Intercropping enhances soil multifunctionality by restructuring microbial community and biogeochemical cycles

Intercropping, a sustainable agricultural cropping system, enhances soil ecosystem multifunctionality (SEMF) including soil fertility and crop yield, via soil microbially-mediated processes. However, the factors driving SEMF in intercropping remain unclear. In the current study, we collected 36 surface soil samples (Ferralic Cambisols) from intercropping and monocropping systems under varying nitrogen (N) gradients (no N, low N [125 kg N ha^-1 maize; 62.5 kg N ha^-1 potato], and high N [375 kg N ha^-1 maize; 187.5 kg N ha^-1 potato]) during the silking stage of summer maize at a long-term experimental site (subtropical monsoon climate) in Southwest China. These samples were analyzed for soil microbial communities via amplicon sequencing and functional gene abundance through quantitative microbial element cycling. We measured 21 soil ecosystem functions, aggregated them into six general functional categories (soil carbon pool, soil aggregate stability, crop productivity, soil gas emission mitigation, nutrient supply, and turnover), and assessed how intercropping and soil microbes regulate SEMF. Specifically, multi-year intercropping enhanced SEMF by 20.3 % without N and 69.6 % under low-N, but showed no effect under high-N. Fungal diversity and community composition were the primary driver of SEMF in intercropping systems. Additionally, intercropping enhanced SEMF by positively regulating keystone taxa (i.e., Sordariomycetes, Planctomycetes, and Actinobacteria) within the network, restructuring community composition, improving fungal diversity, and accelerating biogeochemical cycles. These findings demonstrate that any loss in microbial diversity can impair SEMF, whereas intercropping maximizes SEMF under low-N conditions, thereby establishing a framework for optimized N fertilization in such systems.