Plant diversity induces shifts from microbial generalists to specialist by enhancing niche differentiation, microbiome connectivity, and network stability in a temperate grassland

Background Soil microbiota are key players of terrestrial ecosystem functioning, including decomposition, soil organic matter formation, and nutrient cycling, and interact strongly with plants in the rhizosphere. While several studies have demonstrated the potential of plants to alter soil microbiome assembly and functioning, particularly via the manipulation of soil organic matter pools like root exudates, the implications for sustaining soil ecosystem functioning remain substantial. Using soil from a long-term biodiversity experiment in Jena, Germany, we investigated how soil microbial communities responded to variations in plant species richness (1–16 species), functional group richness (1–4 groups), and functional group identity (grasses, legumes, small herbs, and tall herbs) using 16S rRNA and ITS gene amplicon sequencing. We examined the structures of the bacterial and fungal communities, their metabolic potential, and microbial network architecture to better understand the role of the soil microbiome and its net positive relationship between biodiversity and ecosystem functioning. Results Plant diversity induced gradual shifts in the microbial community composition, while increasing soil organic carbon and nitrogen stocks. Microbial networks exhibited increased connectivity, particularly between bacteria and fungi, while mutualistic and antagonistic functionality increased. Key nodes shifted from generalist taxa at low plant diversity to more specialized communities at high plant diversity. Notably, fungi responded more strongly than bacteria, and their functional potential was driven by plant functional identity rather than species richness. Conclusion At low plant diversity, generalist taxa likely exploit less complex and diverse organic carbon inputs, allowing them to dominate available niches. In contrast, higher plant diversity promotes a variety of specialist taxa that likely benefit from the greater diversity of organic carbon compounds, and thus greater niche availability. As network complexity grows, ecosystem functions are being distributed across more taxa, leading to greater microbiome stability, and ultimately more efficient soil carbon and nutrient cycling. Our findings therein suggest that higher plant diversity strengthens microbial functioning and microbiome resilience.