Plant microhabitats mediate the effects of glacier retreat on soil microbial diversity and community assembly

Soil microorganisms and plants provide together the vast majority of key ecosystem functions and services, but the effects of climate change such as glacier retreat on soil microorganism–plant interactions remain poorly understood. Here, we investigated how plant microhabitats shape fungal and bacterial diversity, community composition, and functional diversity with glacier retreat over space-time. We analysed 234 microbial communities from bulk soil, rhizosphere soil, and plant root endosphere across four deglaciation stages that span c 160 years of glacier retreat. Our results indicate that fungi and bacteria follow distinct spatio-temporal dynamics: bacterial α -diversity declined within 100 years after glacier retreat, whereas fungal α -diversity gradually increased. On the contrary, β -diversity of both bacteria and fungi decreased with glacier retreat, primarily through reduced turnover, indicating directional disassembly and species exclusion. Community composition changed across scales, that is depending on the interactions between glacier retreat and plant microhabitats. Plant roots harbour the most distinct soil microorganism communities, which were particularly constrained at the latest deglaciation stage. Finally, functional diversity analysis revealed that functional guilds varied with deglaciation depending on plant microhabitats. Arbuscular mycorrhizal fungi, epiphytic fungi, plant pathogens, chemo-heterotrophic bacteria and nitrifying bacteria decrease with glacier retreat, while ectomycorrhizal fungi, endophyte, saprotrophic fungi, and cellulolytic bacteria increase with glacier retreat. Our findings reveal that both broad temporal and local spatial factors drive soil microbial community assembly and functions, with implications for plant-microorganism interactions and nutrient cycling dynamics in post-glacial landscapes.