Habitat and lifestyle affect the spatial dynamics of prokaryotic communities along a river-estuary-sea continuum.

Microbial biogeography and its controlling mechanisms are central themes in microbial ecology. However, we still lack a comprehensive understanding of how habitats and lifestyles affect microbial biogeography across complex environmental gradients. In this study, we investigated the planktonic (including free-living [FL] and particle-associated [PA] lifestyles) and benthic prokaryotic communities along a river-estuary-sea continuum of the Changjiang River to explore their distinct spatial dynamics. We observed greater community variability across spatial distances than between habitat and lifestyle types. Spatial variations were evident in FL, PA, and benthic communities, with the highest turnover rates observed in benthic communities, followed by PA, and the lowest turnover rates observed in FL. The replacement effect dominated PA and benthic community variations, whereas the richness effect was more significant in FL communities. Microbial assembly was primarily governed by homogeneous selection and dispersal limitation regardless of habitats/lifestyles, with their ratios decreasing as the spatial distance increased, particularly in the FL fraction. Dispersal limitation had a stronger effect on benthic communities compared to planktonic communities. While heterogeneous selection generally played a minor role, its influence became more pronounced over larger spatial distances and with increasing salinity differences. Finally, we showed that abiotic and biotic factors individually exerted a greater influence on PA communities, whereas their interactions had a stronger effect on FL communities. Our results revealed complex spatial dynamics and assembly mechanisms among microorganisms across different habitats and lifestyles, providing insights into the spatial scaling of community assembly across complex environmental gradients.