Data Sheet 1_Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems.pdf

While soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China’s six major terrestrial ecosystems (41 topsoil samples, 0–20 cm depth), we reveal a counterintuitive pattern: oligotrophic environments (deserts, karst) harbor microbiomes with significantly greater metabolic pathway diversity (KEGG) compared to resource-rich ecosystems. We provide a systematic catalog of key functional genes governing biogeochemical cycles in these soils, identifying: 6 core CAZyme genes essential for soil organic carbon (SOC) decomposition and biosynthesis; 62 nitrogen (N)-cycling genes (KOs) across seven critical enzymatic clusters; 15 sulfur (S)-cycling genes (KOs) within three key enzymatic clusters. These functional gene abundances exhibit distinct, geography-driven clustering patterns, strongly correlated with eight environmental drivers (latitude, NDVI, pH, EC, SOC, TN, C:N ratio, and MAP). This work provides a predictive framework and actionable genetic targets (e.g., specific CAZyme, N/S cycling genes) for potentially manipulating soil microbiomes to enhance ecosystem resilience and biogeochemical functions under stress.

尽管土壤微生物是陆地生态系统功能的核心支撑，但学界对其功能潜力如何随环境梯度发生适应性演化仍知之甚少，针对广布微生物类群的相关研究尤为匮乏。本研究针对中国六大典型陆地生态系统采集了41份0–20厘米深度的表层土壤样品，采用宏基因组学（metagenomics）综合分析方法，揭示了一项反直觉的规律：相较于富营养生态系统，寡营养环境（沙漠、喀斯特（karst））中的微生物组（microbiome）拥有显著更高的代谢通路多样性（KEGG）。本研究构建了调控这些土壤生物地球化学循环的关键功能基因系统编目，共鉴定得到6个调控土壤有机碳（Soil Organic Carbon, SOC）分解与生物合成的核心碳水化合物活性酶（CAZyme）基因、7个关键酶簇下共62个氮（N）循环基因（KOs），以及3个核心酶簇下共15个硫（S）循环基因（KOs）。这些功能基因的丰度呈现出显著的地理驱动聚类特征，与8种环境驱动因子（纬度、归一化植被指数（Normalized Difference Vegetation Index, NDVI）、pH值、电导率（Electrical Conductivity, EC）、SOC、总氮（Total Nitrogen, TN）、碳氮比（C:N ratio）以及年平均降水量（Mean Annual Precipitation, MAP））存在强相关性。本研究构建的预测框架与可操作遗传靶点（如特定CAZyme基因、氮/硫循环基因），可为未来通过调控土壤微生物组以提升胁迫环境下的生态系统恢复力与生物地球化学功能提供理论支撑与实践路径。