Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage

ABSTRACT Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages...

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Autores principales:	Zefeng Zhang, Feng Chen, Xiao Chu, Hao Zhang, Haiwei Luo, Fang Qin, Zhiqiang Zhai, Mingyu Yang, Jing Sun, Yanlin Zhao
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Roseobacter RCA lineage RCA phages viromics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/15d14ade1417467b8debfdfa2ff67ac2
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spelling	oai:doaj.org-article:15d14ade1417467b8debfdfa2ff67ac22021-12-02T18:39:15ZDiverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage10.1128/mSystems.00494-192379-5077https://doaj.org/article/15d14ade1417467b8debfdfa2ff67ac22019-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00494-19https://doaj.org/toc/2379-5077ABSTRACT Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of marine bacteria. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2, and CRP-3) show similar genomic content and architecture as SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology among CRP-1, CRP-2, CRP-3, and HMO-2011 resulted in the contribution of RCA phages to the dominance of the HMO-2011-type group. CRP-4 and CRP-5 are similar to the Cobavirus group roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and represent two new phage groups. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean than most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages and suggests the critical need for isolating phages from the abundant but “unculturable” bacteria. IMPORTANCE The RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups. Two of the four RCA phage groups were found closely related to previously reported SAR116 phage HMO-2011 and Cobavirus group roseophages, respectively. The remaining two groups are novel in the genome contents. Our study also revealed that RCA phages are widely distributed and exhibit high abundance in marine viromic data sets. Altogether, our findings have greatly broadened our understanding of RCA phages and emphasize the ecological and evolutionary importance of RCA phages in the marine virosphere.Zefeng ZhangFeng ChenXiao ChuHao ZhangHaiwei LuoFang QinZhiqiang ZhaiMingyu YangJing SunYanlin ZhaoAmerican Society for MicrobiologyarticleRoseobacterRCA lineageRCA phagesviromicsMicrobiologyQR1-502ENmSystems, Vol 4, Iss 6 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Roseobacter RCA lineage RCA phages viromics Microbiology QR1-502
spellingShingle	Roseobacter RCA lineage RCA phages viromics Microbiology QR1-502 Zefeng Zhang Feng Chen Xiao Chu Hao Zhang Haiwei Luo Fang Qin Zhiqiang Zhai Mingyu Yang Jing Sun Yanlin Zhao Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage
description	ABSTRACT Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of marine bacteria. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2, and CRP-3) show similar genomic content and architecture as SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology among CRP-1, CRP-2, CRP-3, and HMO-2011 resulted in the contribution of RCA phages to the dominance of the HMO-2011-type group. CRP-4 and CRP-5 are similar to the Cobavirus group roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and represent two new phage groups. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean than most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages and suggests the critical need for isolating phages from the abundant but “unculturable” bacteria. IMPORTANCE The RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups. Two of the four RCA phage groups were found closely related to previously reported SAR116 phage HMO-2011 and Cobavirus group roseophages, respectively. The remaining two groups are novel in the genome contents. Our study also revealed that RCA phages are widely distributed and exhibit high abundance in marine viromic data sets. Altogether, our findings have greatly broadened our understanding of RCA phages and emphasize the ecological and evolutionary importance of RCA phages in the marine virosphere.
format	article
author	Zefeng Zhang Feng Chen Xiao Chu Hao Zhang Haiwei Luo Fang Qin Zhiqiang Zhai Mingyu Yang Jing Sun Yanlin Zhao
author_facet	Zefeng Zhang Feng Chen Xiao Chu Hao Zhang Haiwei Luo Fang Qin Zhiqiang Zhai Mingyu Yang Jing Sun Yanlin Zhao
author_sort	Zefeng Zhang
title	Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage
title_short	Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage
title_full	Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage
title_fullStr	Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage
title_full_unstemmed	Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage
title_sort	diverse, abundant, and novel viruses infecting the marine <italic toggle="yes">roseobacter</italic> rca lineage
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/15d14ade1417467b8debfdfa2ff67ac2
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Diverse, Abundant, and Novel Viruses Infecting the Marine <italic toggle="yes">Roseobacter</italic> RCA Lineage

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