Habitats and seasons differentiate the assembly of bacterial communities along a trophic gradient of freshwater lakes.

Freshwater lakes are subject to variable degrees of eutrophication. Within lakes, the planktonic bacterial community (PBC) and sediment bacterial community (SBC) are both significant participants in biogeochemical processes of lake ecosystems. However, how the assembly patterns of bacterial communities vary seasonally along a trophic gradient in freshwater lakes is poorly understood.Here, we collected and analysed water and sediment samples from 13 shallow lakes located in an urban region of China during summer and winter, the trophic states of which ranged from mesotrophic to middle eutrophic in summer and oligo‐mesotrophic to light eutrophic in winter. High‐throughput sequencing of 16S ribosomal RNA genes was used to determine the diversity and composition of bacterial communities.Our results indicated that bacterial communities derived from different habitats and seasons did not exhibit a uniform response to lake trophic states. Linear and nonlinear mixed effect models suggested that the α‐diversity of PBC and SBC, respectively, showed a unimodal and monotonically decreasing trend with increasing eutrophication in summer, whereas that of PBC and SBC, respectively, exhibited no obvious trend or an increased pattern along the trophic gradient in winter. In addition, the taxonomic compositional dissimilarity of the PBC was most significantly related to lake trophic differences in summer. Phylogenetic structure analysis revealed that mostly environmental selection regulated the SBC and PBC in both seasons. Moreover, dispersal limitation and homogenising dispersal contributed more to the assembly of SBC and PBC in both seasons, respectively. Water temperature, associated with seasonal variability, was the most important variable driving the PBC assembly, while sediment pH overwhelmed nutrients in regulating the seasonal patterns of SBC assemblages.Overall, we highlighted that the water and sediments, as well as the seasons, differentiated the diversity patterns and assembly processes of bacterial communities along a trophic gradient of freshwater lakes. Our findings provide novel information for understanding the ecological responses of lacustrine bacterial communities to trophic gradients and seasonal variations. This study also contributes an important reference for predicting the changes of microbial community biodiversity under future scenarios of eutrophication. ​ [ABSTRACT FROM AUTHOR]