Green manure intercropping reshapes beneficial microbial consortia to enhance soil multifunctionality and agroecosystem resilience

Intercropping crops with green manure offers a sustainable strategy to reduce nitrogen fertilizer dependency, enhance yields, and improve land use efficiency. While beneficial soil microorganisms are known to be key drivers of improved soil fertility and crop productivity, the differential responses of specific functional microbial communities to agronomic practices and their precise contributions to overall community structure and ecosystem function remain unclear. Here, we investigate how four key functional groups (NPK nutrient absorption [NPK], pathogen antagonism [PA], drought resisting [DR], and plastic degradation [PD]) driver ecosystem functions in a long-term maize-green manure intercropping field experiment. We found that green manure intercropping significantly decreased the Shannon and Simpson diversity and alterd four soil health-associated functional community composition. Moreover, green manure intercropping improved species connections and increased the network’s overall complexity. Crucially, we identified 11 novel core microbial genera with previously unrecognized roles in underpinning soil multifunctionality. Importantly, green manure-driven restructuring of the bacterial community optimizes functional redundancy, offering a novel pathway for the targeted manipulation of microbial communities and the optimization of agroecosystem functions.