Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions
Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and gree...
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ftpubmed:oai:pubmedcentral.nih.gov:4392320 2023-05-15T18:28:34+02:00 Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions Chow, Cheryl-Emiliane T. Winget, Danielle M. White, Richard A. Hallam, Steven J. Suttle, Curtis A. 2015-04-10 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392320/ https://doi.org/10.3389/fmicb.2015.00265 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392320/ http://dx.doi.org/10.3389/fmicb.2015.00265 Copyright © 2015 Chow, Winget, White, Hallam and Suttle. http://creativecommons.org/licenses/by/4.0/ 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) or licensor 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. CC-BY Microbiology Text 2015 ftpubmed https://doi.org/10.3389/fmicb.2015.00265 2015-04-26T00:01:56Z Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant “nr” database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems. Text Subarctic PubMed Central (PMC) Pacific Frontiers in Microbiology 6 |
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English |
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Microbiology |
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Microbiology Chow, Cheryl-Emiliane T. Winget, Danielle M. White, Richard A. Hallam, Steven J. Suttle, Curtis A. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
topic_facet |
Microbiology |
description |
Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant “nr” database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems. |
format |
Text |
author |
Chow, Cheryl-Emiliane T. Winget, Danielle M. White, Richard A. Hallam, Steven J. Suttle, Curtis A. |
author_facet |
Chow, Cheryl-Emiliane T. Winget, Danielle M. White, Richard A. Hallam, Steven J. Suttle, Curtis A. |
author_sort |
Chow, Cheryl-Emiliane T. |
title |
Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
title_short |
Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
title_full |
Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
title_fullStr |
Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
title_full_unstemmed |
Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
title_sort |
combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
publisher |
Frontiers Media S.A. |
publishDate |
2015 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392320/ https://doi.org/10.3389/fmicb.2015.00265 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Subarctic |
genre_facet |
Subarctic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392320/ http://dx.doi.org/10.3389/fmicb.2015.00265 |
op_rights |
Copyright © 2015 Chow, Winget, White, Hallam and Suttle. http://creativecommons.org/licenses/by/4.0/ 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) or licensor 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. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2015.00265 |
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Frontiers in Microbiology |
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6 |
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