College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany.
BMC Genomics. 2020 Jun 26;21(1):441. doi: 10.1186/s12864-020-06861-y.
Viruses are the most abundant biological entities on earth and play import roles in marine biogeochemical cycles. Here, viral communities in the surface water of the East China Sea (ECS) were collected from three representative regions of Yangshan Harbor (YSH), Gouqi Island (GQI), and the Yangtze River Estuary (YRE) and explored primarily through epifluorescence microscopy (EM), transmission electron microscopy (TEM), and metagenomics analysis.
The virus-like particles (VLPs) in the surface water of the ECS were measured to be 10 to 10 VLPs/ml. Most of the isolated viral particles possessed a head-and-tail structure, but VLPs with unique morphotypes that had never before been observed in the realm of viruses were also found. The sequences related to known viruses in GenBank accounted for 21.1-22.8% of the viromic datasets from YSH, GQI, and YRE. In total, 1029 viral species were identified in the surface waters of the ECS. Among them, tailed phages turn out to make up the majority of viral communities, however a small number of Phycodnaviridae or Mimiviridae related sequences were also detected. The diversity of viruses did not appear to be a big difference among these three aquatic environments but their relative abundance was geographically variable. For example, the Pelagibacter phage HTVC010P accounted for 50.4% of the identified viral species in GQI, but only 9.1% in YSH and 11.7% in YRE. Sequences, almost identical to those of uncultured marine thaumarchaeal dsDNA viruses and magroviruses that infect Marine Group II Euryarchaeota, were confidently detected in the ECS viromes. The predominant classes of virome ORFs with functional annotations that were found were those involved in viral biogenesis. Virus-host connections, inferred from CRISPR spacer-protospacer mapping, implied newly discovered infection relationships in response to arms race between them.
Together, both identified viruses and unknown viral assemblages observed in this study were indicative of the complex viral community composition found in the ECS. This finding fills a major gap in the dark world of oceanic viruses of China and additionally contributes to the better understanding of global marine viral diversity, composition, and distribution.
病毒是地球上最丰富的生物实体，在海洋生物地球化学循环中发挥着重要作用。本研究主要通过荧光显微镜（EM）、透射电子显微镜（TEM）和宏基因组学分析，从洋山港（YSH）、枸杞岛（GQI）和长江口（YRE）三个代表性区域采集了东海（ECS）表层水中的病毒群落。
ECS 表层水中的病毒样颗粒（VLPs）测量值为 10 至 10 VLP/ml。大多数分离出的病毒颗粒具有头-尾结构，但也发现了具有独特形态的 VLPs，这些形态以前从未在病毒领域观察到过。与 GenBank 中已知病毒相关的序列占 YSH、GQI 和 YRE 病毒组数据的 21.1-22.8%。总共在东海表层水中鉴定出 1029 种病毒种。其中，有尾噬菌体构成了病毒群落的大部分，但也检测到少量 Phycodnaviridae 或 Mimiviridae 相关序列。这三个水生环境中的病毒多样性似乎没有太大差异，但它们的相对丰度在地理上是可变的。例如，Pelagibacter 噬菌体 HTVC010P 占 GQI 中鉴定出的病毒种的 50.4%，但在 YSH 中仅占 9.1%，在 YRE 中占 11.7%。在 ECS 病毒组中， confidently 检测到与未培养的海洋 Thaumarchaeota dsDNA 病毒和感染 Marine Group II Euryarchaeota 的 magroviruses 几乎相同的序列。具有功能注释的病毒组 ORFs 主要涉及病毒生物发生。通过 CRISPR 间隔物-原间隔物映射推断的病毒-宿主联系暗示了它们之间军备竞赛导致的新发现的感染关系。
本研究中鉴定出的病毒和观察到的未知病毒组合表明，东海复杂的病毒群落组成。这一发现填补了中国海洋病毒黑暗世界的主要空白，并有助于更好地了解全球海洋病毒的多样性、组成和分布。
