Abstract
Coastal sediment ecosystems function as dynamic interfaces for land-sea interactions, harboring highly complex microbial communities which support vital ecological functions. However, the mechanisms governing microbial diversity maintenance and cross-trophic community assembly at large spatial scales remain poorly explored. In this study, a high-throughput sequencing approach was employed to analyze the bacterial, fungal and protistan communities in surface sediments of the China Seas. As indicated by higher values across most indices, bacterial communities generally exhibited greater richness and alpha diversity compared to fungal and protistan communities. Beta diversity decomposition revealed that species turnover dominated community variations across all three trophic levels, with the highest contribution in bacteria. The neutral community model revealed that stochastic processes exerted a stronger influence on bacterial assembly relative to fungi and protists. Moreover, null model analyses demonstrated that bacterial communities were primarily structured by dispersal limitation, fungal communities by ecological drift, while protistan communities co-regulated by homogeneous selection and homogenizing dispersal. Furthermore, similar latitude-dependent patterns in the α- and β- diversity were observed in bacteria and protists, yet such patterns were distinct for fungi. Finally, based on the correlations between community variations with their assembly mechanisms, regional species pools exerted the strongest influence on bacterial β-diversity, whereas local assembly processes dominated fungal β-diversity. The present study elucidates the trophic-level-dependent assembly rules of coastal microbiomes, thereby establishing a mechanistic foundation for predicting ecosystem responses to global change and informing evidence-based conservation of coastal ecosystems.