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Diverse and unique viruses discovered in the surface water of the East China Sea
BACKGROUND: 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 th...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318539/ https://www.ncbi.nlm.nih.gov/pubmed/32590932 http://dx.doi.org/10.1186/s12864-020-06861-y |
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author | Wu, Shuang Zhou, Liang Zhou, Yifan Wang, Hongming Xiao, Jinzhou Yan, Shuling Wang, Yongjie |
author_facet | Wu, Shuang Zhou, Liang Zhou, Yifan Wang, Hongming Xiao, Jinzhou Yan, Shuling Wang, Yongjie |
author_sort | Wu, Shuang |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: The virus-like particles (VLPs) in the surface water of the ECS were measured to be 10(6) to 10(7) 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. CONCLUSIONS: 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. |
format | Online Article Text |
id | pubmed-7318539 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-73185392020-06-29 Diverse and unique viruses discovered in the surface water of the East China Sea Wu, Shuang Zhou, Liang Zhou, Yifan Wang, Hongming Xiao, Jinzhou Yan, Shuling Wang, Yongjie BMC Genomics Research Article BACKGROUND: 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. RESULTS: The virus-like particles (VLPs) in the surface water of the ECS were measured to be 10(6) to 10(7) 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. CONCLUSIONS: 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. BioMed Central 2020-06-26 /pmc/articles/PMC7318539/ /pubmed/32590932 http://dx.doi.org/10.1186/s12864-020-06861-y Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Wu, Shuang Zhou, Liang Zhou, Yifan Wang, Hongming Xiao, Jinzhou Yan, Shuling Wang, Yongjie Diverse and unique viruses discovered in the surface water of the East China Sea |
title | Diverse and unique viruses discovered in the surface water of the East China Sea |
title_full | Diverse and unique viruses discovered in the surface water of the East China Sea |
title_fullStr | Diverse and unique viruses discovered in the surface water of the East China Sea |
title_full_unstemmed | Diverse and unique viruses discovered in the surface water of the East China Sea |
title_short | Diverse and unique viruses discovered in the surface water of the East China Sea |
title_sort | diverse and unique viruses discovered in the surface water of the east china sea |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318539/ https://www.ncbi.nlm.nih.gov/pubmed/32590932 http://dx.doi.org/10.1186/s12864-020-06861-y |
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