Eutrophication causes microbial community homogenization via modulating generalist species

•Biotic homogenization was observed toward high eutrophication for microbes.•Bray-Curtis distance increased with TSI changes, while fungal LCBD declined with TSI.•Eutrophication was a primary driver of microbial community compositions.•Generalists contributed more to β-diversity and were key for biotic homogenization.•LCBD can be considered as a new parameter to indicate homogenization. Eutrophication substantially influences the community structure of aquatic organisms and has become a major threat to biodiversity. However, whether eutrophication is linked to homogenization of microbial communities and the possible underlying mechanisms are poorly understood. Here, we studied bacterial and fungal communities from water and sediments of 40 shallow lakes in the Yangtze-Huaihe River basin, a representative area characterized by intensifying eutrophication in China, and further examined the beta diversity patterns and underlying mechanisms under eutrophication conditions. Our results indicate that eutrophication generally caused biotic homogenization of bacterial and fungal communities in both habitats showing decreased community variations for the sites with a higher trophic state index (TSI). In the two habitats, community dissimilarities were positively correlated with TSI changes for both taxonomic groups, while the local contribution to beta diversity (LCBD) remarkably declined with increasing TSI for the fungal community. These phenomena were consistent with the pivotal importance of the TSI in statistically accounting for beta diversity of bacterial and fungal communities in both habitats. In addition, we found that physicochemical factors such as water temperature and pH were also important for bacterial and fungal communities in water, while heavy metal elements were important for the communities in sediments. Interestingly, generalist species, rather than specialist species, were revealed to more dominantly affect the variations in beta diversity along the trophic gradient, which were quantified by Bray-Curtis dissimilarity and LCBD. Collectively, our findings reveal the importance of generalist species in contributing to the change of beta diversity of microbial communities along trophic gradients, which have profound implications for a comprehensive understanding of the effects of eutrophication on microbial community. [Display omitted]