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Background: Microorganisms in rivers and lakes are essential for nutrient recycling in aquatic ecosystems. Understanding the ecological processes shaping microbial communities is of crucial importance for aquatic microbial ecology and biogeography. However, the diversity of microorganisms and the forces that control this diversity are poorly understood. This is particularly true within the framework of the river-lake continuum in arid regions. Results: Using a whole catchment-sampling effort, we explored biogeographical patterns and mechanisms of microbial community (bacteria and archaea) assembly within the catchment of the largest inland once freshwater lake (Lake Bosten) in China. Water samples from headstream tributaries, the mainstream of the River Kaidu to downstream Lake Bosten were characterized using amplicon sequencing of 16S rRNA genes. Higher α-diversity was found in mainstream of River Kaidu and in the tributaries compared with Lake Bosten. And the microbial community composition was also significantly different between the lake and its connected river habitats. Canonical correspondence analysis demonstrated that salinity and total suspended solids were the most important environmental factors shaping the community variations. Overall, pure environmental and pure spatial factors explained 13.7 and 5.6% of the community variation, respectively, while 32.0% of the variation was explained by combined environmental and spatial variables. These observations suggested that spatially structured environmental variations mainly shaped the microbial biogeography in this region. Both deterministic and stochastic processes influenced the microbial community assembly in river and lake habitats, and the stochastic pattern was particularly pronounced for microbiome in river habitat. Co-occurrence network analysis revealed more abundant and complicated correlations among frequently occurred taxa in lake habitat compared with the river habitat, implying that ecological multispecies interactions (e.g., competition) shaped lake microbial community structures. Conclusions: Our findings demonstrate an ecological succession along the river-lake continuum of microbial communities across the largest inland once freshwater lake basin in China, and highlight the effects of spatially structured environmental factors on regional microbial β-diversity and species interactions on local community assembly.

Rivers and their tributaries sculpt the earth’s surface, and play an important role in substance circulation and energy flow. Bacteria are involved in most biogeochemical processes in the fluvial ecosystem; however, their pattern distribution in a river and its tributaries has not yet been investigated in detail. In the present study, high-throughput sequencing was employed to examine bacterial communities and their co-occurrence networks between Kaidu River and its nine tributaries in northwestern China. The results obtained demonstrated that both bacterial communities shared a similar dominant sub-community, mainly consisting of Actinobacteria, Bacteroidetes, and Proteobacteria, with Limnohabitans and Variovorax as the dominant genera. In spite of these commonalities, bacterial community structures still significantly differed between these two habitats, which may be related to the distance-related dispersal limitation. Their co-occurrence networks were generally both positively structured. The structural analysis showed that OTUs from the same phyla were more likely to co-occur. Although the keystone genera were taxonomically different between Kaidu River and its tributaries, they both shared common trophic properties in exploiting niches under oligotrophic conditions. We noted that their relative abundances were less than 1%, indicating the over-proportional roles of rare genera in the bacterial community. In addition, the inferred networks showed less nodes and edges, but higher modularity in Kaidu River than its tributaries, suggesting the higher fragmentation of the bacterial community in the mainstream.