Lake and its inflow rivers compose a highly linked river-lake system, within which sediment and water are also closely connected. However, our understanding of this linked and interactive system remains unclear. In this study, we examined bacterial communities in the sediments and surface waters in Poyang Lake and its five tributaries. Bacterial communities were determined while using high-throughput 16S rRNA gene sequencing. The results showed significant differences of bacterial communities between sediments and surface waters, as well as between Poyang lake and its tributaries, suggesting that the river-lake system of Poyang Lake provides diverse and distinct habitats for bacterial communities, including lake water, lake sediment, river water, and river sediment. These biomes harbor distinct bacterial assemblages. Sediments harbor more diverse bacterial taxa than surface waters, but the bacterial communities in surface waters were more different across this river-lake system than those in sediments. In this eutrophic river-lake ecosystem, nitrogen and phosphorus were important drivers in sediment bacterial communities. Nitrogen, phosphorus, and dissolved organic carbon, as well as their stoichiometric ratios affected bacterial communities in surface waters. Moreover, network analysis revealed that the bacterial communities in surface waters were more vulnerable to various disturbances than in sediments, due to lower alpha diversity, high complexity of network, and a small number of key taxa (module hubs and connectors). Nutrient variables had strong influences on individual operational taxonomic units (OTUs) in the network, especially in bacterial network in surface waters. Different groups of taxa responded differently to nutrients, with some modules being more susceptible to nutrient variations. This study increased our current knowledge of linked river-lake ecosystems and provided valuable understanding for effective management and protection of these ecosystems by revealing bacterial communities in sediments and surface waters in Poyang Lake and its tributaries, as well as their responses to nutrients variation.
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