Distinct Composition and Assembly Processes of Bacterial Communities in a River From The Arid Area: Ecotypes or Habitat Types?

Abstract The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, function, and assembly mechanism of the bacterial community in the arid river were analyzed. Four ecotypes were recognized across the three habitats (biofilm, water, and sediment) by Dirichlet multinomial mixture method. The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of Water II to Water I. Significant differences in the composition and function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and function of plastic degradation in Water I than those in Water II. Habitat filtering may play a more important role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominated the assembly process of bacterial communities in water and sediment. In Water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in the Water II. These results would provide conceptual frameworks about how to choose habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.