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Bacterial community structure and the effects of several environmental factors on bacterial community distribution were investigated in the sediment of the macrophyte-dominated and algae-dominated areas in a large, shallow, eutrophic freshwater lake (Lake Taihu, China). Surface sediment samples were collected at 6 sampling sites (3 sites from each of the 2 areas) on 15 February and 15 August 2009. Based on cluster analysis of the DGGE banding patterns, there were significant seasonal variations in the structure of the sediment bacterial community in the macrophyte- and algae-dominated areas, and site-specific variation within an area and between 2 areas. However, there were no significant between-area variations due to the large within-area variation. Analysis of DNA sequences showed that there were differences in the species composition of the sediment bacteria between the macrophyte- and algae-dominated area clone libraries. In the macrophyte-dominated area library, the bacterial community was dominated by Deltaproteobacteria, Verrucomicrobia, Acidobacteria, Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. OP10 was found in the library of this area but not in the algae-dominated area library. The algae-dominated area library was dominated by Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Acidobacteria. Cyanobacteria, Alphaproteobacteria, and Planctomycetes were found in this area library but not in the macrophyte-dominated area library. Canonical correspondence analysis demonstrated that total phosphorus and water temperature were the dominant environmental factors affecting bacterial community composition in the sediment.

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Lake Bosten, a large oligosaline lake in arid northwestern China, has evolved from a freshwater lake and is influenced by eutrophication processes. Since sediments record past limnic changes, the analysis of sedimentary bacteria in Lake Bosten may help elucidate bacterial responses to both salinization and eutrophication. We characterized the intrasystem distribution of sedimentary bacterial communities between freshwater and oligosaline regions of Lake Bosten using denaturing gradient gel electrophoresis and 16S rRNA gene clone libraries. Both principal component analysis and redundancy analysis revealed that salinity was the dominant and pronounced intrasystem factor that shaped the sedimentary bacterial community composition in Lake Bosten. In total, 349 clones and 185 distinct operational taxonomic units were acquired from 4 clone libraries. Proteobacteria (41.5%) was the most abundant phylum, followed by Bacteroidetes (13.5%), Chloroflexi (8.9%), Firmicutes (8.6%) and others. The higher bacterial diversities and proportions of Beta-and Deltaproteobacteria in the oligosaline regions than in the freshwater region reflected the responses of sedimentary bacteria to increased salinity and nutrient levels. The scarceness of typical freshwater bacteria, the relatively high percentage (12.3% of total bacteria) of putative sulfate-reducing bacteria and a high percentage of unclassified bacteria in the sediments all highlight the uniqueness of sedimentary bacterial communities in the early stages of salinization and eutrophication.

The effect of decomposition of Microcystis blooms on the sediment bacterial communities was investigated in a 14-day mesocosm experiments under dark and anoxic condition with three differing levels of Microcystis spp. biomass (from 20 to 2000 µg L(-1)) as measured by chlorophyll-a (Chl-a) concentration in the water column. Sediment samples were collected on days 0 and 14 for bacterial community composition (BCC) analysis, based on rapid decreases in the Chl-a concentration of water column. The BCC was determined by denaturing gradient gel electrophoresis and sequencing of predominant bands. The results showed that after Microcystis decomposition (day 14), the bacterial phylotype diversity in the sediment increased in enclosures with added Microcystis, and the relative abundance of bacteria affiliated with Bacteroidetes and Verrucomicrobia strongly increased. Canonical correspondence analysis showed that organic matter and Chl-a contributed significantly to the changes in sediment bacterial communities during Microcystis decomposition. The present results demonstrate Microcystis decomposition may directly and indirectly influence the BCC of the sediment.

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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.