Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China

Abstract

Bacteria play an important role in the decomposition and cycling of a variety of compounds in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. A unique Chinese eutrophic lake--Dianchi--was selected for study because it has two separate and distinct basins, Caohai with higher organic carbon levels and Waihai with lower organic carbon levels. Sediment bacterial communities were studied in the two basins using samples collected in each season from June 2010 to March 2011. Barcoded pyrosequencing based on the 16 S rRNA gene found that certain common phyla, Proteobacteria, Bacteroidetes, Firmicutes and Chloroflexi, were dominant in the sediments from both basins. However, from the class to genus level, the dominant bacterial groups found in the sediments were distinct between the two basins. Correlation analysis revealed that, among the environmental parameters examined, total organic carbon (TOC) accounted for the greatest proportion of variability in bacterial community. Interestingly, study results suggest that increasing allochthonous organic carbon could enhance bacterial diversity and biomass in the sediment. In addition, analysis of function genes (amoA and nosZ) demonstrated that ammonia-oxidizing bacteria (AOB) were dominant in sediments, with 99% belonging to Nitrosomonas. Denitrifying bacteria were comparatively diverse and were associated with some cultivatable bacteria.

Figure 1. Community analysis using principal coordinate analysis (PCoA) of weighted UniFrac distance matrix.

Figure 2. Relative abundances of dominant phylogenetic groups in sediments derived from Caohai and Waihai sampling sites.

Phylogenetic groups accounting for <1% of all classified sequences are summarized as “other” in the figure.

Figure 3. Phylogenetic trees with the (a) amoA and (b) nosZ representative sequences (OTUs) from Dianchi Lake sediments (Sampled in Dec. of 2010).

The numbers on the branch nodes represent percentage of bootstrap resamplings based on 1000 replicates (only ≥50% are shown). The scale bar indicates the number of nucleotide substitutions per site. The relative abundance of each OTU (comprising 2 or more clones) in the amoA or nosZ clone library is shown in parentheses. Additional symbols for abundance are (▪) Caohai and (▴) Waihai.

Figure 4. Quantitive analysis of 16 S rRNA, amoA, and nosZ gene in the sediments (computed in dry weight).

Black bars represent Caohai and grey bars represent Waihai. Error bars represent standard deviation from three independent experiments.

Figure 5. Principal components analysis (PCA) and Redundancy analysis (RDA) with of bacterial communities as affected by sediment properties, based on the relative abundance of dominant bacterial phyla and proteobacterial classes.

Total-N represents NH₃-N+NO₂ ⁻-N+NO₃ ⁻-N. Abbreviations in figure: Temp, temperature; Actinobac., Actinobacteria; Alphapro., Alphaproteobacteria; Betapro., Betaproteobacteria; Deltapro., Deltaproteobacteria; Gammapro.,Gammaproteobacteria; Acidobac., Acidobacteria; Unclassified bac., Unclassified bacteria; Unclassified Pro., Unclassified Proteobacteria. Epsilonpro., Epsilonproteobacteria.