Microhabitat-specific restructuring of soil protist communities along a tropical land-use intensification gradient

Microhabitat-specific responses of soil organisms to land-use intensification remain a major blind spot in biodiversity research. Here, we assessed how protists—key regulators of microbial diversity and nutrient cycling—differ in composition and roles across litter, rhizosphere and bulk soil along a land-use gradient of increasing management intensity, from rainforest to shrubland, rubber plantations, and oil palm plantations in Sumatra, Indonesia. High-throughput sequencing revealed that rhizosphere protists responded most strongly to land-use intensification, with a 39.6% increase in Shannon index and marked shifts in community composition. Bulk soil protists showed similar but weaker responses, while litter protists exhibited compositional shifts without significant α-diversity changes. Notably, protist community composition was differentially structured by abiotic and biotic drivers across microhabitats independent of land-use type, with biotic dominance in the rhizosphere, abiotic dominance in litter, and joint control in bulk soil. To assess functional turnover, we applied an ecological niche framework (generalist–specialist–opportunist). Generalists remained stable in litter, whereas specialists showed reduced niche breadth and richness in rhizosphere and bulk soil, particularly in oil palm plantations, and opportunists showed intermediate responses. These findings demonstrate that land-use intensification restructures belowground communities in a microhabitat-specific and functionally predictable manner. By explicitly separating litter, rhizosphere, and bulk soil microhabitats, our study reveals microhabitat-specific assembly processes overlooked in conventional bulk-soil analyses and provides new insights into protist responses to land-use intensification in tropical soils. These findings highlight the need to incorporate microhabitat-scale processes when assessing soil biodiversity and ecosystem functioning under environmental change.