Decoding the microbial assembly and environmental drivers along the phyllosphere-rhizosphere continuum of leguminous green manure Astragalus sinicus

Green manure crops are increasingly recognized not only for their contributions to soil fertility but also for their role in shaping plant-associated microbiome. Astragalus sinicus, a widely used leguminous green manure in East Asian paddy fields, harbors distinct microbial assemblages across plant compartments, yet the ecological processes driving microbiome assembly along its phyllosphere-rhizosphere continuum remain unclear. In this study, we profiled microbiome composition across the rhizospheric, phyllospheric, and soil compartments of A. sinicus using 16S rRNA gene amplicon sequencing targeting the region south of the Yangtze River, analyzing 315 samples collected from seven rice-growing regions. We found that Proteobacteria predominated all sampled compartments, with Mesorhizobium (75.85-96.93%) constituting the predominant taxon in the root microbiome. The leaf microbiome showed higher variability, dominated by Vibrionimonas (0.31-46.6%), Pantoea (0.71-46.61%), Pseudomonas (0.07-24.6%) and Bradyrhizobium (0.06-8.45%). Co-occurrence networks revealed a distinct gradient, including expansive yet weakly connected soil networks, moderately sized and highly modular leaf networks, and compact, highly robust root consortia, delineating a shift from environmentally driven complexity to host-filtered stability. Root and leaf microbiome assembly was primarily governed by stochastic processes (- 2 < β-NTI < 2, NCM r² > 70%) and plant- mediated selection (DI = 0.01/0.02, DSI = 0.09/0.14), with soil nutrient conditions, particularly total nitrogen, organic carbon, available phosphorus, and available potassiu, playing significant roles in shaping microbiome composition (p < 0.05). These core plant-associated ASVs were selectively enriched by the plant from the soil in over 70% of the sampled regions. Among these, Mesorhizobium in roots and Methylobacterium-Methylorubrum in leaves were found to be critical for nitrogen fixation and nutrient cycling, as evidenced by previous studies. Our results highlight the intricate interactions between plants, microbes, and their environment, underscoring the importance of plant-mediated selection and soil nutrient conditions in shaping the microbiome of A. sinicus, with significant implications for sustainable agricultural practices.