Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

ABSTRACT Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage)...

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Autores principales:	Lin-Xing Chen, Yanlin Zhao, Katherine D. McMahon, Jiro F. Mori, Gerdhard L. Jessen, Tara Colenbrander Nelson, Lesley A. Warren, Jillian F. Banfield
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	SAR11 LD12 Fonsibacter freshwater phage Pelagiphage genome-resolved metagenomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1cfbd2f61965420292b00d5d506da909
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spelling	oai:doaj.org-article:1cfbd2f61965420292b00d5d506da9092021-12-02T19:46:17ZWide Distribution of Phage That Infect Freshwater SAR11 Bacteria10.1128/mSystems.00410-192379-5077https://doaj.org/article/1cfbd2f61965420292b00d5d506da9092019-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00410-19https://doaj.org/toc/2379-5077ABSTRACT Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter. A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria. IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.Lin-Xing ChenYanlin ZhaoKatherine D. McMahonJiro F. MoriGerdhard L. JessenTara Colenbrander NelsonLesley A. WarrenJillian F. BanfieldAmerican Society for MicrobiologyarticleSAR11LD12Fonsibacterfreshwater phagePelagiphagegenome-resolved metagenomicsMicrobiologyQR1-502ENmSystems, Vol 4, Iss 5 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	SAR11 LD12 Fonsibacter freshwater phage Pelagiphage genome-resolved metagenomics Microbiology QR1-502
spellingShingle	SAR11 LD12 Fonsibacter freshwater phage Pelagiphage genome-resolved metagenomics Microbiology QR1-502 Lin-Xing Chen Yanlin Zhao Katherine D. McMahon Jiro F. Mori Gerdhard L. Jessen Tara Colenbrander Nelson Lesley A. Warren Jillian F. Banfield Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria
description	ABSTRACT Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter. A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria. IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.
format	article
author	Lin-Xing Chen Yanlin Zhao Katherine D. McMahon Jiro F. Mori Gerdhard L. Jessen Tara Colenbrander Nelson Lesley A. Warren Jillian F. Banfield
author_facet	Lin-Xing Chen Yanlin Zhao Katherine D. McMahon Jiro F. Mori Gerdhard L. Jessen Tara Colenbrander Nelson Lesley A. Warren Jillian F. Banfield
author_sort	Lin-Xing Chen
title	Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria
title_short	Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria
title_full	Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria
title_fullStr	Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria
title_full_unstemmed	Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria
title_sort	wide distribution of phage that infect freshwater sar11 bacteria
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/1cfbd2f61965420292b00d5d506da909
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Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

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