Metagenomic study of microbial communities in the South China Sea

The South China Sea (SCS) harbours a wide range of marine habitats within which exists a rich biodiversity. However, few studies have been published on its diverse communities, particularly in regards to its microbial counterparts. As the key players behind many of the vital processes that are carried out in the ocean, marine prokaryotes have thus been made the focus of this study, placing emphasis on community composition and structure, as well as their metabolic potential. By employing next generation shotgun sequencing technologies, we assessed the taxonomic structure of the prokaryotic communities in the surface waters collected from four characteristic sites located along the coast of Singapore, Malaysia and the Philippines. All studied locations were dominated by members of the Proteobacteria (Alpha- and Gamma-) and Cyanobacteria (Synechococcus sp. and Prochlorococcus sp.). The highest proportion of Gammaproteobacteria was found in Sarawak, representing an approximate 20% of total sequences. The class consisted of Alteromonodales, Pseudomonadales, Oceanospirillales and Enterobacteriales across all sites, which is similar to previous studies, except in Singapore where Vibrionales made up 50% of the group. Archaeal assemblages were made up largely of Euryarchaeota and unclassified sequences, while Crenarchaeota and Thaumarchaeota were present in much smaller proportions, except in Philippines where Thaumarchaeota made up almost 40% of the entire taxa. Based on physicochemical parameters, the prokaryotic communities in the seawater samples collected from both Singapore and Sarawak appeared to be subject to an anthropogenic influence (shipping harbour and river runoff), resulting in a significant difference in community structure compared to the other sites. Through our findings, we also observed that the majority of the microbial communities adhered to a core set of genes across the different locations. Among all the different sites, the Singapore (S1605) sample appeared to be the furthest removed in terms of functional similarities. The proportion of the major metabolic functions found in these waters differed from the other sites (Sarawak, Kota Kinabalu, Philippines), where amino acid metabolism was the most dominant but with a significantly lower count of protein metabolism genes. The biogeochemically relevant genes found here also differed substantially from the other locations, with two-fold the number of phosphate, and lipid and glycan metabolism genes. Based on the patterns observed, the environmental parameters appeared to play a larger role in determining the structure of these microbial communities rather than geographical variation. The results obtained from this study provide the first comparison of prokaryotic communities found in the surface waters of the eastern region of the South China Sea and will serve as a good platform for many prospective areas of study.