Legume integration into rice cropping systems buffers topsoil functional potential against microbial diversity loss

Intensive cropping systems pose a growing threat to soil microbial diversity, potentially impairing essential agroecosystem functions. Introducing legume crops or implementing fallow periods into these systems are promising strategies to alleviate such negative impacts. However, how these strategies affect the resilience of soil functions to microbial diversity loss remains largely unexplored, particularly in deeper soil layers. In this study, we employed a dilution-to-extinction approach to simulate microbial diversity loss and investigated its effect on functional potential in both topsoil (0–20 cm) and subsoil (40–60 cm) under three crop rotation systems (i.e., rice-fallow, rice-wheat, rice-milk vetch). Soil functional potential was indicated by measuring the copy number of functional genes using high-throughput qPCR. Our results indicate that microbial diversity loss significantly reduced abundance of genes associated with C degradation, C fixation, N mineralization, nitrification, and denitrification in the topsoil of rice-fallow and rice-wheat systems. In contrast, the rice-milk vetch system preserved abundance of these functional genes in the topsoil following microbial diversity loss, highlighting the potential of tailored cropping strategies to counteract the adverse effect of intensive agriculture. Furthermore, while abundance of genes associated with nitrification was also reduced in subsoil by microbial diversity loss, that of genes associated with C degradation and denitrification generally increased for all cropping systems. This highlights the vulnerability of subsoil function potential to microbial diversity loss, potentially enhancing greenhouse gas emissions and contributing to positive climate feedbacks. We concluded that integrating legume crops can maintain soil functional potential in topsoil even in the face of reduced microbial diversity, which is crucial for developing sustainable agricultural practices and ensuring long-term agroecosystem resilience.