Shuo Jiao

Understanding how fungal biogeography shapes ecosystem processes is central to predicting biogeochemical responses to environmental change. However, the properties of saprotrophic fungi that link their distribution patterns to belowground carbon cycling remain unclear. Here, we provide a comprehensive assessment linking widespread (high-occurrence) and narrowly distributed (low-occurrence) saprotrophic fungi (saprotrophs) to carbon decomposition processes across a broad latitudinal gradient from tropical to boreal zones. Our results show that the diversity of saprotrophic fungi is shaped by distinct community assembly processes, which in turn generate contrasting geographic patterns across latitudes. Widespread saprotrophs are mainly structured by large-scale climatic and local soil variables (environmental filtering) and show increasing diversity toward higher latitudes, whereas narrow-ranged saprotrophs are primarily constrained by the regional species pool (dispersal filtering), leading to declining diversity with latitude. By integrating large-scale biogeographic data with DNA stable isotope probing experiment, we provide evidence that fungal taxa actively participating in straw decomposition are dominated by widespread saprotrophs, underscoring their essential role in carbon cycling. Our findings highlight occupancy as a key biogeographic attribute regulating fungal contributions to carbon cycling and provide a predictive framework for understanding how belowground biodiversity shapes soil carbon dynamics under global change.

Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural–natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.

Global nitrogen (N) enrichment promotes soil organic carbon (SOC) accumulation but often causes biodiversity loss in plants and soil microbes, creating a central challenge for achieving co-benefits of carbon accumulation and biodiversity conservation. The extent to which biodiversity contributes to SOC accumulation, and how these trade-offs can be mitigated under N enrichment remains poorly understood. Here, we conduct a global meta-analysis of N enrichment experiments encompassing 2141 observations from 275 studies to evaluate the contributions of plant, bacterial, and fungal diversity to SOC accumulation and to determine associated ecological thresholds. Our findings indicate that biodiversity, especially in plant communities, is the most important factor for SOC accumulation. We identify three distinct N thresholds characterized by different ecological responses: biodiversity loss accelerates at 50 kg N ha⁻¹ yr⁻¹, soil degradation persists at 200 kg N ha⁻¹ yr⁻¹, and SOC accumulation declines beyond this point. Given that the promoting effects of bacterial, fungal, and plant diversity on SOC diminish or even reverse at 50, 67, and 74 kg N ha⁻¹ yr⁻¹, respectively, we suggest limiting fertilization to around 50 kg N ha⁻¹ yr⁻¹, as the trade-off between biodiversity loss and SOC accumulation under N enrichment is potentially minimized.

Niche breadth variation represents a kind of evolutionary trade‐off among traits on resource utility and stress tolerance, which constrains the taxa not to be widely distributed. Regional species pools provide a reservoir of genetic material for organisms with different niche breadths, yet their role in niche breadth variation remains unclear. Here we conducted a large‐scale soil survey across China, including agricultural, forest, grassland, and wetland soils, to explore how the regional species pool influences bacterial niche breadth variation, specifically, the transition between generalists (wider niche breadth) and specialists (narrower niche breadth), and further examined functional traits of frequently transitioning taxa. We found that generalists decreased bacterial beta‐diversity, while specialists enhanced bacterial beta‐diversity. Regional species pools were the primary factors affecting the transition rate from generalists to specialists in agricultural and natural ecosystems. In contrast, the reverse transition rate from specialists to generalists was predominantly influenced by soil pH in agricultural fields, standardised phylogenetic diversity in forests and wetlands, and soil moisture in grasslands. Additionally, the phylotypes transitioning from natural generalists to agricultural specialists were enriched in quorum sensing genes, the biosynthesis of microbial cell constituents' genes, as well as starch metabolism and C‐fixation genes, compared to those transitioning from natural specialists to agricultural generalists. Collectively, our study demonstrates that regional species pools play a crucial role in shaping the variation in niche breadth among soil microbes, representing a fundamental force in the formation of highly specialised microbial communities.

Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.

The ecological niche represents a fundamental property of organisms, reflecting their diversity of utilized resources or environmental tolerances across space and time. Despite a wealth of studies revealing that not all bacteria being everywhere, the key traits that determine niche breadth have remained unclear. Here, bacterial niche breadth based on a large‐scale soil survey across a wide range of environmental gradients at a national‐scale is characterized, and evaluated their life‐history traits utilizing over 2000 bacterial genomic datasets from the Genome Taxonomy Database (GTDB). A positive relationship between gene functional diversity and niche breadth is found, and identified a key set of bacterial traits associated with niche breadth, which are assigned to five life‐history categories, encompassing growth, competition, stress tolerance, resource acquisition, and dispersal ability. The traits of these categories are captured by distinct clusters in the full dimensionality of trait space, suggesting that a broad‐niche taxon may indeed possess multiple facets of life history strategies essential for survival in diverse environments. Bacterial taxa with wider niche breadth maximized a diversity of traits associated with different life history strategies, whereas specialists tended to harbor a smaller number of traits associated with fewer life history strategies. Together, this study offers new insights into developing a trait‐based understanding of bacterial niche breadth from the perspective of life history theory.

Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.