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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ftdoajarticles:oai:doaj.org/article:31b5d964e4be4ab5879622158a5f915c 2023-05-15T18:28:34+02:00 Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions Cheryl-Emiliane Tien Chow Danielle M Winget Richard Allen White III Steven J Hallam Curtis A Suttle 2015-04-01T00:00:00Z https://doi.org/10.3389/fmicb.2015.00265 https://doaj.org/article/31b5d964e4be4ab5879622158a5f915c EN eng Frontiers Media S.A. http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00265/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2015.00265 https://doaj.org/article/31b5d964e4be4ab5879622158a5f915c Frontiers in Microbiology, Vol 6 (2015) Metagenomics microbial ecology Single Cell Genomics virome Reference genome Fosmid Microbiology QR1-502 article 2015 ftdoajarticles https://doi.org/10.3389/fmicb.2015.00265 2022-12-31T02:02:45Z 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 (10m) and oxygen-starved basin (200m) 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. Article in Journal/Newspaper Subarctic Directory of Open Access Journals: DOAJ Articles Pacific Frontiers in Microbiology 6 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Metagenomics microbial ecology Single Cell Genomics virome Reference genome Fosmid Microbiology QR1-502 |
spellingShingle |
Metagenomics microbial ecology Single Cell Genomics virome Reference genome Fosmid Microbiology QR1-502 Cheryl-Emiliane Tien Chow Danielle M Winget Richard Allen White III Steven J Hallam Curtis A Suttle Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions |
topic_facet |
Metagenomics microbial ecology Single Cell Genomics virome Reference genome Fosmid Microbiology QR1-502 |
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 (10m) and oxygen-starved basin (200m) 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 |
Article in Journal/Newspaper |
author |
Cheryl-Emiliane Tien Chow Danielle M Winget Richard Allen White III Steven J Hallam Curtis A Suttle |
author_facet |
Cheryl-Emiliane Tien Chow Danielle M Winget Richard Allen White III Steven J Hallam Curtis A Suttle |
author_sort |
Cheryl-Emiliane Tien Chow |
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 |
https://doi.org/10.3389/fmicb.2015.00265 https://doaj.org/article/31b5d964e4be4ab5879622158a5f915c |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Subarctic |
genre_facet |
Subarctic |
op_source |
Frontiers in Microbiology, Vol 6 (2015) |
op_relation |
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00265/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2015.00265 https://doaj.org/article/31b5d964e4be4ab5879622158a5f915c |
op_doi |
https://doi.org/10.3389/fmicb.2015.00265 |
container_title |
Frontiers in Microbiology |
container_volume |
6 |
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1766211097776357376 |