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Genomic diversity and ecological distribution of marine Pseudoalteromonas phages
Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Ps...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Nature Singapore
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232697/ https://www.ncbi.nlm.nih.gov/pubmed/37275543 http://dx.doi.org/10.1007/s42995-022-00160-z |
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author | Zheng, Kaiyang Dong, Yue Liang, Yantao Liu, Yundan Zhang, Xinran Zhang, Wenjing Wang, Ziyue Shao, Hongbing Sung, Yeong Yik Mok, Wen Jye Wong, Li Lian McMinn, Andrew Wang, Min |
author_facet | Zheng, Kaiyang Dong, Yue Liang, Yantao Liu, Yundan Zhang, Xinran Zhang, Wenjing Wang, Ziyue Shao, Hongbing Sung, Yeong Yik Mok, Wen Jye Wong, Li Lian McMinn, Andrew Wang, Min |
author_sort | Zheng, Kaiyang |
collection | PubMed |
description | Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-022-00160-z. |
format | Online Article Text |
id | pubmed-10232697 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Springer Nature Singapore |
record_format | MEDLINE/PubMed |
spelling | pubmed-102326972023-06-02 Genomic diversity and ecological distribution of marine Pseudoalteromonas phages Zheng, Kaiyang Dong, Yue Liang, Yantao Liu, Yundan Zhang, Xinran Zhang, Wenjing Wang, Ziyue Shao, Hongbing Sung, Yeong Yik Mok, Wen Jye Wong, Li Lian McMinn, Andrew Wang, Min Mar Life Sci Technol Research Paper Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-022-00160-z. Springer Nature Singapore 2023-01-20 /pmc/articles/PMC10232697/ /pubmed/37275543 http://dx.doi.org/10.1007/s42995-022-00160-z Text en © The Author(s) 2023, corrected publication 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Paper Zheng, Kaiyang Dong, Yue Liang, Yantao Liu, Yundan Zhang, Xinran Zhang, Wenjing Wang, Ziyue Shao, Hongbing Sung, Yeong Yik Mok, Wen Jye Wong, Li Lian McMinn, Andrew Wang, Min Genomic diversity and ecological distribution of marine Pseudoalteromonas phages |
title | Genomic diversity and ecological distribution of marine Pseudoalteromonas phages |
title_full | Genomic diversity and ecological distribution of marine Pseudoalteromonas phages |
title_fullStr | Genomic diversity and ecological distribution of marine Pseudoalteromonas phages |
title_full_unstemmed | Genomic diversity and ecological distribution of marine Pseudoalteromonas phages |
title_short | Genomic diversity and ecological distribution of marine Pseudoalteromonas phages |
title_sort | genomic diversity and ecological distribution of marine pseudoalteromonas phages |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232697/ https://www.ncbi.nlm.nih.gov/pubmed/37275543 http://dx.doi.org/10.1007/s42995-022-00160-z |
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