In eutrophic lakes, heterotrophic bacteria are closely associated with algal detritus and play a crucial role in nutrient cycling. However, the seasonal and spatial dynamics of free‐living (FL) and particle‐attached (PA) bacteria and the environmental factors shaping this relationship remain poorly understood. To address this issue, we explored the spatiotemporal patterns of bacterial community composition (BCC) in Lake Taihu, China, using terminal restriction fragment length polymorphism (T‐RFLP) and 454‐tag pyrosequencing of 16S rRNA gene. We generated a total of 218,027 high quality non‐cyanobacterial sequence reads that resulted in 4940 OTUs (97% cutoff), with Actinobacteria, β‐ and α‐proteobacteria being the predominant taxa. Although PA communities contained significantly higher alpha‐diversity than FL ones, we found that 59% of OTUs, that accounted for 96% of the total reads, were shared by both communities. The high degree of overlap between FL and PA communities indicates a high rate of dispersal potential, highlighting an underestimated connectivity and potentially similar ecological role for these two components. Distinct seasonal trends were recorded in both FL and PA communities, while spatial differences in BCC were small. In addition, both FL and PA bacterial communities exhibited similar patterns and synchrony, correlated to water temperature, nitrate and total suspended solids (TSS). Accordingly, the effects of eutrophication and hydrodynamics on the phylogenetic overlap and diversity between FL and PA communities were discussed.

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.

Due to the recent decades of climate change and intensive human activities, endorheic lakes are threatened by both salinization and eutrophication. However, knowledge of the aquatic bacterial community’s response to simultaneous increasing salinity and trophic status is still poor. To address this knowledge gap, we collected 40 surface water samples from five lakes and six rivers on the semi-arid Inner Mongolia Plateau, and investigated their bacterial communities using 16S rRNA gene-targeted amplicon sequencing. We found that bacterial species diversity significantly decreased from the mesotrophic freshwater river habitat to the eutrophic high-brackish lake habitat; salinity was more important than trophic status in explaining this decreased diversity. Salinity was the most important environmental factor in shaping community composition, while increased nitrogen loading was more important in structuring predicted functional composition. Within the lake habitats, the impact of environmental filtering on bacterial community assembly increased with the increasing salinity. The results suggested that the elevated salinity and nutrients have combined effects on the aquatic bacterial community, resulting in dramatic declines in species diversity, and promoted the importance of deterministic processes in community assembly. Our findings provide new insights into bacterial communities’ responses to the intensified climate-driven and anthropogenic environmental changes in aquatic ecosystems.

Eutrophication affects bacterial communities by fueling them with nutrients and carbon sources. While the influence of physicochemical conditions on bacterial communities is well studied, little is known about how dissolved organic matter (DOM) quality affects bacterial interspecific interactions and community composition with increasing eutrophication. Here, we examined the relative importance of physicochemical conditions and chromophoric DOM (CDOM) composition for bacterial community variation across trophic gradients using 109 samples data collected in 33 lakes of the Yangtze‐Huaihe River basin. We found a notable increase of bacterial abundance, elevated modularity of co‐occurrence networks, and decreased habitat niche breadths from mesotrophic sites to hyper‐eutrophic sites, suggesting changes in co‐occurrence patterns with eutrophication. Variation partitioning revealed that the proportion purely explained by CDOM composition was higher at the moderate‐ and hyper‐eutrophic sites than at the mesotrophic sites. Moreover, the module structures of the networks correlated significantly with CDOM composition at the eutrophic sites but not at the mesotrophic sites. The significant negative correlation between community‐level habitat niche breadths and the intensities of the protein‐like components at the moderate‐ and hyper‐eutrophic sites indicates a strong association between biolabile protein‐like compounds and habitat specialists in nutrient and substrate enriched lake systems. Our results suggest that consideration of DOM composition can strengthen the identification of links between environmental factors and bacterial community composition and interspecific interactions, especially under resource‐rich conditions.