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.
Highlights
The bacterioplankton phylotypes of a-Proteobacteria are among the largest heterotrophic marine bacteria and often detected in various marine regions on Earth [1,2]
Studies on marine microbial populations have suggested that Order Rhodobacterales (a-Proteobacteria) members are ubiquitous in marine environments and can account for .25% of total marine bacterioplankton [2,3,4]
gene transfer agent (GTA) is a small phage-like particle released by bacteria; each particle contains a random ca. 4.5 kb fragment of bacterial genomic DNA [9] that can be transferred between cells [10]
Summary
The bacterioplankton phylotypes of a-Proteobacteria are among the largest heterotrophic marine bacteria and often detected in various marine regions on Earth [1,2]. Studies on marine microbial populations have suggested that Order Rhodobacterales (a-Proteobacteria) members are ubiquitous in marine environments and can account for .25% of total marine bacterioplankton [2,3,4]. The complete genome sequences of Rhodobacterales contain gene transfer agent (GTA) gene clusters [7,8]; these genes are not found in other major bacterioplankton groups. GTAs are present in phylogenetically diverse prokaryotes, indicating that this mode of DNA transfer may be important in shaping microbial genomes and communities [6]. A capsid protein-encoding gene (g5) of GTA has been used as a marker to estimate the diversity of Rhodobacterales in temperate and cold waters because GTA genes are conserved in Rhodobacterales [5,6]
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