Identification and genomic analysis of temperate Pseudomonas bacteriophage PstS-1 from the Japan trench at a depth of 7000 m

Yoshida, Mitsuhiro; Yoshida-Takashima, Yukari; Nunoura, Takuro; Takai, Ken

doi:10.1016/j.resmic.2015.05.001

Cited by 13 publications

(8 citation statements)

References 74 publications

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“…Compared to viruses in coastal and estuarine environments, lysogeny seems to be more prevalent in the deep biosphere, as indicated by the presence of high amounts of temperate phages [ 25 ]. Although attempts to isolate phages from deep-sea bacteria have been successful in several cases [ 26 – 28 ], these remain largely unexplored because only a few hosts have been cultivated. To date, our understanding of deep-sea roseobacter phages is limited.…”

Section: Introductionmentioning

confidence: 99%

Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

et al. 2017

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BackgroundMarine phages are spectacularly diverse in nature. Dozens of roseophages infecting members of Roseobacter clade bacteria were isolated and characterized, exhibiting a very high degree of genetic diversity. In the present study, the induction of two temperate bacteriophages, namely, vB_ThpS-P1 and vB_PeaS-P1, was performed in Roseobacter clade bacteria isolated from the deep-sea water, Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014, respectively. Two novel phages in morphological, genomic and proteomic features were presented, and their phylogeny and evolutionary relationships were explored by bioinformatic analysis.ResultsElectron microscopy showed that the morphology of the two phages were similar to that of siphoviruses. Genome sequencing indicated that the two phages were similar in size, organization, and content, thereby suggesting that these shared a common ancestor. Despite the presence of Mu-like phage head genes, the phages are more closely related to Rhodobacter phage RC1 than Mu phages in terms of gene content and sequence similarity. Based on comparative genomic and phylogenetic analysis, we propose a Mu-like head phage group to allow for the inclusion of Mu-like phages and two newly phages. The sequences of the Mu-like head phage group were widespread, occurring in each investigated metagenomes. Furthermore, the horizontal exchange of genetic material within the Mu-like head phage group might have involved a gene that was associated with phage phenotypic characteristics.ConclusionsThis study is the first report on the complete genome sequences of temperate phages that infect deep-sea roseobacters, belonging to the Mu-like head phage group. The Mu-like head phage group might represent a small but ubiquitous fraction of marine viral diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3886-0) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

et al. 2017

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“…A recent study has shown that hadal viruses (mainly bacteriophages) harbor unprecedented genomic novelty and are ecologically important ( Jian et al., 2021 ). Nevertheless, only a single phage, PstS-1, was previously isolated from the abyssal environment (the seawater of the Japan Trench at a depth of 7000 m) ( Yoshida et al., 2015 ). In the present study, we isolated a temperate bacteriophage that infects a Halomonas strain derived from hadal sediment.…”

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confidence: 99%

Isolation and characterization of a novel linear-plasmid phage from the sediment of the Mariana Trench

et al. 2022

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“…(3) Use of CRISPR as a marker to track microbe-virus interactions in the ocean. Strikingly, comparative analysis of CRISPR sequences in prokaryotic genomes and viral genomes enables the identification of host–virus pairs, uncovering new infection relationships, and analyzing virus–host interactions [ 59 , 90 , 104 , 109 , 139 , 140 , 141 , 142 , 143 ]. For instance, thy A gene, a fragment of the cold-active Colwelliaphage 9A, was discovered in the CRISPR sequences of Syntrophus aciditrophicus , suggesting a history of viral infection in the organism [ 113 ].…”

Section: Applications On Marine Prokaryotic Microbesmentioning

confidence: 99%

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Li,

Wu,

Zhang

et al. 2024

Microorganisms

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Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of ‘dark’ genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

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Identification and genomic analysis of temperate Pseudomonas bacteriophage PstS-1 from the Japan trench at a depth of 7000 m

Cited by 13 publications

References 74 publications

Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

Isolation and characterization of a novel linear-plasmid phage from the sediment of the Mariana Trench

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

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