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Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global envir...

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Autores principales: Hopkins, Max, Kailasan, Shweta, Cohen, Allison, Roux, Simon, Tucker, Kimberly Pause, Shevenell, Amelia, Agbandje-McKenna, Mavis, Breitbart, Mya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184009/
https://www.ncbi.nlm.nih.gov/pubmed/24694711
http://dx.doi.org/10.1038/ismej.2014.43
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author Hopkins, Max
Kailasan, Shweta
Cohen, Allison
Roux, Simon
Tucker, Kimberly Pause
Shevenell, Amelia
Agbandje-McKenna, Mavis
Breitbart, Mya
author_facet Hopkins, Max
Kailasan, Shweta
Cohen, Allison
Roux, Simon
Tucker, Kimberly Pause
Shevenell, Amelia
Agbandje-McKenna, Mavis
Breitbart, Mya
author_sort Hopkins, Max
collection PubMed
description The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.
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spelling pubmed-41840092014-10-03 Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein Hopkins, Max Kailasan, Shweta Cohen, Allison Roux, Simon Tucker, Kimberly Pause Shevenell, Amelia Agbandje-McKenna, Mavis Breitbart, Mya ISME J Original Article The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles. Nature Publishing Group 2014-10 2014-04-03 /pmc/articles/PMC4184009/ /pubmed/24694711 http://dx.doi.org/10.1038/ismej.2014.43 Text en Copyright © 2014 International Society for Microbial Ecology http://creativecommons.org/licenses/by-nc-sa/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/
spellingShingle Original Article
Hopkins, Max
Kailasan, Shweta
Cohen, Allison
Roux, Simon
Tucker, Kimberly Pause
Shevenell, Amelia
Agbandje-McKenna, Mavis
Breitbart, Mya
Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
title Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
title_full Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
title_fullStr Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
title_full_unstemmed Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
title_short Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
title_sort diversity of environmental single-stranded dna phages revealed by pcr amplification of the partial major capsid protein
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184009/
https://www.ncbi.nlm.nih.gov/pubmed/24694711
http://dx.doi.org/10.1038/ismej.2014.43
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