The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands

Cooling has stimulated soil carbon storage in forest ecosystems

The interactive effect of soil cooling and nitrogen (N) addition can accurately simulate climatic and anthropogenic effects on terrestrial and other land-based ecosystems, but direct empirical measurements on the effects of cooling and N addition on soil carbon (C) and N are lacking. Hence, transplanting soils into colder regions was used to evaluate the effects of cooling and N addition on soil C and N. We used PVCs of 30 cm in height and 8 cm in diameter to extract soil samples. Soil C and N were significantly (P < 0.05) increased by transplanting soils into colder regions. In contrast, cooling has insignificantly (P > 0.05) increased the soil dissolved organic C (DOC) and dissolved organic (DON), but the effect was negatively significant on soil pH compared to the C/N ratio. Similarly, N addition significantly increased the measured soil N stock. However, the effect was negatively significant on soil pH (P < 0.05) compared to the C/N ratio (P > 0.05). Nevertheless, the interaction of cooling and N addition did not affect the soil C and N storage. A similar effect was observed on the soil DOC and DON. The results presented here illustrate that transplanting soils into colder regions and N deposition has perfectly simulated the effects of climate-forcing factors on soil C and N storage in terrestrial and other land-based ecosystems. Accordingly, this study suggests that low temperatures have stimulated the accumulation of the measured soil organic and dissolved properties, but the effect is less consequential when low temperature interacts with N addition in high-elevation areas where ecosystem structures and functions are limited by temperature and may serve as a baseline for future research on land feedbacks to the climate system.

Effects of nitrogen addition on rhizosphere priming: The role of stoichiometric imbalance

Nitrogen (N) input has a significant impact on the availability of carbon (C), nitrogen (N), and phosphorus (P) in the rhizosphere, leading to an imbalanced stoichiometry in microbial demands. This imbalance can result in energy or nutrient limitations, which, in turn, affect C dynamics during plant growth. However, the precise influence of N addition on the C:N:P imbalance ratio and its subsequent effects on rhizosphere priming effects (RPEs) remain unclear. To address this gap, we conducted a 75-day microcosm experiment, varying N addition rates (0, 150, 300 kg N ha-1), to examine how microbes regulate RPE by adapting to stoichiometry and maintaining homeostasis in response to N addition, using the 13C natural method. Our result showed that N input induced a stoichiometric imbalance in C:N:P, leading to P or C limitation for microbes during plant growth. Microbes responded by adjusting enzymatic stoichiometry and functional taxa to preserve homeostasis, thereby modifying the threshold element ratios (TERs) to cope with the C:N:P imbalance. Microbes adapted to the stoichiometric imbalance by reducing TER, which was attributed to a reduction in carbon use efficiency. Consequently, we observed higher RPE under P limitation, whereas the opposite trend was observed under C or N limitation. These results offer novel insights into the microbial regulation of RPE variation under different soil nutrient conditions and contribute to a better understanding of soil C dynamics.

Vegetation type, not the legacy of warming, modifies the response of microbial functional genes and greenhouse gas fluxes to drought in Oro-Arctic and alpine regions

Climate warming and summer droughts alter soil microbial activity, affecting greenhouse gas (GHG) emissions in Arctic and alpine regions. However, the long-term effects of warming, and implications for future microbial resilience, are poorly understood. Using one alpine and three Arctic soils subjected to in situ long-term experimental warming, we simulated drought in laboratory incubations to test how microbial functional-gene abundance affects fluxes in three GHGs: carbon dioxide, methane, and nitrous oxide. We found that responses of functional gene abundances to drought and warming are strongly associated with vegetation type and soil carbon. Our sites ranged from a wet, forb dominated, soil carbon-rich systems to a drier, soil carbon-poor alpine site. Resilience of functional gene abundances, and in turn methane and carbon dioxide fluxes, was lower in the wetter, carbon-rich systems. However, we did not detect an effect of drought or warming on nitrous oxide fluxes. All gene-GHG relationships were modified by vegetation type, with stronger effects being observed in wetter, forb-rich soils. These results suggest that impacts of warming and drought on GHG emissions are linked to a complex set of microbial gene abundances and may be habitat-specific.

Disentangling the assembly mechanisms of bacterial communities in a transition zone between the alpine steppe and alpine meadow ecosystems on the Tibetan Plateau

Alpine meadows and alpine steppes are two major grassland types distributed on the Tibetan Plateau. Due in large part to the differences in hydrothermal and nutrient conditions following the thawing of lakeshore permafrost, alpine meadows and alpine steppes which are characterized by disparate above- and below-ground biomass, could emerge together in the grassland transition zone between meadows and steppes of the Tibetan Plateau. Bacterial communities are essential components of alpine grassland ecosystems and respond rapidly to environmental changes. Despite their ecological significance, it remains poorly elucidated whether and how the assembly patterns of bacterial communities differed between alpine meadows and alpine steppes. Here, to disentangle the assembly mechanisms of bacterial communities from alpine meadows and alpine steppes, we collected samples from three diverse habitats (i.e., sediments, rhizosphere soils and bulk soils) in both alpine meadow and steppe ecosystems on the Tibetan Plateau. Our results indicated that in both meadows and steppes, rhizosphere bacterial communities exhibited higher alpha-diversity but lower beta-diversity compared to the bacterial communities in sediments and bulk soils. However, the close relationships of bacterial communities between different habitats weakened from meadows to steppes. Null model analysis indicated that the importance of environmental selection shaping bacterial community assemblages in all habitats decreased from meadows to steppes, whereas the role of dispersal limitation showed an opposite pattern. Moreover, pH was the primary driver of phylogenetic turnover of bacterial communities in the steppes across all habitats, whereas the dominant drivers of phylogenetic turnover of bacterial communities in meadows varied with habitat types. Overall, our findings provide novel insights into understanding the differences in microbial communities between meadows and steppes in the grassland transition zone on the Tibetan Plateau.

Activation effect of catechol on biotic and abiotic factors of humus formation during chicken manure composting

In this present study, catechol was added to promote humus formation in chicken manure composting using 12.5-L working volume lab-scale reactors. Chicken manure composting were carried out on two treatments, control (CK) and 0.5% (w/w) catechol treated group. Results showed that catechol addition reduced organic matter loss and improved the content of recalcitrant components. Humus and humic acid (HA) contents were, respectively, 69.2% and 82.3% higher in catechol treated-compost than in the control. With the addition of catechol, the bacterial community composition and richness was changed, e.g., the relative percentage of Bacillus and Sinibacillus were increased, which might contribute to humus and HA formation. Additionally, the activities of polyphenol oxidase and laccase (related to humus formation) were increased by the addition of catechol. Importantly, the catechol addition reduced the polyphenol content by 39.6% compared to control. Overall, the addition of catechol enhanced the biotic and abiotic factors to promote the humification process during composting, which might be a promising approach for accelerating the humification process and reducing contamination of phenolic compounds.

Experimental Warming Has Not Affected the Changes in Soil Organic Carbon During the Growing Season in an Alpine Meadow Ecosystem on the Qinghai-Tibet Plateau

The effects of climate warming and season on soil organic carbon (SOC) have received widespread attention, but how climate warming affects the seasonal changes of SOC remains unclear. Here, we established a gradient warming experiment to investigate plant attributes and soil physicochemical and microbial properties that were potentially associated with changes in SOC at the beginning (May) and end (August) of the growing season in an alpine meadow ecosystem on the Qinghai-Tibet Plateau. The SOC of August was lower than that of May, and the storage of SOC in August decreased by an average of 18.53 million grams of carbon per hectare. Warming not only failed to alter the content of SOC regardless of the season but also did not affect the change in SOC during the growing season. Among all the variables measured, microbial biomass carbon was highly coupled to the change in SOC. These findings indicate that alpine meadow soil is a source of carbon during the growing season, but climate warming has no significant impact on it. This study highlights that in the regulation of carbon source or pool in alpine meadow ecosystem, more attention should be paid to changes in SOC during the growing season, rather than climate warming.

Fast and persistent responses of alpine permafrost microbial communities to in situ warming

Global warming in mid-latitude alpine regions results in permafrost thawing, together with greater availability of carbon and nutrients in soils and frequent freeze-thaw cycles. Yet it is unclear how these multifactorial changes will shape the 1 m-deep permafrost microbiome in the future, and how this will in turn modulate microbially-mediated feedbacks between mountain soils and climate (e.g. soil CO₂ emissions). To unravel the responses of the alpine permafrost microbiome to in situ warming, we established a three-year experiment in a permafrost monitoring summit in the Alps. Specifically, we simulated conditions of warming by transplanting permafrost soils from a depth of 160 cm either to the active-layer topsoils in the north-facing slope or in the warmer south-facing slope, near the summit. qPCR-based and amplicon sequencing analyses indicated an augmented microbial abundance in the transplanted permafrost, driven by the increase in copiotrophic prokaryotic taxa (e.g. Noviherbaspirillum and Massilia) and metabolically versatile psychrotrophs (e.g. Tundrisphaera and Granulicella); which acclimatized to the changing environment and potentially benefited from substrates released upon thawing. Metabolically restricted Patescibacteria lineages vastly decreased with warming, as reflected in the loss of α-diversity in the transplanted soils. Ascomycetous sapro-pathotrophs (e.g. Tetracladium) and a few lichenized fungi (e.g. Aspicilia) expanded in the transplanted permafrost, particularly in soils transplanted to the warmer south-facing slope, replacing basidiomycetous yeasts (e.g. Glaciozyma). The transplantation-induced loosening of microbial association networks in the permafrost could potentially indicate lesser cooperative interactions between neighboring microorganisms. Broader substrate-use microbial activities measured in the transplanted permafrost could relate to altered soil C dynamics. The three-year simulated warming did not, however, enhance heterotrophic respiration, which was limited by the carbon-depleted permafrost conditions. Collectively, our quantitative findings suggest the vulnerability of the alpine permafrost microbiome to warming, which might improve predictions on microbially-modulated transformations of mountain soil ecosystems under the future climate.

Decreased growth of wild soil microbes after 15 years of transplant-induced warming in a montane meadow

The carbon stored in soil exceeds that of plant biomass and atmospheric carbon and its stability can impact global climate. Growth of decomposer microorganisms mediates both the accrual and loss of soil carbon. Growth is sensitive to temperature and given the vast biological diversity of soil microorganisms, the response of decomposer growth rates to warming may be strongly idiosyncratic, varying among taxa, making ecosystem predictions difficult. Here, we show that 15 years of warming by transplanting plant-soil mesocosms down in elevation, strongly reduced the growth rates of soil microorganisms, measured in the field using undisturbed soil. The magnitude of the response to warming varied among microbial taxa. However, the direction of the response-reduced growth-was universal and warming explained twofold more variation than did the sum of taxonomic identity and its interaction with warming. For this ecosystem, most of the growth responses to warming could be explained without taxon-specific information, suggesting that in some cases microbial responses measured in aggregate may be adequate for climate modeling. Long-term experimental warming also reduced soil carbon content, likely a consequence of a warming-induced increase in decomposition, as warming-induced changes in plant productivity were negligible. The loss of soil carbon and decreased microbial biomass with warming may explain the reduced growth of the microbial community, more than the direct effects of temperature on growth. These findings show that direct and indirect effects of long-term warming can reduce growth rates of soil microbes, which may have important feedbacks to global warming.

Divergent effects of hydrological alteration and nutrient addition on greenhouse gas emissions in the water level fluctuation zone of the Three Gorges Reservoir, China

Changes in global rainfall patterns and construction of artificial dams have led to widespread alteration of hydrological processes in riparian ecosystems. At the same time, many riparian ecosystems, such as those associated with the Yangtze, are being subjected to enhanced inputs of nitrogen (N) and phosphorus (P) due to intensified agricultural activity in surrounding uplands. Together, these environmental changes may alter the magnitude and direction of greenhouse gasses (GHGs) fluxes from riparian soils. We conducted an in situ experiment combined with quantitative PCR approach (qPCR) to elucidate the effects of hydrological alterations (continuous flooding (CF), periodic flooding (PF), and no flooding (NF)) and nutrient addition (N addition (urea, 100 kg N ha^-1 y^-1), P addition (P₂O₅, 20 kg ha^-1y^-1), N + P addition, and control (CK)) on three major GHGs including carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) fluxes as well as the underlying mechanisms. Our results showed that hydrological alterations greatly affected GHGs emissions, possibly by altering soil moisture, soil organic C, and C:N ratios. The CF, with higher soil moisture and lower C:N ratio, increased CH₄ emissions 13-fold and reduced CO₂ and N₂O emissions by 37.3% and 72.2% averaged over the growing seasons compared with no flooding. PF enhanced CH₄ emissions 5.7-fold and decreased N₂O emissions by 69.0% in comparison with no flooding. Nutrient additions had no significant effect on CO₂ or CH₄ flux, but P addition significantly lowered N₂O flux. Interactions between hydrological alterations and nutrient additions were not detected for any GHGs. As a result, hydrological alterations and nutrient additions affected the global warming potential (GWP) of growing season GHG budgets on a 100-year time horizon, mainly by changing the CO₂ emissions. CF reduced GWP from 597 to 439 g CO₂-eq m^-2, and N + P addition enhanced GWP from 489 to 625 g CO₂-eq m^-2. The qPCR analysis revealed that decreased CH₄ oxidation potential may lead to the enrichment of CH₄ emissions under the hydrological alterations, and reduced nitrification and denitrification potential contributed to the reduction of N₂O fluxes under all the treatments. Our study indicates that continuous flooding could curb the contribution of riparian GHGs fluxes to global warming but that the combination of N and P additions may increase the greenhouse effect mainly by regulating the CO₂ emissions of growing season in riparian ecosystem.

Temperature sensitivity of SOM decomposition is linked with a K-selected microbial community

Temperature sensitivity (Q₁₀ ) of soil organic matter (SOM) decomposition is a crucial parameter to predict the fate of soil carbon (C) under global warming. Nonetheless, the response pattern of Q₁₀ to continuous warming and the underlying mechanisms are still under debate, especially considering the complex interactions between Q₁₀ , SOM quality, and soil microorganisms. We examined the Q₁₀ of SOM decomposition across a mean annual temperature (MAT) gradient from -1.9 to 5.1°C in temperate mixed forest ecosystems in parallel with SOM quality and bioavailability, microbial taxonomic composition, and functional genes responsible for organic carbon decomposition. Within this temperature gradient of 7.0°C, the Q₁₀ values increased with MAT, but decreased with SOM bioavailability. The Q₁₀ values increased with the prevalence of K-strategy of soil microbial community, which was characterized by: (i) high ratios of oligotrophic to copiotrophic taxa, (ii) ectomycorrhizal to saprotrophic fungi, (iii) functional genes responsible for degradation of recalcitrant to that of labile C, and (iv) low average 16S rRNA operon copy number. Because the recalcitrant organic matter was mainly utilized by the K-strategists, these findings independently support the carbon quality-temperature theory from the perspective of microbial taxonomic composition and functions. A year-long incubation experiment was performed to determine the response of labile and recalcitrant C pools to warming based on the two-pool model. The decomposition of recalcitrant SOM was more sensitive to increased temperature in southern warm regions, which might attribute to the dominance of K-selected microbial communities. It implies that climate warming would mobilize the larger recalcitrant pools in warm regions, exacerbating the positive feedback between increased MAT and CO₂ efflux. This is the first attempt to link temperature sensitivity of SOM decomposition with microbial eco-strategies by incorporating the genetic information and disentangling the complex relationship between Q₁₀ and soil microorganisms.

High microbial diversity stabilizes the responses of soil organic carbon decomposition to warming in the subsoil on the Tibetan Plateau

Soil microbes are directly involved in soil organic carbon (SOC) decomposition, yet the importance of microbial biodiversity in regulating the temperature sensitivity of SOC decomposition remains elusive, particularly in alpine regions where climate change is predicted to strongly affect SOC dynamics and ecosystem stability. Here we collected topsoil and subsoil samples along an elevational gradient on the southeastern Tibetan Plateau to explore the temperature sensitivity (Q₁₀ ) of SOC decomposition in relation to changes in microbial communities. Specifically, we tested whether the decomposition of SOC would be more sensitive to warming when microbial diversity is low. The estimated Q₁₀ value ranged from 1.28 to 1.68, and 1.80 to 2.10 in the topsoil and subsoil, respectively. The highest Q₁₀ value was observed at the lowest altitude of forests in the topsoil, and at the highest altitude of alpine meadow in the subsoil. Variations in Q₁₀ were closely related to changes in microbial properties. In the topsoil the ratio of gram-positive to gram-negative bacteria (G+:G-) was the predominant factor associated with the altitudinal variations in Q₁₀ . In the subsoil, SOC decomposition showed more resilience to warming when the diversity of soil bacteria (both whole community and major groups) and fungi was higher. Our results partly support the positive biodiversity-ecosystem stability hypothesis. Structural equation modeling further indicates that variations in Q₁₀ in the subsoil were directly related to changes in microbial diversity and community composition, which were affected by soil pH. Collectively our results provide compelling evidence that microbial biodiversity plays an important role in stabilizing SOC decomposition in the subsoil of alpine montane ecosystems. Conservation of belowground biodiversity is therefore of great importance in maintaining the stability of ecosystem processes under climate change in high-elevation regions of the Tibetan Plateau.

Microbial metabolic response to winter warming stabilizes soil carbon

Current consensus on global climate change predicts warming trends with more pronounced temperature changes in winter than summer in the Northern Hemisphere at high latitudes. Moderate increases in soil temperature are generally related to faster rates of soil organic carbon (SOC) decomposition in Northern ecosystems, but there is evidence that SOC stocks have remained remarkably stable or even increased on the Tibetan Plateau under these conditions. This intriguing observation points to altered soil microbial mediation of carbon-cycling feedbacks in this region that might be related to seasonal warming. This study investigated the unexplained SOC stabilization observed on the Tibetan Plateau by quantifying microbial responses to experimental seasonal warming in a typical alpine meadow. Ecosystem respiration was reduced by 17%-38% under winter warming compared with year-round warming or no warming and coincided with decreased abundances of fungi and functional genes that control labile and stable organic carbon decomposition. Compared with year-round warming, winter warming slowed macroaggregate turnover rates by 1.6 times, increased fine intra-aggregate particulate organic matter content by 75%, and increased carbon stabilized in microaggregates within stable macroaggregates by 56%. Larger bacterial "necromass" (amino sugars) concentrations in soil under winter warming coincided with a 12% increase in carboxyl-C. These results indicate the enhanced physical preservation of SOC under winter warming and emphasize the role of soil microorganisms in aggregate life cycles. In summary, the divergent responses of SOC persistence in soils exposed to winter warming compared to year-round warming are explained by the slowing of microbial decomposition but increasing physical protection of microbially derived organic compounds. Consequently, the soil microbial response to winter warming on the Tibetan Plateau may cause negative feedbacks to global climate change and should be considered in Earth system models.

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils

Climate change is strongly affecting high-mountain soils and warming in particular is associated with pronounced changes in microbe-mediated C and N cycling, affecting plant-soil interactions and greenhouse gas balances and therefore feedbacks to global warming. We used shotgun metagenomics to assess changes in microbial community structures, as well as changes in microbial C- and N-cycling potential and stress response genes and we linked these data with changes in soil C and N pools and temperature-dependent measurements of bacterial growth rates. We did so by incubating high-elevation soil from the Swiss Alps at 4°C, 15°C, 25°C, or 35°C for 1 month. We found no shift with increasing temperature in the C-substrate-degrader community towards taxa more capable of degrading recalcitrant organic matter. Conversely, at 35°C, we found an increase in genes associated with the degradation and modification of microbial cell walls, together with high bacterial growth rates. Together, these findings suggest that the rapidly growing high-temperature community is fueled by necromass from heat-sensitive taxa. This interpretation was further supported by a shift in the microbial N-cycling potential towards N mineralization and assimilation under higher temperatures, along with reduced potential for conversions among inorganic N forms. Microbial stress-response genes reacted inconsistently to increasing temperature, suggesting that the high-temperature community was not severely stressed by these conditions. Rather, soil microbes were able to acclimate by changing the thermal properties of membranes and cell walls as indicated by an increase in genes involved in membrane and cell wall modifications as well as a shift in the optimum temperature for bacterial growth towards the treatment temperature. Overall, our results suggest that high temperatures, as they may occur with heat waves under global warming, promote a highly active microbial community capable of rapid mineralization of microbial necromass, which may transiently amplify warming effects.

The microbial network property as a bio-indicator of antibiotic transmission in the environment

Interspecies interaction is an essential mechanism for bacterial communities to develop antibiotic resistance via horizontal gene transfer. Nonetheless, how bacterial interactions vary along the environmental transmission of antibiotics and the underpinnings remain unclear. To address it, we explore potential microbial associations by analyzing bacterial networks generated from 16S rRNA gene sequences and functional networks containing a large number of antibiotic-resistance genes (ARGs). Antibiotic concentration decreased by more than 4000-fold along the environmental transmission chain from manure samples of swine farms to aerobic compost, compost-amended agricultural soils, and neighboring agricultural soils. Both bacterial and functional networks became larger in nodes and links with decreasing antibiotic concentrations, likely resulting from lower antibiotics stress. Nonetheless, bacterial networks became less clustered with decreasing antibiotic concentrations, while functional networks became more clustered. Modularity, a key topological property that enhances system resilience to antibiotic stress, remained high for functional networks, but the modularity values of bacterial networks were the lowest when antibiotic concentrations were intermediate. To explain it, we identified a clear shift from deterministic processes, particularly variable selection, to stochastic processes at intermediate antibiotic concentrations as the dominant mechanism in shaping bacterial communities. Collectively, our results revealed microbial network dynamics and suggest that the modularity value of association networks could serve as an important indicator of antibiotic concentrations in the environment.

Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition

Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.

Altered microbial structure and function after thermokarst formation

Permafrost thaw could induce substantial carbon (C) emissions to the atmosphere, and thus trigger a positive feedback to climate warming. As the engine of biogeochemical cycling, soil microorganisms exert a critical role in mediating the direction and strength of permafrost C-climate feedback. However, our understanding about the impacts of thermokarst (abrupt permafrost thaw) on microbial structure and function remains limited. Here we employed metagenomic sequencing to analyze changes in topsoil (0-15 cm) microbial communities and functional genes along a permafrost thaw sequence (1, 10, and 16 years since permafrost collapse) on the Tibetan Plateau. By combining laboratory incubation and a two-pool model, we then explored changes in soil labile and stable C decomposition along the thaw sequence. Our results showed that topsoil microbial α-diversity decreased, while the community structure and functional gene abundance did not exhibit any significant change at the early stage of collapse (1 year since collapse) relative to non-collapsed control. However, as the time since the collapse increased, both the topsoil microbial community structure and functional genes differed from the control. Abundances of functional genes involved in labile C degradation decreased while those for stable C degradation increased at the late stage of collapse (16 years since collapse), largely driven by changes in substrate properties along the thaw sequence. Accordingly, faster stable C decomposition occurred at the late stage of collapse compared to the control, which was associated with the increase in relative abundance of functional genes for stable C degradation. These results suggest that upland thermokarst alters microbial structure and function, particularly enhances soil stable C decomposition by modulating microbial functional genes, which could reinforce a warmer climate over the decadal timescale.

Long-term active restoration of extremely degraded alpine grassland accelerated turnover and increased stability of soil carbon

Soil nutrient contents and organic carbon (C) stability are key indicators for restoration of degraded grassland. However, the effects of long-term active restoration of extremely degraded grassland on soil parameters have been equivocal. The aims of this study were to evaluate the impact of active restoration of degraded alpine grassland on: (a) soil organic matter (SOM) mineralization; and (b) the importance of biotic factors for temperature sensitivity (Q₁₀ ) of SOM mineralization. Soils were sampled from intact, degraded and restored alpine grasslands at altitudes ranging between 3,900 and 4,200 m on the Tibetan Plateau. The samples were incubated at 5, 15 and 25°C, and Q₁₀ values of SOM mineralization were determined. Structural equation modeling was used to evaluate the importance of vegetation, soil physico-chemical properties and microbial parameters for Q₁₀ regulation. The Q₁₀ of N mineralization was similar among intact, degraded and restored soils (0.84-1.24) and was higher in topsoil (1.09) than in subsoil (0.92). The best predictive factor of CO₂ -Q₁₀ for intact grassland was microbial biomass, for degraded grassland was basal microbial respiration, and for restored grassland was soil bulk density. Restoration by planting vegetation decreased the Q₁₀ of SOM mineralization as soil bulk density, the most important negative predictor, increased in restored grassland. The Q₁₀ of SOM mineralization in topsoil was 14% higher than in subsoil because of higher microbial abundance and exo-enzyme activities. The NH₄ ⁺ content was greatest in intact soil, while NO₃ ^- content was greatest in degraded soil. The SOM mineralization rate decreased with grassland degradation and increased after long-term (>10 years) restoration. In conclusion, extremely degraded grassland needs proper long-term management in active restoration projects, especially for improvement of soil nutrients in a harsh environment.

Effect of increasing precipitation and warming on microbial community in Tibetan alpine steppe

Soil microorganisms play an important role in regulating the feedback of Alpine steppe ecosystems to future climate change. However, the interaction effect of warming and increasing precipitation on soil microorganisms remains unclear, in the face of an ongoing warmer and wetter climate on the Tibetan Plateau. In this study, we investigate the multi-factorial effects on soil microbial diversity, community structure, and microbial interactions in a three-year climate change experiment established in an Alpine steppe on the Tibetan Plateau, involving warming (+2 °C), +15% increasing precipitation and +30% increasing precipitation. Compared to warming, warming plus increasing precipitation alleviated the decrease in microbial diversity, and increased the dissimilarities in microbial community structures, largely influenced by water and substrate availability. We further observed differences in moisture increased the differences in microbial diversity and dissimilarities in microbial community structures across different precipitation levels under ambient temperature. Interestingly, warming plus increasing precipitation could create more ecological niches for microbial species to coexist but may lessen the strength of microbial interactions in contrast to increasing precipitation alone. Collectively, our findings indicate that microbial responses to future climate change in Alpine steppe soils will be more complex than those under single-climate-factor conditions.

Aggregational differentiation of ureolytic microbes in an Ultisol under long-term organic and chemical fertilizations

Ureolytic microorganisms play a crucial role in soil nitrogen transformation. Soil aggregates and associated microbes are reported to modify the impact of agricultural management on soil nutrient cycling. However, the responses of ureolytic microbial communities in various soil aggregates to long-term fertilization regimes are still unclear in acid soils. In this study, we characterized the ureolytic microflora as well as urease activity in three soil aggregate fractions (2-0.25, 0.25-0.053, <0.053 mm) from an Ultisol with 26-year fertilization experiment. The results showed that long-term chemical fertilization (NPK) significantly decreased the abundance, richness and activity of ureolytic microbial community across soil aggregates (P < .05) due to strong soil acidification. While manure application (M and MNPK) could mitigate these negative impacts and markedly (P < .05) improved the abundance, α-diversity and activity of soil ureolytic microflora. Long-term fertilization regimes also drove the differentiation of ureolytic microbial compositions in soil aggregates (Adonis, F = 17.4, P = .001, R² = 33.6%), and manure application appeared to be the most important driver. This variation partly contributed to the aberrance of soil urease activity (structure equation model, path coefficient: 0.45, P = .008). No significant differences were found for ureolytic microbial community among soil aggregates, which was in accordance with the distribution patterns of soil nutrients, indicating the dominant role of resources availability in determining ureolytic microbiota in micro-environment. The ureolytic microbial community among different soil aggregates responded uniformly to long-term fertilizations. Our study revealed that manure application was a sustainable fertilization regime to alleviate the loss of soil ureolytic microbial diversity and activity in acid soils.

Potential feedback mediated by soil microbiome response to warming in a glacier forefield

Mountain glaciers are retreating at an unprecedented rate due to global warming. Glacier retreat is widely believed to be driven by the physiochemical characteristics of glacier surfaces; however, the current knowledge of such biological drivers remains limited. An estimated 130 Tg of organic carbon (OC) is stored in mountain glaciers globally. As a result of global warming, the accelerated microbial decomposition of OC may further accelerate the melting process of mountain glaciers by heat production with the release of greenhouse gases, such as carbon dioxide (CO₂ ) and methane. Here, using short-term aerobic incubation data from the forefield of Urumqi Glacier No. 1, we assessed the potential climate feedback mediated by soil microbiomes at temperatures of 5°C (control), 6.2°C (RCP 2.6), 11°C (RCP 8.5), and 15°C (extreme temperature). We observed enhanced CO₂ -C release and heat production under warming conditions, which led to an increase in near-surface (2 m) atmospheric temperatures, ranging from 0.9°C to 3.4°C. Warming significantly changed the structures of the RNA-derived (active) and DNA-derived (total) soil microbiomes, and active microbes were more sensitive to increased temperatures than total microbes. Considering the positive effects of temperature and deglaciation age on the CO₂ -C release rate, the alterations in the active microbial community structure had a negative impact on the increased CO₂ -C release rate. Our results revealed that glacial melting could potentially be significantly accelerated by heat production from increased microbial decomposition of OC. This risk might be true for other high-altitude glaciers under emerging warming, thus improving the predictions of the effects of potential feedback on global warming.

Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance

Although biotic interactions among members of microbial communities have been conceived to be crucial for community assembly, it remains unclear how changes in environmental conditions affect microbial interaction and consequently system performance. Here, we adopted a random matrix theory-based network analysis to explore microbial interactions in triplicate anaerobic digestion (AD) systems, which is widely applied for organic pollutant treatments. The digesters were operated with incremental organic loading rates (OLRs) from 1.0 g volatile solids (VS)/liter/day to 1.3 g VS/liter/day and then to 1.5 g VS/liter/day, which increased VS removal and methane production proportionally. Higher resource availability led to networks with higher connectivity and shorter harmonic geodesic distance, suggestive of more intense microbial interactions and quicker responses to environmental changes. Strikingly, a number of topological properties of microbial network showed significant (P < 0.05) correlation with AD performance (i.e., methane production, biogas production, and VS removal). When controlling for environmental parameters (e.g., total ammonia, pH, and the VS load), node connectivity, especially that of the methanogenic archaeal network, still correlated with AD performance. Last, we identified the Methanothermus, Methanobacterium, Chlorobium, and Haloarcula taxa and an unclassified Thaumarchaeota taxon as keystone nodes of the network.IMPORTANCE AD is a biological process widely used for effective waste treatment throughout the world. Biotic interactions among microbes are critical to the assembly and functioning of the microbial community, but the response of microbial interactions to environmental changes and their influence on AD performance are still poorly understood. Using well-replicated time series data of 16S rRNA gene amplicons and functional gene arrays, we constructed random matrix theory-based association networks to characterize potential microbial interactions with incremental OLRs. We demonstrated striking linkage between network topological features of methanogenic archaea and AD functioning independent of environmental parameters. As the intricate balance of multiple microbial functional groups is responsible for methane production, our results suggest that microbial interaction may be an important, previously unrecognized mechanism in determining AD performance.

Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

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.

High variations of methanogenic microorganisms drive full-scale anaerobic digestion process

Anaerobic digestion is one of the most successful waste management strategies worldwide, wherein microorganisms play an essential role in reducing organic pollutants and producing renewable energy. However, variations of microbial community in full-scale anaerobic digesters, particularly functional groups relevant to biogas production, remain elusive. Here, we examined microbial community in a year-long monthly time series of 3 full-scale anaerobic digesters. We observed substantial diversification in community composition, with only a few abundant OTUs (e.g. Clostridiales, Anaerolineaceae and Methanosaeta) persistently present across different samples. Similarly, there were high variations in relative abundance of methanogenic archaea and methanogenic genes, which were positively correlated (r² = 0.530, P < 0.001). Variations of methanogens explained 55.7% of biogas producing rates, much higher than the explanatory percentage of environmental parameters (16.4%). Hydrogenotrophic methanogens, especially abundant Methanomicrobiales taxa, were correlated with biogas production performance (r = 0.665, P < 0.001) and nearly all methanogenic genes (0.430 < r < 0.735, P < 0.012). Given that methanogenic archaea or genes are well established for methanogenesis, we conclude that high variations in methanogenic traits (e.g. taxa or genes) are responsible for biogas production variations in full-scale anaerobic digesters.

Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils

With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N₂ fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.

Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N₂ fixation is the major source of biologically available N, the soil N₂-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.

Short-Term Response of the Soil Microbial Abundances and Enzyme Activities to Experimental Warming in a Boreal Peatland in Northeast China

Global warming is likely to influence the soil microorganisms and enzyme activity and alter the carbon and nitrogen balance of peatland ecosystems. To investigate the difference in sensitivities of carbon and nitrogen cycling microorganisms and enzyme activity to warming, we conducted three-year warming experiments in a boreal peatland. Our findings demonstrated that both mcrA and nirS gene abundance in shallow soil and deep soil exhibited insensitivity to warming, while shallow soil archaea 16S rRNA gene and amoA gene abundance in both shallow soil and deep soil increased under warming. Soil pmoA gene abundance of both layers, bacterial 16S rRNA gene abundance in shallow soil, and nirK gene abundance in deep soil decreased due to warming. The decreases of these gene abundances would be a result of losing labile substrates because of the competitive interactions between aboveground plants and underground soil microorganisms. Experimental warming inhibited β-glucosidase activity in two soil layers and invertase activity in deep soil, while it stimulated acid phosphatase activity in shallow soil. Both temperature and labile substrates regulate the responses of soil microbial abundances and enzyme activities to warming and affect the coupling relationships of carbon and nitrogen. This study provides a potential microbial mechanism controlling carbon and nitrogen cycling in peatland under climate warming.

Soil organic carbon and total nitrogen stocks in alpine ecosystems of Altun Mountain National Nature Reserve in dry China

The Altun Mountain National Nature Reserve (AMNNR), characterized by complex topography, is located on the northern edge of the Qinghai-Tibetan Plateau. The stocks of soil organic carbon (SOC) and total nitrogen (TN) are critically important for carbon and nitrogen sequestration in dry alpine ecosystems of the AMNNR, which is a "natural laboratory" for assessing the carbon and nitrogen storage without human disturbance. We explored the stocks of SOC and TN in soils of different dry alpine ecosystems by sampling 23 sites across the AMNNR during 2013. The results showed that the SOC and TN stocks of AMNNR varied significantly with ecosystem types. The SOC stocks of 0-15 cm were highest in the alpine wet meadow (7.96 kg/m²), followed by alpine steppe (2.63 kg/m²). The stocks of SOC and TN in 0-5 and 5-10 cm soils of alpine wet meadow were significantly (P < 0.05) higher than those in the soils of other dry alpine ecosystems. In the whole AMNNR, total storage of SOC and TN were approximately 80.97 and 4.48 Tg, 34.25% of SOC and 24.01% of TN were stored in the alpine steppe, 21.51% of SOC and 26.01% of TN were stored in the alpine scrub, the largest ecosystem in the AMNNR. Our findings suggested it is important to protect the soil and vegetation of the dry alpine ecosystems, particularly the alpine wet meadow and alpine scrub to promote the carbon storage.

Elevated CO2 and Warming Altered Grassland Microbial Communities in Soil Top-Layers

As two central issues of global climate change, the continuous increase of both atmospheric CO₂ concentrations and global temperature has profound effects on various terrestrial ecosystems. Microbial communities play pivotal roles in these ecosystems by responding to environmental changes through regulation of soil biogeochemical processes. However, little is known about the effect of elevated CO₂ (eCO₂) and global warming on soil microbial communities, especially in semiarid zones. We used a functional gene array (GeoChip 3.0) to measure the functional gene composition, structure, and metabolic potential of soil microbial communities under warming, eCO₂, and eCO₂ + warming conditions in a semiarid grassland. The results showed that the composition and structure of microbial communities was dramatically altered by multiple climate factors, including elevated CO₂ and increased temperature. Key functional genes, those involved in carbon (C) degradation and fixation, methane metabolism, nitrogen (N) fixation, denitrification and N mineralization, were all stimulated under eCO₂, while those genes involved in denitrification and ammonification were inhibited under warming alone. The interaction effects of eCO₂ and warming on soil functional processes were similar to eCO₂ alone, whereas some genes involved in recalcitrant C degradation showed no significant changes. In addition, canonical correspondence analysis and Mantel test results suggested that NO₃-N and moisture significantly correlated with variations in microbial functional genes. Overall, this study revealed the possible feedback of soil microbial communities to multiple climate change factors by the suppression of N cycling under warming, and enhancement of C and N cycling processes under either eCO₂ alone or in interaction with warming. These findings may enhance our understanding of semiarid grassland ecosystem responses to integrated factors of global climate change.

Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stability

Eutrophication and climate warming, induced by anthropogenic activities, are simultaneously occurring worldwide and jointly affecting soil carbon stability. Therefore, it is of great interest to examine whether and how they interactively affect soil microbial community, a major soil carbon driver. Here, we showed that climate warming, simulated by southward transferring Mollisol soil in agricultural ecosystems from the cold temperate climate zone (N) to warm temperate climate (C) and subtropical climate zone (S), decreased soil organic matter (SOM) by 6%-12%. In contrast, amendment with nitrogen, phosphorus and potassium enhanced plant biomass by 97% and SOM by 6% at the N site, thus stimulating copiotrophic taxa but reducing oligotrophic taxa in relative abundance. However, microbial responses to nutrient amendment were overridden by soil transfer in that nutrient amendment had little effect at the C site but increased recalcitrant carbon-degrading fungal Agaricomycetes and Microbotryomycetes taxa derived from Basidiomycota by 4-17 folds and recalcitrant carbon-degrading genes by 23%-40% at the S site, implying a possible priming effect. Consequently, SOM at the S site was not increased by nutrient amendment despite increased plant biomass by 108%. Collectively, we demonstrate that soil transfer to warmer regions overrides microbial responses to nutrient amendment and weakens soil carbon sequestration.

Microbial functional gene patterns related to soil greenhouse gas emissions in oil contaminated areas

Linking microbial community structure to physiology and ecological processes is a critical focus of microbial ecology. To understand the microbial functional gene patterns related to soil greenhouse gas [carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O)] emissions under oil contamination, we used functional gene array (GeoChip 5.0) analysis and network methods to investigate the feedback responses of soil microbial functional gene patterns and identify keystone genes in Shengli Oilfield, China. The microbial functional gene number, relative abundance and diversity involved in carbon degradation and nitrogen cycling decreased consistently with the reduced CO₂ and N₂O flux in oil contaminated soils, whereas the gene number and relative abundance of methane-production related genes increased with contamination. Functional molecular ecological networks were built based on random matrix theory, where network structures and properties showed significantly variation between oil contaminated and uncontaminated soils (P<0.05). Network nodes, connectivity and complexity all reduced under oil contamination. The sensitive and the highest connective genes in the network were identified as keystone genes, based on Mann-Whitney U tests and network analysis. Our findings improved the understanding of the microbe-mediated mechanisms affecting soil greenhouse gas emissions.

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010-2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices.

No significant changes in topsoil carbon in the grasslands of northern China between the 1980s and 2000s

The grasslands of northern China store a large amount of soil organic carbon (SOC), and the small changes in SOC stock could significantly affect the regional C cycle. However, recent estimates of SOC changes in this region are highly controversial. In this study, we examined the changes in the SOC density (SOCD) in the upper 30cm of the grasslands of northern China between the 1980s and 2000s, using an improved approach that integrates field-based measurements into machine learning algorithms (artificial neural network (ANN) and random forest (RF)). The RF-generated SOCD averaged 5.55kgCm^-2 in the 1980s and 5.53kgCm^-2 in the 2000s, and the change ranged from -0.17 to 0.22kgCm^-2 at the 95% confidence level, suggesting that the overall SOCD did not vary significantly during the study period. However, the change in SOCD exhibited large regional variability; the topsoil of the Inner Mongolian grasslands experienced significant C loss (4.86 vs. 4.33kgCm^-2), while that of the Xinjiang grasslands exhibited an accumulation of C (5.55 vs. 6.46kgCm^-2). Furthermore, the topsoil C in the Tibetan alpine grasslands remained relatively stable (6.12 vs. 6.06kgCm^-2). A comparison of the different grassland types indicated that SOCD significantly decreased in typical steppe, whereas it increased in mountain meadow, and remained stable in the other grasslands (alpine meadow, alpine steppe, mountain steppe and desert steppe). Climate change could partly explain the changes in the SOCD of the different grassland types. Increases in precipitation could lead to SOC accumulation in temperate grasslands and SOC loss in alpine grasslands, while climate warming is likely to cause SOC loss in temperate grasslands. Overall, our study suggests that the grasslands of northern China remained a neutral SOC sink between the 1980s and 2000s.

Evaluating the microbial ecology and metabolite profile in Kazak artisanal cheeses from Xinjiang, China

Kazak artisanal cheese is one of the famous fermented food in Uighur Autonomy Region of Xinjiang, China. However, the microbial ecology in Kazak artisanal cheeses across different regions is unclear. In this study, we determined the microbial community composition through amplicon sequencing and measured the flavor profile of 10 cheese samples from different regions of Xinjiang. The associations between microbial communities, flavors and environmental factors were examined by redundancy analysis and Monte Carlo permutation test. Cheeses from different regions had different microbial communities, which was mainly reflected in the relative abundance of Lactobacillus, Streptococcus, Issatchenkia, Debaryomyces and Kluyveromyces. In addition, Pichia and Torulaspora were also the key microbial groups, according to the high relative abundance and large co-occurrence incidence in the correlation network. Using the microbe-metabolites correlation analysis, the major flavor-producing taxa were identified as Kluyveromyces, Anoxybacillus, Torulaspora, Lactobacillus, Streptococcus and Dipodascus. Environmental factors accounted for the majority of the microbial community variations, 88.54% for bacteria and 75.71% for fungi. Compared to physico-chemical factors (temperature, moisture, and pH), geographical factors (longitude, latitude and elevation) had a stronger effect on microbial communities in cheese samples from different regions of Xinjiang.

Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau

Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0.079 to 0.89) of the Plateau, to assess how changes in aridity affect the abundance, community composition, and diversity of bacteria, ammonia-oxidizers, and denitrifers (nirK/S and nosZ genes-containing communities) as well as nitrogen (N) turnover enzyme activities. We found V-shaped or inverted V-shaped relationships between the aridity index (AI) and soil microbial parameters (gene abundance, community structures, microbial diversity, and N turnover enzyme activities) with a threshold at AI = 0.27. The increasing or decreasing rates of the microbial parameters were higher in areas with AI < 0.27 (alpine steppes) than in mesic areas with 0.27 < AI < 0.89 (alpine meadow and swamp meadow). The results indicated that the projected warming and wetting have a strong impact on soil microbial communities in the alpine steppes.

Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment

Microbial decomposition of soil organic carbon (SOC) in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III) reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05) associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol), methane and CO₂ production, and Fe(III) reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO₂) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.

Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space

BACKGROUND

Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage-host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells.

RESULTS

Equipped with high-throughput, cutting-edge environmental genomics techniques, we examined phage and prokaryotic community composition of four anaerobic digesters in full-scale wastewater treatment plants across China. Despite the relatively stable process performance in biogas production, phage and prokaryotic groups fluctuated monthly over a year of study period, showing significant correlations between those two groups at the α- and β-diversity levels. Strikingly, phages explained 40.6% of total variations of the prokaryotic community composition, much higher than the explanatory power by abiotic factors (14.5%). Consequently, phages were significantly (P < 0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed phage-prokaryote pairs were shallowly conserved since they were detected only within small viral clades.

CONCLUSIONS

Those results collectively demonstrate phages as a major biotic factor in controlling prokaryotic composition and process performance. Therefore, phages may play a larger role in shaping prokaryotic community dynamics and process performance of anaerobic digesters than currently appreciated.

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling

As climate cooling is increasingly regarded as important natural variability of long-term global warming trends, there is a resurging interest in understanding its impact on biodiversity and ecosystem functioning. Here, we report a soil transplant experiment from lower to higher elevations in a Tibetan alpine grassland to simulate the impact of cooling on ecosystem community structure and function. Three years of cooling resulted in reduced plant productivity and microbial functional potential (for example, carbon respiration and nutrient cycling). Microbial genetic markers associated with chemically recalcitrant carbon decomposition remained unchanged despite a decrease in genes associated with chemically labile carbon decomposition. As a consequence, cooling-associated changes correlated with a decrease in soil organic carbon (SOC). Extrapolation of these results suggests that for every 1 °C decrease in annual average air temperature, 0.1 Pg (0.3%) of SOC would be lost from the Tibetan plateau. These results demonstrate that microbial feedbacks to cooling have the potential to differentially impact chemically labile and recalcitrant carbon turnover, which could lead to strong, adverse consequences on soil C storage. Our findings are alarming, considering the frequency of short-term cooling and its scale to disrupt ecosystems and biogeochemical cycling.

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.

Variations of Soil Microbial Community Structures Beneath Broadleaved Forest Trees in Temperate and Subtropical Climate Zones

Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRI (Net Relatedness Index) values increased from -0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomy-based association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-for-time substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.

Molecular mechanisms of water table lowering and nitrogen deposition in affecting greenhouse gas emissions from a Tibetan alpine wetland

Rapid climate change and intensified human activities have resulted in water table lowering (WTL) and enhanced nitrogen (N) deposition in Tibetan alpine wetlands. These changes may alter the magnitude and direction of greenhouse gas (GHG) emissions, affecting the climate impact of these fragile ecosystems. We conducted a mesocosm experiment combined with a metagenomics approach (GeoChip 5.0) to elucidate the effects of WTL (-20 cm relative to control) and N deposition (30 kg N ha^-1  yr^-1 ) on carbon dioxide (CO₂ ), methane (CH₄ ) and nitrous oxide (N₂ O) fluxes as well as the underlying mechanisms. Our results showed that WTL reduced CH₄ emissions by 57.4% averaged over three growing seasons compared with no-WTL plots, but had no significant effect on net CO₂ uptake or N₂ O flux. N deposition increased net CO₂ uptake by 25.2% in comparison with no-N deposition plots and turned the mesocosms from N₂ O sinks to N₂ O sources, but had little influence on CH₄ emissions. The interactions between WTL and N deposition were not detected in all GHG emissions. As a result, WTL and N deposition both reduced the global warming potential (GWP) of growing season GHG budgets on a 100-year time horizon, but via different mechanisms. WTL reduced GWP from 337.3 to -480.1 g CO₂ -eq m^-2 mostly because of decreased CH₄ emissions, while N deposition reduced GWP from 21.0 to -163.8 g CO₂ -eq m^-2 , mainly owing to increased net CO₂ uptake. GeoChip analysis revealed that decreased CH₄ production potential, rather than increased CH₄ oxidation potential, may lead to the reduction in net CH₄ emissions, and decreased nitrification potential and increased denitrification potential affected N₂ O fluxes under WTL conditions. Our study highlights the importance of microbial mechanisms in regulating ecosystem-scale GHG responses to environmental changes.

Tillage practices and straw-returning methods affect topsoil bacterial community and organic C under a rice-wheat cropping system in central China

The objective of this study was to investigate how the relationships between bacterial communities and organic C (SOC) in topsoil (0–5 cm) are affected by tillage practices [conventional intensive tillage (CT) or no-tillage (NT)] and straw-returning methods [crop straw returning (S) or removal (NS)] under a rice-wheat rotation in central China. Soil bacterial communities were determined by high-throughput sequencing technology. After two cycles of annual rice-wheat rotation, compared with CT treatments, NT treatments generally had significantly more bacterial genera and monounsaturated fatty acids/saturated fatty acids (MUFA/STFA), but a decreased gram-positive bacteria/gram-negative bacteria ratio (G⁺/G⁻). S treatments had significantly more bacterial genera and MUFA/STFA, but had decreased G⁺/G⁻ compared with NS treatments. Multivariate analysis revealed that Gemmatimonas, Rudaea, Spingomonas, Pseudomonas, Dyella, Burkholderia, Clostridium, Pseudolabrys, Arcicella and Bacillus were correlated with SOC, and cellulolytic bacteria (Burkholderia, Pseudomonas, Clostridium, Rudaea and Bacillus) and Gemmationas explained 55.3% and 12.4% of the variance in SOC, respectively. Structural equation modeling further indicated that tillage and residue managements affected SOC directly and indirectly through these cellulolytic bacteria and Gemmationas. Our results suggest that Burkholderia, Pseudomonas, Clostridium, Rudaea, Bacillus and Gemmationas help to regulate SOC sequestration in topsoil under tillage and residue systems.

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO₂ efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Author Video: An author video summary of this article is available.

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau

Soil microbial communities are influenced by climate change drivers such as warming and altered precipitation. These changes create abiotic stresses, including desiccation and nutrient limitation, which act on microbes. However, our understanding of the responses of microbial communities to co-occurring climate change drivers is limited. We surveyed soil bacterial and fungal diversity and composition after a 1-year warming and altered precipitation manipulation in the Tibetan plateau alpine grassland. In isolation, warming and decreased precipitation treatments each had no significant effects on soil bacterial community structure; however, in combination of both treatments altered bacterial community structure (p = 0.03). The main effect of altered precipitation specifically impacted the relative abundances of Bacteroidetes and Gammaproteobacteria compared to the control, while the main effect of warming impacted the relative abundance of Betaproteobacteria. In contrast, the fungal community had no significant response to the treatments after 1-year. Using structural equation modeling (SEM), we found bacterial community composition was positively related to soil moisture. Our results indicate that short-term climate change could cause changes in soil bacterial community through taxonomic shifts. Our work provides new insights into immediate soil microbial responses to short-term stressors acting on an ecosystem that is particularly sensitive to global climate change.

Stronger warming effects on microbial abundances in colder regions

Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra, and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our findings therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions.

Microbial responses to southward and northward Cambisol soil transplant

Soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse‐scale taxonomic diversity at both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO₃¯‐N) showed strong correlations with microbial communities. In addition, abundances of ammonium‐oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO₃¯‐N contents, suggesting that microbial responses to soil transplant could alter microbe‐mediated biogeochemical cycle at the ecosystem level.