Microbial-microhabitat interactions drive shrub and herb diversity along an altitudinal gradient in a mountainous birch secondary forest

Mountain ecosystems are highly sensitive to climate change, and vegetation-soil-microbe interactions are essential for their ecological functioning. This study was carried out in a Betula platyphylla secondary forest in the Han Mountain National Nature Reserve, Inner Mongolia, with the main goal of unraveling the moisture-driven “microbe-nutrient-vegetation” cascade mechanism along an altitudinal gradient. Sampling was conducted along an altitudinal gradient: low (1225 ± 50 m), middle (1375 ± 50 m), and high (1525 ± 50 m) zones. This study used a metagenomic approach to identify microbial communities. By integrating soil microenvironment properties, microbial functional traits, nutrient availability, and understory plant diversity, we used multivariate statistics and Partial Least Squares Path Modeling (PLS-PM) to unravel the moisture-driven “microbe-nutrient-vegetation” cascade mechanism. (1) Soil water content significantly decreased with altitude, triggering a microbial shift from low-altitude copiotrophic bacteria (e.g., Proteobacteria and Actinobacteria) to high-altitude stress-tolerant fungi (e.g., Cortinarius and Mortierella ). With increasing elevation along the altitudinal gradient, microbial metabolic limitation shifted, with phosphorus limitation weakening (vector angle decreased by 2.81 %) and carbon limitation strengthening (vector length increased by 11.32 %). (2) Moisture-regulated nutrient dynamics through microbial traits: Higher moisture at low altitudes enhanced bacterial diversity and carbon/nitrogen accumulation (e.g., dissolved organic carbon (DOC) and available nitrogen (AN)), whereas moisture deficit at high altitudes favored fungi associated with the P cycle (microbial biomass phosphorus (MBP) accumulation). Mid-altitude showed complementary microbial nutrient use, resulting in a peak in available phosphorus (AP) content. (3) Shrub diversity peaked at low altitudes (Chao1 = 6.01) and was mainly promoted by bacteria associated with the C/N cycle. Herb diversity exhibited a mid-altitude bulge (Chao1 = 20.19) and was strongly associated with fungal-driven phosphorus availability (AP contribution rate = 30.1 %). (4) The PLS-PM model (goodness of fit = 0.78) verified that soil water content (total effect β = 0.80) indirectly influenced vegetation diversity by regulating microbial community structure (β = −0.98) and nutrient availability (β = 0.89), forming a core “moisture → microbe → nutrient” cascade pathway. This study elucidates the mechanistic pathways linking moisture, microbes, nutrients, and plants along elevational gradients, deepens our mechanistic understanding of how future climate change may affect soil microbial diversity, and provides a theoretical foundation for developing forward-looking strategies to conserve vegetation diversity. • Microbial dominance shifts from bacteria to fungi dominance with altitude. • Soil moisture governs microbial functions and nutrient cycling. • Shrub and herb diversity peaks exhibit altitudinal mismatch. • Identifies two pathways: resource activation and functional reorganization.