Vertical diversity of sediment bacterial communities in two different trophic states of the eutrophic Lake Taihu, China

Vertical diversity of sediment bacterial communities in 2 different trophic states (macrophyte-dominated and algae-dominated) of the large shallow eutrophic Lake Taihu, China, were investigated using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA sequence analysis. Clustering analysis of DGGE profiles showed that different clusters were recognized in different depths of sediment cores in the 2 lake trophic states. Analyses of the bacterial diversity, as estimated by the Shannon index (H'), showed that different sediment layers of the macrophyte-dominated state had higher diversity than the algae-dominated state. In addition, bacterial diversity of the sediment in the macrophyte-dominated state changed abruptly throughout the layers, but bacterial diversity of the algae-dominated state decreased gradually with sediment depth. Phylogenetic analysis showed that Proteobacteria was the most abundant phylum in the middle sediment of the 2 lake trophic states. In the macrophyte-dominated state, clone sequences related to Betaproteobacteria (50.0%) were the most abundant, followed by Epsilonproteobacteria (21.1%), Acidobacteria (7.9%), Deltaproteobacteria (7.9%), Chloroflexi (7.9%), and Bacteroidetes (5.3%); whereas in the algae-dominated state, sequences affiliated with Betaproteobacteria (84.4%) were predominant, followed by Deltaproteobacteria (12.5%) and Acidobacteria (3.1%). Canonical correspondence analysis showed that organic matter and pH play key roles in driving the vertical changes of bacterial community composition.