Networks of lakes and streams are linked by downslope flows of material and energy within catchments. Understanding how bacterial assemblages are associated with nutrients and stoichiometric gradients in lakes and streams is essential for understanding biogeochemical cycling in freshwater ecosystems. In this study, we conducted field sampling of bacterial communities from lake water and stream biofilms in Erhai Lake watershed. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and explored the relationship between bacterial composition and environmental factors using networking analysis, canonical correspondence analysis (CCA), and variation partitioning analysis (VPA). Physicochemical parameters, nutrients, and nutrient ratios gradients between the lake and the streams were strongly associated with the differences in community composition and the dominant taxa. Cyanobacteria dominated in Erhai Lake, while Proteobacteria dominated in streams. The stream bacterial network was more stable with multiple stressors, including physicochemical-factors and nutrient-factors, while the lake bacterial network was more fragile and susceptible to human activities with dominant nutrients (phosphorus). Negative correlations between bacterial communities and soluble reactive phosphorus (SRP) as well as positive correlations between bacterial communities and dissolved organic carbon (DOC) in the network indicated these factors had strong effect on bacterial succession. Erhai Lake is in a eutrophic state, and high relative abundances of Synechococcus (40.62%) and Microcystis (16.2%) were noted during the course of our study. CCA indicated that nutrients (phosphorus) were key parameters driving Cyanobacteria-dominated community structure. By classifying the environmental factors into five categories, VPA analyses identified that P-factor (total phosphorus (TP) and SRP) as well as the synergistic effect of C-factor (DOC), N-factor (NO3−
), and P-factor (TP and SRP) played a central role in structuring the bacterial communities in Erhai Lake. Heterogeneous physicochemical conditions explained the variations in bacterial assemblages in streams. This study provides a picture of stream–lake linkages from the perspective of bacterial community structure as well as key factors driving bacterial assemblages within lakes and streams at the whole watershed scale. We further argue that better management of phosphorus on the watershed scale is needed for ameliorating eutrophication of Erhai Lake.
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