Phylogenetic diversity of bacterial communities in South China Sea mesoscale cyclonic eddy perturbations

Eddy pumping drives a set of biogeochemical processes by lifting deep waters into the euphotic zone. To address the potential effect of such physical processes upon the bacterial community, phylogenetic diversity was determined in two cold-core cyclonic eddies in the South China Sea. 16S rDNA terminal restriction fragment length polymorphism analysis of the microbial communities through the whole water column showed a wider depth range for the intermediate transition water mass at sites inside the eddies than for those outside. This water mass contained a relatively more complex community than the euphotic and deep-water zones. Stratification of prokaryotic populations between the surface and chlorophyll maximum layer of eddy-related sites versus homogeneity of communities in the euphotic zone of the reference site, revealed by statistical analysis of 16S rDNA libraries, is most likely a reflection of isopycnal displacement induced by differing water movement inside and outside eddies. Phylogenetic analysis revealed that eddy center sites were characterized by deep-water group Alteromonadales-affiliated clones, the psychrophilic genus Octadecabacter cluster and the nitrogen-fixing phototrophic Rhodospirillaceae cluster, while Paracoccus, an important functional group, abundantly existed at the reference site outside eddies. Our analysis revealed that bacterial community structure was significantly influenced by cyclonic eddy perturbations.