Genetic diversity of bacterial communities and gene transfer agents in northern South China Sea

Abstract

Pyrosequencing of the 16S ribosomal RNA gene (rDNA) amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS) and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS) than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA) major capsid gene (g5) was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS), temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments.

Figure 1. Map of sampling stations in the northern South China Sea.

Figure 2. Bacterial compositions of the different samples in the nSCS.

Figure 3. Bacterial compositions of the different communities in the nSCS.

Figure 4. Neighbor-joining phylogenetic tree based on partial g5 amino acid sequences (ca. 250 aa) showing the phylogenetic diversity of g5 in the northern South China Sea.

Figure 5. Two-dimensional plots of MDS analysis from g5 gene clone library to compare broad-scale differences between Rhodobacterales communities.

Figure 6. Biogeographic distribution of g5 gene OTUs in the nSCS (red) compared with those from Subartic North Atlantic Ocean (cold water), the Arctic Ocean (cold water) and Chesapeake Bay (temperate water).