Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean
Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80...
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ftpubmed:oai:pubmedcentral.nih.gov:3105770 2023-05-15T17:31:03+02:00 Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean Tucker, Kimberly P Parsons, Rachel Symonds, Erin M Breitbart, Mya 2011-05 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105770 http://www.ncbi.nlm.nih.gov/pubmed/21124487 https://doi.org/10.1038/ismej.2010.188 en eng Nature Publishing Group http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105770 http://www.ncbi.nlm.nih.gov/pubmed/21124487 http://dx.doi.org/10.1038/ismej.2010.188 Copyright © 2011 International Society for Microbial Ecology Original Article Text 2011 ftpubmed https://doi.org/10.1038/ismej.2010.188 2013-09-03T15:22:54Z Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem. Text North Atlantic PubMed Central (PMC) The ISME Journal 5 5 822 830 |
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Original Article Tucker, Kimberly P Parsons, Rachel Symonds, Erin M Breitbart, Mya Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean |
topic_facet |
Original Article |
description |
Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem. |
format |
Text |
author |
Tucker, Kimberly P Parsons, Rachel Symonds, Erin M Breitbart, Mya |
author_facet |
Tucker, Kimberly P Parsons, Rachel Symonds, Erin M Breitbart, Mya |
author_sort |
Tucker, Kimberly P |
title |
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean |
title_short |
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean |
title_full |
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean |
title_fullStr |
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean |
title_full_unstemmed |
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean |
title_sort |
diversity and distribution of single-stranded dna phages in the north atlantic ocean |
publisher |
Nature Publishing Group |
publishDate |
2011 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105770 http://www.ncbi.nlm.nih.gov/pubmed/21124487 https://doi.org/10.1038/ismej.2010.188 |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105770 http://www.ncbi.nlm.nih.gov/pubmed/21124487 http://dx.doi.org/10.1038/ismej.2010.188 |
op_rights |
Copyright © 2011 International Society for Microbial Ecology |
op_doi |
https://doi.org/10.1038/ismej.2010.188 |
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The ISME Journal |
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5 |
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5 |
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830 |
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1766128358467305472 |