Rainfall Shapes the Diversity of Soil Nitrogen‐Fixing Microorganisms Worldwide

Beyond diversity: the functional mechanisms of microbial adapations under climate change in alpine deserts

The functional responses of soil microbiomes to concurrent warming and altered precipitation in alpine deserts remain poorly understood, hindering predictions of these fragile ecosystem to climate change. Specifically, the mechanisms by which microbial communities maintain ecosystem function potential despite climate-induced biodiversity changes are unclear. A three-year field manipulation experiment in an alpine desert grassland on the Qinghai-Xizang Plateau showed that warming and watering acted as distinct ecological drivers. Warming restructured prokaryotic and fungal communities, favored stress-associated taxa, and increasing interkingdom network complexity, indicating tighter microbial associations under climate stress. Although warming reduced microbial richness and diversity, it did not diminish the overall potential for soil nutrient cycling. Instead, functional stability was associated with sustained microbial abundance, network reorganization, and selective changes in nutrient-cycling genes, particularly those involved in nitrogen and phosphorus transformation hosted by specific bacterial phyla. In contrast, watering did not significantly increase mean soil moisture, but altered soil nutrient availability, affecting key microbial groups and their functions, showing an indirect regulation pathway. Functional stability in alpine deserts under climate change was maintained not by taxonomic diversity alone, but through abundance-based compensation, community reorganization, and pathway-specific functional shifts. This study provides a mechanistic framework linking climate drivers to microbial community structure and nutrient-cycling potential, offering predictive insights into the responses of cold-arid ecosystems to future climate change.

Decadal Resampling Reveals Widespread Increases in Soil Microbial Diversity Associated With Nitrogen Deposition.

Simulated manipulation experiments, such as nitrogen addition to mimic atmospheric nitrogen deposition, are widely used in global change research. However, experimental manipulations may differ from real-world environmental change in their intensity, duration, and co-occurrence, leaving long-term changes in soil microbial communities and soil health insufficiently understood. To address this gap, we resampled soils from 38 forest and grassland ecosystems across eastern China in 2009 and 2019 and assessed microbial taxonomic and functional diversity using shotgun metagenomics. Microbial diversity increased by 17% over the decade, accompanied by clear shifts in community composition. Among the environmental variables considered, nitrogen deposition (~19 kg nitrogen ha-1 year-1 across ecosystems) was the strongest predictor of changes in seven of 12 microbial community metrics. Larger nitrogen deposition was also associated with increased relative abundances of nitrogen-cycling genes and reduced spatial turnover in microbial community composition. These effects were consistent with a potential alleviation of nitrogen limitation and weakening of deterministic community assembly, although these mechanisms could not be directly established. In addition, increases in genes associated with carbon degradation and phosphorus cycling, together with declines in the relative abundances of pathogens, antibiotic resistance genes, and DNA viruses, coincided with the raise of the composite soil health index. Our findings demonstrate widespread decadal increases in soil microbial diversity and soil health across eastern China, with nitrogen deposition emerging as their strongest environmental factor. These results highlight that microbial responses to long-term ambient environmental change can differ markedly from responses inferred from short-term or high-intensity manipulation experiments.

Heterotrophic respiration by soil microbes in a changing climate

Functional diversity mediates the nonlinear relationship between tree species richness and soil denitrification in young subtropical forests

Soil denitrification is strongly linked to soil nitrogen availability and influences nitrate leaching and greenhouse gas emissions. In turn, it can be regulated by ecosystem productivity through plant nitrogen uptake and organic matter inputs. However, the specific effects of tree diversity on soil denitrification and the underlying mechanisms remain poorly understood in forest ecosystems. Here, we investigated the effects of tree species richness (across five levels: 1, 4, 8, 16 and 32 species) and the corresponding functional structure on soil denitrification through a large biodiversity experiment in young subtropical forests (3‐year‐old). Our results revealed a unimodal relationship between tree species richness and denitrification potential, with the peak at four species. The structural equation model indicated that tree species richness was positively associated with the functional dispersion of leaf dry matter content, which in turn increased ground basal area, thereby promoting denitrification potential by enhancing soil water‐filled pore space, elevating the abundance of the nirK gene and reducing the soil C:N ratio. Additionally, the community‐weighted means of root tissue density and specific leaf area positively and negatively influenced soil denitrification potential, respectively. Synthesis and applications . Our results suggest that soil denitrification is more pronounced in young forest communities characterized by high productivity and dominated by resource‐conservative species with high root tissue density and low specific leaf area. We recommend that forest managers prioritize high functional trait diversity rather than tree species richness to maximize niche complementarity in planted forests, an approach that would improve both economic and ecological benefits. These findings provide a foundation grounded in evidence for integrating biodiversity, nutrient cycling and selection principles based on traits into afforestation and stand transformation.

Interaction Mechanisms Among Soil Environmental Factors, Microbial Communities, and Nitrogen-Cycling Functional Genes in Cool-Climate Maize Fields

Cool-climate maize fields are characterized by low soil temperatures, strong seasonal hydrothermal fluctuations, and peat-influenced soil profiles, which may lead to patterns of nitrogen (N) cycling distinct from those in conventional agricultural soils. During maize growth, soils from three depths were characterized using physicochemical measurements, N-transformation and enzyme-activity assays, metagenomic sequencing, Mantel tests, variation partitioning analysis, and partial least squares path modeling (PLS-PM). Soil environmental factors varied significantly over time and with depth; soil organic matter (SOM) and total nitrogen (TN) increased with depth, while ammonium nitrogen (NH4+-N) predominated early and nitrate nitrogen (NO3−-N) predominated during the middle and late growth stages. The nitrogen fixation rate (NFR), nitrification rate (NitR), and denitrification rate (DNR) all peaked in August and showed a spatial pattern characterized by nitrogen fixation in the deepest layer and denitrification in the upper and middle layers. Bacterial communities varied less spatiotemporally than fungal communities. The genes nifK, hao, nirS/nirK, NR, nrfC, and hzsA/hzsC were identified as key nitrogen-cycling functional genes. Mantel tests and PLS-PM further characterized these relationships, with PLS-PM showing that soil physicochemical properties were positively associated with bacterial community composition (β = 0.87, p < 0.01), which, in turn, was negatively associated with N-cycling functional genes (β = −0.97, p < 0.001). Together, these pathways were associated with variation in N-cycling processes. Overall, this study advances an integrated understanding of N-cycling patterns and their potential controls in cool-climate maize fields and provides a scientific basis for optimizing N management strategies.

Plant functional diversity promotes ecosystem multifunctionality in abandoned karst farmland under changing rainfall patterns

Introduction Global climate change is altering the frequency and intensity of rainfall, with consequent effects on ecosystem multifunctionality (EMF). However, under more frequent extreme rainfall conditions, it remains unclear whether abiotic and biotic factors exert identical effects on EMF, and what the primary drivers of EMF are. Methods In this study, we quantified EMF using both averaging and multiple-threshold approaches. Within the framework of Hill-Chao numbers, plant biodiversity and soil microbial diversity were measured. We explored the effects of abiotic factors, plant diversity, and soil microbial diversity on EMF in abandoned karst farmland by simulating changes in the frequency of rainfall events of varying intensities. By manipulating rainfall frequency across different intensities while maintaining natural annual rainfall totals, we assessed its influence on multifunctionality and identified the primary drivers of variation. Results Increased frequency of heavy rainfall reduced plant biodiversity but had positive effects on the maintenance of EMF, although these effect were not significant (P > 0.05). Among abiotic factors, soil moisture content exhibited a positive relationship with EMF. Notably, plant functional diversity emerged as a primary driver, with its positive effect on EMF strengthening at higher functional thresholds (e.g., EMFT50 and EMFT90). Furthermore, abiotic factors affected EMF through both direct and indirect pathways, with the indirect effects primarily mediated by functional diversity, particularly under high-threshold multifunctionality. Discussion These findings suggest that, under projected future increases in extreme rainfall events, enhancing plant functional diversity should be a priority during the early succession of abandoned karst farmland. Strategies aimed at increasing plant functional diversity may benefit the restoration of ecosystem functions in degraded landscapes.