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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Microbiol. | doi: 10.3389/fmicb.2019.01951

Metagenomic analysis of the diversity of DNA viruses in the surface and deep-sea of the South China Sea

 Yantao Liang1,  Long Wang1, Zengmeng Wang1, Jiulong Zhao1,  Qingwei Yang2,  Min Wang2,  Kaiguang Yang3, Lihua Zhang3,  Nianzhi Jiao4 and  Yongyu Zhang1*
  • 1Qingdao Institute of Bioenergy and Bioprocess Technology (CAS), China
  • 2Ocean University of China, China
  • 3Dalian Institute of Chemical Physics (CAS), China
  • 4Xiamen University, China

Abstract: A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 meters below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July–August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4 and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.

Keywords: marine viruses, South China Sea, deep sea, Metagenomics, community structure

Received: 25 Apr 2019; Accepted: 08 Aug 2019.

Edited by:

Jie Xu, South China Sea Institute of Oceanology (CAS), China

Reviewed by:

Huiluo Cao, The University of Hong Kong, Hong Kong
Alejandra Prieto-Davó, Facultad de Química, Unidad Sisal, Universidad Nacional Autónoma de México, Mexico  

Copyright: © 2019 Liang, Wang, Wang, Zhao, Yang, Wang, Yang, Zhang, Jiao and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Yongyu Zhang, Qingdao Institute of Bioenergy and Bioprocess Technology (CAS), Qingdao, 266101, Shandong Province, China, zhangyy@qibebt.ac.cn