Regional Species Pools Drive the Transition Rate of Soil Bacterial Specialisation

Niche breadth variation represents a kind of evolutionary trade-off among traits on resource utility and stress tolerance, which constrains the taxa not to be widely distributed. Regional species pools provide a reservoir of genetic material for organisms with different niche breadths, yet their role in niche breadth variation remains unclear. Here we conducted a large-scale soil survey across China, including agricultural, forest, grassland, and wetland soils, to explore how the regional species pool influences bacterial niche breadth variation, specifically, the transition between generalists (wider niche breadth) and specialists (narrower niche breadth), and further examined functional traits of frequently transitioning taxa. We found that generalists decreased bacterial beta-diversity, while specialists enhanced bacterial beta-diversity. Regional species pools were the primary factors affecting the transition rate from generalists to specialists in agricultural and natural ecosystems. In contrast, the reverse transition rate from specialists to generalists was predominantly influenced by soil pH in agricultural fields, standardised phylogenetic diversity in forests and wetlands, and soil moisture in grasslands. Additionally, the phylotypes transitioning from natural generalists to agricultural specialists were enriched in quorum sensing genes, the biosynthesis of microbial cell constituents' genes, as well as starch metabolism and C-fixation genes, compared to those transitioning from natural specialists to agricultural generalists. Collectively, our study demonstrates that regional species pools play a crucial role in shaping the variation in niche breadth among soil microbes, representing a fundamental force in the formation of highly specialised microbial communities.