Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

ABSTRACT The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of m...

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Autores principales:	Asier Zaragoza-Solas, Francisco Rodriguez-Valera, Mario López-Pérez
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Fonsibacter pelagiphages SAR11 genome-resolved metagenomics myophages Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/689aff9d9069488a8f22ecb01f939891
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spelling	oai:doaj.org-article:689aff9d9069488a8f22ecb01f9398912021-12-02T18:39:46ZMetagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments10.1128/mSystems.00905-192379-5077https://doaj.org/article/689aff9d9069488a8f22ecb01f9398912020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00905-19https://doaj.org/toc/2379-5077ABSTRACT The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear. IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.Asier Zaragoza-SolasFrancisco Rodriguez-ValeraMario López-PérezAmerican Society for MicrobiologyarticleFonsibacterpelagiphagesSAR11genome-resolved metagenomicsmyophagesMicrobiologyQR1-502ENmSystems, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Fonsibacter pelagiphages SAR11 genome-resolved metagenomics myophages Microbiology QR1-502
spellingShingle	Fonsibacter pelagiphages SAR11 genome-resolved metagenomics myophages Microbiology QR1-502 Asier Zaragoza-Solas Francisco Rodriguez-Valera Mario López-Pérez Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments
description	ABSTRACT The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear. IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.
format	article
author	Asier Zaragoza-Solas Francisco Rodriguez-Valera Mario López-Pérez
author_facet	Asier Zaragoza-Solas Francisco Rodriguez-Valera Mario López-Pérez
author_sort	Asier Zaragoza-Solas
title	Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments
title_short	Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments
title_full	Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments
title_fullStr	Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments
title_full_unstemmed	Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments
title_sort	metagenome mining reveals hidden genomic diversity of pelagimyophages in aquatic environments
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/689aff9d9069488a8f22ecb01f939891
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Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

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