Genomic diversity and ecological distribution of marine Pseudoalteromonas phages.

IF 5.8 2区生物学 Q1 MARINE & FRESHWATER BIOLOGY

Marine Life Science & Technology Pub Date : 2023-01-20 eCollection Date: 2023-05-01 DOI:10.1007/s42995-022-00160-z

Kaiyang Zheng, Yue Dong, Yantao Liang, Yundan Liu, Xinran Zhang, Wenjing Zhang, Ziyue Wang, Hongbing Shao, Yeong Yik Sung, Wen Jye Mok, Li Lian Wong, Andrew McMinn, Min Wang

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引用次数: 3

Abstract

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.

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海洋拟交替单胞菌噬菌体的基因组多样性和生态分布。

假交替单胞菌属是数量最多的海洋细菌属之一，分布广泛。它在深海和极地海洋中特别丰富，在那里它被发现具有广泛的代谢能力和与其他生物独特的共存策略。然而，到目前为止，只有少数假交替单胞菌噬菌体被分离和研究，其基因组多样性和分布模式仍不清楚。在此，基于微生物和病毒基因组以及宏基因组数据集，系统分析了拟交替单胞菌噬菌体的基因组、分类特征和分布模式。共鉴定出143个完整或接近完整的假交替单胞菌相关噬菌体基因组（PSAPGs），包括34个假交替单孢菌噬菌体分离株、24个前病毒和85个假交替双胞菌相关未培养病毒基因组（UViGs）；这些病毒在属水平上被分配到47个病毒簇。许多整合前病毒（n = 24），并检测到丝状噬菌体（n = 32），表明假交替单胞菌中存在病毒溶原性生命周期。PSAPGs编码66种类型的249个与肽酶和核苷酸代谢有关的潜在辅助代谢基因（AMG）。它们还可能通过操纵宿主的新陈代谢参与海洋生物地球化学循环，特别是磷和硫循环。细胞病毒和丝状PSAPG是在极地发现的主要病毒谱系，而一些编码转座酶的肌肉病毒和细胞病毒PSAPG在深海中更丰富。这项研究扩大了我们对海洋拟交替单胞菌噬菌体的分类学、系统发育和生态范围的理解，加深了我们对病毒对拟交替单孢菌影响的了解。它将为研究海洋中噬菌体和假交替单胞菌之间的相互作用提供一个基线。补充信息：在线版本包含补充材料，请访问10.1007/s42995-022-00160-z。

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来源期刊

Marine Life Science & Technology MARINE & FRESHWATER BIOLOGY-

CiteScore

9.60

自引率

10.50%

发文量

期刊介绍： Marine Life Science & Technology (MLST), established in 2019, is dedicated to publishing original research papers that unveil new discoveries and theories spanning a wide spectrum of life sciences and technologies. This includes fundamental biology, fisheries science and technology, medicinal bioresources, food science, biotechnology, ecology, and environmental biology, with a particular focus on marine habitats. The journal is committed to nurturing synergistic interactions among these diverse disciplines, striving to advance multidisciplinary approaches within the scientific field. It caters to a readership comprising biological scientists, aquaculture researchers, marine technologists, biological oceanographers, and ecologists.