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) 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 providemore »
- Authors:
-
[1];
[8];
- Univ. of California, Berkeley, CA (United States)
- Fujian Agriculture and Forestry Univ. (China)
- Univ. of Wisconsin, Madison, WI (United States)
- Univ. of Toronto, ON (Canada); Yokohama City Univ. (Japan)
- Univ. of Toronto, ON (Canada); Univ. Austral de Chile, Valdivia (Chile)
- Univ. of Toronto, ON (Canada)
- Univ. of Toronto, ON (Canada); McMaster Univ., Hamilton, ON (Canada)
- Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chan Zuckerberg Biohub, San Francisco, CA (United States); Innovative Genomics Institute at UC Berkeley, CA (United States); Univ. of Melbourne (Australia)
- Univ. of Hawaii at Manoa, Honolulu, HI (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); Genome Canada Large Scale Applied Research; Ontario Fund-Research Excellence; NSERC Canada and Syncrude Canada
- OSTI Identifier:
- 1581379
- Grant/Contract Number:
- AC02-05CH11231; CRDPJ 403361-10
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mSystems
- Additional Journal Information:
- Journal Volume: 4; Journal Issue: 5; Journal ID: ISSN 2379-5077
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; SAR11; LD12; Fonsibacter; freshwater phage; Pelagiphage; genome-resolved metagenomics
Citation Formats
Chen, Lin-Xing, Zhao, Yanlin, McMahon, Katherine D., Mori, Jiro F., Jessen, Gerdhard L., Nelson, Tara Colenbrander, Warren, Lesley A., Banfield, Jillian F., and Rappe, Michael S. Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria. United States: N. p., 2019.
Web. doi:10.1128/mSystems.00410-19.
Chen, Lin-Xing, Zhao, Yanlin, McMahon, Katherine D., Mori, Jiro F., Jessen, Gerdhard L., Nelson, Tara Colenbrander, Warren, Lesley A., Banfield, Jillian F., & Rappe, Michael S. Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria. United States. https://doi.org/10.1128/mSystems.00410-19
Chen, Lin-Xing, Zhao, Yanlin, McMahon, Katherine D., Mori, Jiro F., Jessen, Gerdhard L., Nelson, Tara Colenbrander, Warren, Lesley A., Banfield, Jillian F., and Rappe, Michael S. Tue .
"Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria". United States. https://doi.org/10.1128/mSystems.00410-19. https://www.osti.gov/servlets/purl/1581379.
@article{osti_1581379,
title = {Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria},
author = {Chen, Lin-Xing and Zhao, Yanlin and McMahon, Katherine D. and Mori, Jiro F. and Jessen, Gerdhard L. and Nelson, Tara Colenbrander and Warren, Lesley A. and Banfield, Jillian F. and Rappe, Michael S.},
abstractNote = {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. 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.},
doi = {10.1128/mSystems.00410-19},
journal = {mSystems},
number = 5,
volume = 4,
place = {United States},
year = {Tue Oct 22 00:00:00 EDT 2019},
month = {Tue Oct 22 00:00:00 EDT 2019}
}
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