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

Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake

Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.

Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities

Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.

Microbial necromass and glycoproteins for determining soil carbon formation under arbuscular mycorrhiza symbiosis

Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and critically modulate soil organic carbon (C) dynamics. Whether AMF promote soil C storage and stability is, however, largely unknown. Since microbial necromass C (MNC) and glomalin-related soil protein (GRSP) are stable microbial-derived C in soils, we therefore evaluated how AMF symbiosis alters both soil C pools and their contributions to soil organic C (SOC) under nitrogen fertilization, based on a 16-weeks mesocosm experiment using a mutant tomato with highly reduced AMF symbiosis. Results showed that SOC content is 4.5 % higher following AMF symbiosis. Additionally, the content of MNC and total GRSP were 47.5 % and 22.3 % higher under AMF symbiosis than at AMF absence, respectively. The accumulations of GRSP and microbial necromass in soil were closely associated with mineral-associated organic C and the abundance of AMF. The increased soil living microbial biomass under AMF symbiosis was mainly derived from AMF biomass, and fungal necromass C significantly contributed to SOC accumulation, as evidenced by the higher fungal:bacterial necromass C ratio under AMF symbiosis. On the contrary, bacterial necromass was degraded to compensate for the increased microbial nutrient demand because of the aggravated nutrient limitation under AMF symbiosis, leading to a decrease in bacterial necromass. Redundancy analysis showing that bacterial necromass was negatively correlated with soil C:N ratio supported this argument. Moreover, the relative change rate of total GRSP was consistently greater in nitrogen-limited soil than that of microbial necromass. Our findings suggested GRSP accumulates faster and contributes more to SOC pools under AMF symbiosis than microbial necromass. The positive correlation between the contributions of GRSP and MNC to SOC further provided valuable information in terms of enhancing our understanding of mechanisms underlying the maintenance of SOC stocks through microbial-derived C.

Vertical fungal community distribution patterns along a stratified soil profile in subalpine Larix principis-rupprechtii plantations on China's Luya mountain

Soil microorganisms play important roles in the biogeochemical cycling of terrestrial ecosystems. Recent studies found that soil fungal composition and diversity varied significantly with soil depth. However, little is known about the vertical distribution patterns of soil fungal communities and their associated drivers. For this study, we collected soil samples from six soil layers (i.e., litter layer (P), humus layer (P0), 0-10 cm layer (P1), 10-20 cm layer (P2), 20-40 cm layer (P3), and 40-80 cm layer (P4)) within Larix principis-rupprechtii plantations to investigate fungal community composition, diversity, and associated drivers using Illumina MiSeq high-throughput sequencing. Results showed that the top 10 dominant genera with the highest relative abundance belonged to Ascomycota, Basidiomycota, and Mortierellomycota. A decreasing α-diversity trend was observed along with soil depth. Moreover, correlation analysis showed that ammonia nitrogen (NH4+-N), pH, total carbon (TC), and total nitrogen (TN) content markedly correlated with fungal α-diversity. Significant β-diversity differences were found in soil fungal communities. Additionally, TN and total phosphorus (TP) content were the main environmental drivers that influenced the spatial distribution pattern of fungal communities. The βNTI showed a gradual increase with soil depth. In the surface layers of soil, the dominant factor of fungal community assembly was homogeneous selection, while in the deep layers of soil, it was variable selection. Co-occurrence network analysis showed that fungal community interactions in the deepest soil layer (40-80 cm) were more complex and were more positive. Results from this study provide a theoretical basis and data support to understand the mechanisms of soil fungal community assembly processes more deeply in L. principis-rupprechtii plantations.

Bacterial necromass as the main source of organic matter in saline soils

Soil salinity poses a major threat to crop growth, microbial activity, and organic matter accumulation in agroecosystems in arid and semiarid regions. The limitations of carbon (C) accrual due to salinity can be partly mitigated by the application of organic fertilizers. Although microorganisms are crucial for soil organic carbon (SOC) stabilization, the relationships between living and dead microbial C pools and the community features of SOC accrual in saline soils are not known. A two-year field experiment was conducted to examine the effects of organic fertilizers on the microbial regulatory mechanisms of C sequestration in saline soil (chloride-sulfate salinity). Compared to manure addition alone, manure plus commercial humic acid increased SOC stock by 11% and decreased CO2 emissions by 10%, consequently facilitated soil C sequestration. We explain these results by greater bacterial necromass formation due to the dominance of r-strategists with faster turnover rate (growth and death), as well as larger necromass stability as supported by the increased aggregate stability under the addition of humic acids with manure. Humic acids increased the abundance of bacterial phylum Proteobacteria (copiotrophs) and decreased Acidobacteria (oligotrophs) compared with straw, indicating that r-strategists outcompeted K-strategists, leading to bacterial necromass accumulation. With larger C/N ratio (88), straw increased leucine aminopeptidase to mine N-rich substrates (i.e., from necromass and soil organic matter) and consequently reduced SOC stock by 8%. The decreased salinity and increased organic C availability under straw with manure addition also led to a 13% higher CO2 flux compared with manure application alone. Thus, humic acids added with manure benefited to SOC accumulation by raising bacterial necromass C and reducing CO2 emissions.

Asymmetric winter warming reduces microbial carbon use efficiency and growth more than symmetric year-round warming in alpine soils

Asymmetric seasonal warming trends are evident across terrestrial ecosystems, with winter temperatures rising more than summer ones. Yet, the impact of such asymmetric seasonal warming on soil microbial carbon metabolism and growth remains poorly understood. Using 18O isotope labeling, we examined the effects of a decade-long experimental seasonal warming on microbial carbon use efficiency (CUE) and growth in alpine grassland ecosystems. Moreover, the quantitative stable isotope probing with 18O-H2O was employed to evaluate taxon-specific bacterial growth in these ecosystems. Results show that symmetric year-round warming decreased microbial growth rate by 31% and CUE by 22%. Asymmetric winter warming resulted in a further decrease in microbial growth rate of 27% and microbial CUE of 59% compared to symmetric year-round warming. Long-term warming increased microbial carbon limitations, especially under asymmetric winter warming. Long-term warming suppressed the growth rates of most bacterial genera, with asymmetric winter warming having a stronger inhibition on the growth rates of specific genera (e.g., Gp10, Actinomarinicola, Bosea, Acidibacter, and Gemmata) compared to symmetric year-round warming. Bacterial growth was phylogenetically conserved, but this conservation diminished under warming conditions, primarily due to shifts in bacterial physiological states rather than the number of bacterial species and community composition. Overall, long-term warming escalated microbial carbon limitations, decreased microbial growth and CUE, with asymmetric winter warming having a more pronounced effect. Understanding these impacts is crucial for predicting soil carbon cycling as global warming progresses.

Direct Evidence for Microbial Regulation of the Temperature Sensitivity of Soil Carbon Decomposition

Soil physicochemical protection, substrates, and microorganisms are thought to modulate the temperature sensitivity of soil carbon decomposition (Q10), but their regulatory roles have yet to be distinguished because of the confounding effects of concurrent changes of them. Here, we sought to differentiate these effects through microorganism reciprocal transplant and aggregate disruption experiments using soils collected from seven sites along a 5000-km latitudinal transect encompassing a wide range of climatic conditions and from a 4-year laboratory incubation experiment. We found direct microbial regulation of Q10, with a higher Q10 being associated with greater fungal:bacterial ratios. However, no significant direct effects of physicochemical protection and substrate were observed on the variation in Q10 along the latitudinal transect or among different incubation time points. These findings highlight that we should move forward from physicochemical protection and substrate to microbial mechanisms regulating soil carbon decomposition temperature sensitivity to understand and better predict soil carbon-climate feedback.

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

IMPORTANCE

As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Biogeographic and co-occurrence network differentiation of fungal communities in warm-temperate montane soils

Studying the biogeographic patterns of fungal communities across altitudinal and soil depth gradients is essential for understanding how environmental variations shape the diversity and functionality of these complex ecological assemblages. Here, we evaluated the response and assembly patterns of fungal communities to altitude and soil depth, and the co-occurrence patterns influencing soil fungal metabolic preferences on Dongling Mountain. We observed significant variations in fungal β-diversity, driven by elevation and soil depth, with climatic parameters (MAT and MAP) and nutrient concentrations (TOC, TP, and TN) serving as prominent influencers. Additionally, we found that the multiple substrate-induced respiration rate of fungi degrading various carbon substrates was diminished in high-altitude and subsurface soils compared to low-altitude and surface soils. Stochastic processes play a more important role in controlling fungal community assembly than deterministic processes, with dispersal limitation emerging as the main driver of community assembly. While greater network complexity was evident in the topsoil compared to the subsoil, both layers harbored altitude-sensitive OTUs (asOTUs) that belonging to distinct modules. Moreover, fungal groups sensitive to the same altitude exhibited similar metabolic preferences. The asOTUs designated for lower altitude areas favored unstable carbon substrates (glucose and sucrose), while those designated as higher altitude areas exhibited a preference for recalcitrant carbon (xylan and lignin). This evidence suggests that soil fungal communities respond to environmental changes by trading off their life strategies and metabolic characteristics.

Excessive climate warming exacerbates nitrogen limitation on microbial metabolism in an alpine meadow of the Tibetan Plateau: Evidence from soil ecoenzymatic stoichiometry

Soil ecoenzymatic stoichiometry reflects the dynamic equilibrium between microorganism's nutrient requirements and resource availability. However, uncertainties persist regarding the key determinants of nutrient restriction in relation to microbial metabolism under varying degrees of warming. Our long-term and multi-level warming field experiment (control treatment, +0.42 °C, +1.50 °C, +2.55 °C) in a typical alpine meadow unveiled a decline in carbon (C)- and nitrogen (N)-acquired enzymes with escalating warming magnitudes, while phosphorus (P)-acquired enzymes displayed an opposite trend. Employing enzymatic stoichiometry modeling, we assessed the nutrient limitations of microbial metabolic activity and found that C and N co-limited microbial metabolic activities in the alpine meadow. Remarkably, high-level warming (+2.55 °C) exacerbated microbe N limitation, but alleviate C limitations. The structural equation modeling further indicated that alterations in soil extracellular enzyme characteristics (SES) were more effectively elucidated by microbial characteristics (microbial biomass C, N, P, and their ratios) rather than by soil nutrients (total nutrient contents and their ratios). However, the microbial control over SES diminished with higher levels of warming magnitude. Overall, our results provided novel evidence that the factors driving microbe metabolic limitation may vary with the degree of warming in Tibet alpine grasslands. Changes in nutrient demand for microorganism's metabolism in response to warming should be considered to improve nutrient management in adapting to different future warming scenarios.

Vegetation restoration in an alpine meadow: Insights from soil microbial communities and resource limitation across soil depth

Aboveground vegetation restoration shapes the soil microbial community structure and affects microbial resource acquisition. However, the changes in soil microbial resource limitation in subsoil during vegetation restoration are still unclear. In this study, the microbial community structure and resource limitation in an alpine meadow soil profile that had undergone natural restoration for short-term (4-year) and long-term (10-year) restoration in response to vegetation restoration were explored through high-throughput sequencing analysis and extracellular enzyme stoichiometry (EES). There was no significant difference in microbial composition and α diversity between short- and long-term restoration soils. Soil microorganisms in this alpine meadow were mainly limited by phosphorus. Carbon limitation of soil microorganisms was significantly decreased in each layer (0-15, 15-30, 30-45, 45-60, and 60-80 cm corresponding to L1, L2, L3, L4, and L5, respectively) of long-term restoration soils when compared to that of the short-term restoration soil layers, while phosphorus limitation of microorganisms in subsoil (60-80 cm) was significantly increased by 17.38%. Soil nutrients, pH, moisture content, and microbial composition are the main drivers of microbial resource limitation in restoration, and their effects on microbial resource limitation were different in short- and long-term restoration. Meanwhile, key microbial taxa have a significant impact on microbial resource limitation, especially in short-term restoration soils. This study suggested that vegetation restoration significantly affected soil microbial resource limitation, and could alleviate microbial resource limitations by adding nutrients, thus accelerating the process of vegetation restoration in alpine ecosystems.

Conservation tillage facilitates the accumulation of soil organic carbon fractions by affecting the microbial community in an eolian sandy soil

Conservation tillage (CT) is an important agronomic measure that facilitates soil organic carbon (SOC) accumulation by reducing soil disturbance and plant residue mulching, thus increasing crop yields, improving soil fertility and achieving C neutrality. However, our understanding of the microbial mechanism underlying SOC fraction accumulation under different tillage practices is still lacking. Here, a 6-year in situ field experiment was carried out to explore the effects of CT and traditional tillage (CK) practices on SOC fractions in an eolian sandy soil. Compared with CK, CT increased the particulate OC (POC) content in the 0-30 cm soil layer and the mineral-associated OC (MAOC) content in the 0-20 cm soil layer. Moreover, tillage type and soil depth had significant influences on the bacterial, fungal and protistan community compositions and structures. The co-occurrence network was divided into 4 ecological modules, and module 1 exhibited significant correlations with the POC and MOC contents. After determining their topological roles, we identified the keystone taxa in the network. The results indicated that the most common bacterial taxa may result in SOC loss due to low C use efficiency, while specific fungal (Cephalotrichum) and protistan (Cercozoa) species could facilitate SOC fraction accumulation by promoting macroaggregate formation and predation. Therefore, the increase in keystone fungi and protists, as well as the reduction in bacteria, drove module 1 community function, which in turn promoted SOC sequestration under CT. These results strengthen our understanding of microbial functions in the accrual of SOC fractions, which contributes to the development of conservation agriculture on the Northeast China Plain.

Long-term conservation tillage enhances microbial carbon use efficiency by altering multitrophic interactions in soil

Microbial carbon (C) use efficiency (CUE) plays a key role in soil C storage. The predation of protists on bacteria and fungi has potential impacts on the global C cycle. However, under conservation tillage conditions, the effects of multitrophic interactions on soil microbial CUE are still unclear. Here, we investigate the multitrophic network (especially the keystone ecological cluster) and its regulation of soil microbial CUE and soil organic C (SOC) under different long-term (15-year) tillage practices. We found that conservation tillage (CT) significantly enhanced microbial CUE, turnover, and SOC (P < 0.05) compared to traditional tillage (control, CK). At the same time, tillage practice and soil depth had significant effects on the structure of fungal and protistan communities. Furthermore, the soil biodiversity of the keystone cluster was positively correlated with the microbial physiological traits (CUE, microbial growth rate (MGR), microbial respiration rate (Rs), microbial turnover) and SOC (P < 0.05). Protistan richness played the strongest role in directly shaping the keystone cluster. Compared with CK, CT generally enhanced the correlation between microbial communities and microbial physiological characteristics and SOC. Overall, our results illustrate that the top-down control (the organisms at higher trophic levels affect the organisms at lower trophic levels) of protists in the soil micro-food web plays an important role in improving microbial CUE under conservation tillage. Our findings provide a theoretical basis for promoting the application of protists in targeted microbial engineering and contribute to the promotion of conservation agriculture and the improvement of soil C sequestration potential.

Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China

Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain. Our results showed significant altitudinal distribution patterns concerning bacterial diversity and structure in the surface soil. The bacterial diversity exhibited a consistent decrease, while specific taxa demonstrated unique patterns along the altitudinal gradient. However, no altitudinal dependence was observed for bacterial diversity and community structure in the subsurface soil. Additionally, a shift in bacterial ecological groups is evident with changing soil depth. Copiotrophic taxa thrive in surface soils characterized by higher carbon and nutrient content, while oligotrophic taxa dominate in subsurface soils with more limited resources. Bacterial community characteristics exhibited strong correlations with soil organic carbon in both soil layers, followed by pH in the surface soil and soil moisture in the subsurface soil. With increasing depth, there is an observable increase in taxa-taxa interaction complexity and network structure within bacterial communities. The surface soil exhibits greater sensitivity to environmental perturbations, leading to increased modularity and an abundance of positive relationships in its community networks compared to the subsurface soil. Furthermore, the bacterial community at different depths was influenced by combining deterministic and stochastic processes, with stochasticity (homogenizing dispersal and undominated) decreasing and determinism (heterogeneous selection) increasing with soil depth.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.

Microbial responses to long-term warming differ across soil microenvironments

Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.

Oligotrophic microbes are recruited to resist multiple global change factors in agricultural subsoils

An increasing number of anthropogenic pressures can have negative effects on biodiversity and ecosystem functioning. However, our understanding of how soil microbial communities and functions in response to multiple global change factors (GCFs) is still incomplete, particularly in less frequently disturbed subsoils. In this study, we examined the impact of different levels of GCFs (0-9) on soil functions and bacterial communities in both topsoils (0-20 cm) and subsoils (20-40 cm) of an agricultural ecosystem, and characterized the intrinsic factors influencing community resistance based on microbial life history strategy. Our experimental results showed a decline in soil multifunctionality, bacterial diversity, and community resistance as the number of GCFs increased, with a more drastic reduction in community resistance of subsoils. Specifically, we observed a significantly positive relationship between the oligotroph/copiotroph ratio and community resistance in subsoils, which was also verified by the negative correlation between 16S rRNA operon (rrn) copy number and community resistance. Structural equation modeling further revealed the direct effects of community resistance in promoting the ecosystem functioning, regardless of top- and subsoils. Therefore, these results suggested that subsoils may recruit more oligotrophic microbes to enhance their originally weaker community resistance under multiple GCFs, which was essential for maintaining sustainable agroecological functions and services. Overall, our study represents a significant advance in linking microbial life history strategy to the resistance of belowground microbial community and functionality.

Climate Warming-Driven Changes in the Molecular Composition of Soil Dissolved Organic Matter Across Depth: A Case Study on the Tibetan Plateau

Dissolved organic matter (DOM) is critical for soil carbon sequestration in terrestrial ecosystems. DOM molecular composition varies with soil depth. However, the spatial heterogeneity of depth-dependent DOM in response to climate warming remains unclear, especially in alpine ecosystems. In this study, the DOM of alpine meadow soil samples was characterized comprehensively by using spectroscopy and mass spectrometry, and open-top chambers (OTCs) were employed to simulate warming. It was found that climate warming had the greatest impact on the upper layer (0-30 cm), followed by the lower layer (60-80 cm), while the middle layer (30-60 cm) was the most stable among the three soil layers. The reasons for the obvious changes in DOM in the upper and lower layers of soil were further explained based on biotic and abiotic factors. Specifically, soil nutrients (NH4+-N, NO3--N, TC, and TP) affected the molecular composition of DOM in layer L1 (0-15 cm), while pH affected layer L5 (60-80 cm). Gemmatimonadetes, Proteobacteria, and Actinobacteria played important roles in the composition of DOM in the L5 layer (60-80 cm), while the dominant fungal groups affecting the DOM composition increased in the L1 layer (0-15 cm) under warming. In summary, this research has contributed to a deeper understanding of depth-dependent changes in DOM molecular composition in alpine ecosystems.

Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China

To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.

Whole-soil-profile warming does not change microbial carbon use efficiency in surface and deep soils

The paucity of investigations of carbon (C) dynamics through the soil profile with warming makes it challenging to evaluate the terrestrial C feedback to climate change. Soil microbes are important engines driving terrestrial biogeochemical cycles; their carbon use efficiency (CUE), defined as the proportion of metabolized organic C allocated to microbial biomass, is a key regulator controlling the fate of soil C. It has been theorized that microbial CUE should decline with warming; however, empirical evidence for this response is scarce, and data from deeper soils are particularly scarce. Here, based on soil samples from a whole-soil-profile warming experiment (0 to 1 m, +4 °C) and 18O tracing approach, we examined the vertical variation of microbial CUE and its response to ~3.3-y experimental warming in an alpine grassland on the Qinghai-Tibetan Plateau. Microbial CUE decreased with soil depth, a trend that was primarily controlled by soil C availability. However, warming had limited effects on microbial CUE regardless of soil depth. Similarly, warming had no significant effect on soil C availability, as characterized by extractable organic C, enzyme-based lignocellulose index, and lignin phenol-based ratios of vanillyls, syringyls, and cinnamyls. Collectively, our work suggests that short-term warming does not alter microbial CUE in either surface or deep soils, and emphasizes the regulatory role of soil C availability on microbial CUE.

Metagenomes and Metagenome-Assembled Genome Sequences from Nitrogen-Fixing Alder Nodules

Bacterial nitrogen (N) fixation in alder nodules is a key process providing nitrogen to nutrient-limited arctic biomes. Here, 45 prokaryotic metagenome-assembled genome (MAG) sequences from root nodules of arctic alder are reported.

The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales

Microorganisms exist throughout the soil profile and those microorganisms living in deeper soil horizons likely play key roles in regulating biogeochemical processes. However, the vertical differentiations of microbes along soil depth and their global biogeographical patterns remain poorly understood. Herein, we conducted a global meta-analysis to clarify the vertical changes of microbial biomass, diversity, and microbial relative abundance across the soil profiles. Data was collected from 43 peer-reviewed articles of 110 soil profiles (467 observations in total) from around the world. We found soil microbial biomass and bacterial diversity decreased with depth in soils. Among examined edaphic factors, the depth variation in soil pH exhibited significant negative associations with the depth change in microbial biomass and bacterial Shannon index, while soil total organic carbon (TOC) and total nitrogen (TN) exhibited significant positive associations. For the major bacteria phyla, the relative abundances of Proteobacteria and Bacteroidetes decreased with soil depth, while Chloroflexi, Gemmatimonadetes, and Nitrospirae increased. We found both parallels and differences in the biogeographical patterns of microbial attribute of topsoil vs. subsoil. Microbial biomass was significantly controlled by the soil nutrient concentrations in both topsoil and subsoil compared with climatic factors, while bacterial Shannon index was significantly controlled by the edaphic factors and across latitudes or climatic factors. Moreover, mean annual precipitation can also be used as a predictor of microbial biomass in subsoil which is different from topsoil. Collectively, our results provide a novel integrative view of how microbial biomass and bacterial community response to soil depth change and clarify the controlling factors of the global distribution patterns of microbial biomass and diversity, which are critical to enhance ecosystem simulation models and for formulating sustainable ecosystem management and conservation policies.

Soil bacterial communities associated with multi-nutrient cycling under long-term warming in the alpine meadow

Introduction

The functions of terrestrial ecosystems are mainly maintained by bacteria, as a key component of microorganisms, which actively participate in the nutrient cycling of ecosystems. Currently, there are few studies have been carried out on the bacteria contributing to the soil multi-nutrient cycling in responding to climate warming, which hampers our obtainment of a comprehensive understanding of the ecological function of ecosystems as a whole.

Methods

In this study, the main bacteria taxa contributing to the soil multi-nutrient cycling under the long-term warming in an alpine meadow was determined based onphysichemical properties measurement and high-throughput sequencing, and the potential reasons that warming altered the main bacteria contributing to the soil multi-nutrient cycling were further analyzed.

Results

The results confirmed that the bacterial β-diversity was crucial to the soil multi-nutrient cycling. Furthermore, Gemmatimonadetes, Actinobacteria, and Proteobacteria were the main contributors to the soil multi-nutrient cycling, and played pivotal roles as keystone nodes and biomarkers throughout the entire soil profile. This suggested that warming altered and shifted the main bacteria contributing to the soil multi-nutrient cycling toward keystone taxa.

Discussion

Meanwhile, their relative abundance was higher, which could make them have the advantage of seizing resources in the face of environmental pressures. In summary, the results demonstrated the crucial role of keystone bacteria in the multi-nutrient cycling under the climate warming in the alpine meadow. This has important implications for understanding and exploring the multi-nutrient cycling of alpine ecosystems under the global climate warming.

Warmer and drier ecosystems select for smaller bacterial genomes in global soils

Bacterial genome size reflects bacterial evolutionary processes and metabolic lifestyles, with implications for microbial community assembly and ecosystem functions. However, to understand the extent of genome-mediated microbial responses to environmental selections, we require studies that observe genome size distributions along environmental gradients representing different conditions that soil bacteria normally encounter. In this study, we used surface soils collected from 237 sites across the globe and analyzed how environmental conditions (e.g., soil carbon and nutrients, aridity, pH, and temperature) affect soil bacterial occurrences and genome size at the community level using bacterial community profiling. We used a joint species distribution model to quantify the effects of environments on species occurrences and found that aridity was a major regulator of genome size with warmer and drier environments selecting bacteria with smaller genomes. Drought-induced physiological constraints on bacterial growth (e.g., water scarcity for cell metabolisms) may have led to these correlations. This finding suggests that increasing cover by warmer and drier ecosystems may result in bacterial genome simplifications by a reduction of genome size.

An overlooked mechanism underlying the attenuated temperature response of soil heterotrophic respiration

Biogeochemical reactions occurring in soil pore space underpin gaseous emissions measured at macroscopic scales but are difficult to quantify due to their complexity and heterogeneity. We develop a volumetric-average method to calculate aerobic respiration rates analytically from soil with microscopic soil structure represented explicitly. Soil water content in the model is the result of the volumetric-average of the microscopic processes, and it is nonlinearly coupled with temperature and other factors. Since many biogeochemical reactions are driven by oxygen (O₂) which must overcome various resistances before reaching reactive microsites from the atmosphere, the volumetric-average results in negative feedback between temperature and soil respiration, with the magnitude of the feedback increasing with soil water content and substrate quality. Comparisons with various experiments show the model reproduces the variation of carbon dioxide emission from soils under different water content and temperature gradients, indicating that it captures the key microscopic processes underpinning soil respiration. We show that alongside thermal microbial adaptation, substrate heterogeneity and microbial turnover and carbon use efficiency, O₂ dissolution and diffusion in water associated with soil pore space is another key explanation for the attenuated temperature response of soil respiration and should be considered in developing soil organic carbon models.

Reduced precipitation neutralizes the positive impact of soil warming on soil microbial community in a temperate oak forest

Changes in soil microbial community play an irreplaceable role in regulating nutrient cycling that shapes forest ecosystem responses to climate change. However, if the effect of experimental warming on soil microorganisms depends upon soil water availability, which is closely related to soil depth is generally not well decumented. We conducted an in situ simulation experiment in an oak forest to determine the response pattern of soil microbial community to manipulated drought and warming at different soil depths. The responses of soil microbial communities to reduced precipitation and soil warming were highly dependent upon soil depth. Reduced precipitation remarkably elevated top-soil microbial biomass carbon (MBC) and nitrogen (MBN) in the unwarmed plots but no effects occured in the warmed plots. Soil warming showed positive effects on top-soil MBC and MBN under ambient precipitation, whereas negative ones were found under decreased precipitation. Neither reduced precipitation nor soil warming displayed effects on sub-soil MBC and MBN. Reduced precipitation notably increased soil total phospholipid fatty acids (PLFA) as well as that of bacterial and gram-negative bacterial only at top-soil in the unwarmed plots. Soil warming showed positive effects on total PLFA, bacterial PLFA, and gram-negative bacterial PLFA at both top- and sub-soil under ambient precipitation. We found that the interactive effects of climate change on soil microorganisms varied with soil depth, indicating that multilayer soil models should be considered while assessing the relationship between soil and atmosphere carbon exchange. Further research is expected to explore the long-term response of soil microorganisms in soil vertical profiles to climate change.

Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile

Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/Q₁₀ and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity (V_max) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. V_max and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/Q₁₀ and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.

Depth dependence of climatic controls on soil microbial community activity and composition

Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on subsoil microbial communities is limited. Here, we investigated the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and extracellular enzyme activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We found that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we found that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.

Characteristics of microbial community composition and its relationship with carbon, nitrogen and sulfur in sediments

Microorganisms play an important role in the biogeochemical cycles of lacustrine sediments. However, little is known about their vertical responses to sedimentary depths and their contributions to important element cycles such as carbon, nitrogen and sulfur. Here, we investigated the community features of sedimental prokaryotes along with vertical profiles (i.e., sedimental depths of 0-230 cm) in the Dongting watershed. In the entire profile, the bacterial diversity wavelike decreased with increasing sediment depths, whereas archaeal diversity increased monotonically in the deep layer (100-230 cm). Bacteria were more sensitive to sedimental depths than archaea (B: P < 0.001, R = 0.534; A: P < 0.001, R = 0.327). The relative abundance of the primary phylum of bacteria (e.g. Proteobacteria) and archaea (e.g. Thaumarchaeota) changed significantly with sediment layers (P < 0.05). The vertical distribution of prokaryotes in sediments was related to the changes in sediment properties (P < 0.05, e.g., the content of nutrients, pH, texture, etc.). The co-occurrence network analysis further indicated that the superficial (0-40 cm) and deep (100-230 cm) networks contained more tightly connected node groups (more modules number), while the tighter connections (shorter APL) and more complex networks (higher avgK) were seen in sub-deep (40-100 cm) sediments. Based on the FAPROTAX database, we found that the predicted prokaryotic microbial functional groups involved in the N cycle had the highest abundance (87.47%), followed by the C cycle (9.48%) and the S cycle (2.39%). In addition, these groups were enriched in the superficial and deep layers. Taken together, these results reveal a new perspective on the vertical spatial variation in microorganisms at the fine-scale of the lake sediments. Distinct microbiome response patterns may have important implications for carbon, nitrogen and sulfur cycling along with the sediment profile in Dongting lake ecosystems.