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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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