copper tube was inserted into the wetland and filled with ethanol and dry ice to freeze the surrounding soil. Biological structure and function could be analyzed, and labile compounds such as mRNA were recovered.