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Widespread yet persistent low abundance of TIM5‐like cyanophages in the oceans
Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundanc...
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| Published in: | Environmental microbiology 2022-12, Vol.24 (12), p.6476-6492 |
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| container_title | Environmental microbiology |
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| creator | Baran, Nava Carlson, Michael C. G. Sabehi, Gazalah Peleg, Margalit Kondratyeva, Kira Pekarski, Irena Lindell, Debbie |
| description | Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundance of the TIM5‐like cyanophages. The sequencing of three new TIM5‐like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid‐phase polymerase chain reaction assay, to quantify TIM5‐like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5‐like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between |
| doi_str_mv | 10.1111/1462-2920.16210 |
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G. ; Sabehi, Gazalah ; Peleg, Margalit ; Kondratyeva, Kira ; Pekarski, Irena ; Lindell, Debbie</creator><creatorcontrib>Baran, Nava ; Carlson, Michael C. G. ; Sabehi, Gazalah ; Peleg, Margalit ; Kondratyeva, Kira ; Pekarski, Irena ; Lindell, Debbie</creatorcontrib><description>Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundance of the TIM5‐like cyanophages. The sequencing of three new TIM5‐like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid‐phase polymerase chain reaction assay, to quantify TIM5‐like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5‐like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml−1. Occasional peaks in abundance of 10‐ to 100‐fold were observed, reaching 71,000 viruses·ml−1. These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. These characteristics of low diversity and abundance, as well as variable outbreaks, distinguishes the TIM5‐like lineage from other major cyanophage lineages and illuminates that rare virus lineages can be persistent and widespread in the oceans.</description><identifier>ISSN: 1462-2912</identifier><identifier>EISSN: 1462-2920</identifier><identifier>DOI: 10.1111/1462-2920.16210</identifier><identifier>PMID: 36116015</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Abundance ; Annual cycles ; Annual variations ; Bacteriophages - genetics ; Conserved sequence ; Ecosystem ; Euphotic zone ; Expeditions ; Genomes ; Indian Ocean ; Marine ecosystems ; Microorganisms ; Multiship expeditions ; Nucleotide sequence ; Oceans ; Oceans and Seas ; PCR ; Phylogeny ; Polymerase chain reaction ; Synechococcus - genetics ; Viruses</subject><ispartof>Environmental microbiology, 2022-12, Vol.24 (12), p.6476-6492</ispartof><rights>2022 The Authors. published by Society for Applied Microbiology and John Wiley & Sons Ltd.</rights><rights>2022 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.</rights><rights>2022. This article is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). 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We adapted the polony method, a solid‐phase polymerase chain reaction assay, to quantify TIM5‐like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5‐like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml−1. Occasional peaks in abundance of 10‐ to 100‐fold were observed, reaching 71,000 viruses·ml−1. These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. 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The sequencing of three new TIM5‐like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid‐phase polymerase chain reaction assay, to quantify TIM5‐like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5‐like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml−1. Occasional peaks in abundance of 10‐ to 100‐fold were observed, reaching 71,000 viruses·ml−1. These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. 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| ispartof | Environmental microbiology, 2022-12, Vol.24 (12), p.6476-6492 |
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| subjects | Abundance Annual cycles Annual variations Bacteriophages - genetics Conserved sequence Ecosystem Euphotic zone Expeditions Genomes Indian Ocean Marine ecosystems Microorganisms Multiship expeditions Nucleotide sequence Oceans Oceans and Seas PCR Phylogeny Polymerase chain reaction Synechococcus - genetics Viruses |
| title | Widespread yet persistent low abundance of TIM5‐like cyanophages in the oceans |
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