Environmental change increases the contribution of rare microbial species to ecosystem functioning in agricultural soils.

Understanding the responses of soil microbial communities to environmental change, as well as their contributions to ecosystem functioning under disturbed conditions, is of fundamental importance. Yet, the relative roles of rare and abundant microbes in sustaining soil functions under environmental changes remain poorly understood, particularly in agricultural ecosystems. Here, we sampled soils from 50 agricultural fields across eastern China to examine the response patterns of rare and abundant sub-communities, encompassing multitrophic soil organisms, including bacteria, fungi, and protists, to climate warming, dry-wet cycles, and nutrient enrichment, and assessed their relative contributions to ecosystem multifunctionality. We found that, unlike abundant taxa, rare species diversity significantly decreased with dry-wet cycles but increased with nutrient addition. In addition, the community resistance of abundant species was significantly higher than that of rare species under all of treatments. Co-occurrence network analysis showed that species associations increased under environmental changes in both abundant and rare sub-communities, while the shift was more pronounced in rare species. Notably, rare species emerged as the main drivers of ecosystem function, with their contributions becoming more pronounced under environmental changes. Collectively, these results highlight the pivotal role of rare species in supporting and enhancing agricultural ecosystem functioning under global change scenarios.