Isolation and Characterization of the First Temperate Virus Infecting Psychrobacillus from Marine Sediments

Abstract

Viruses are far more abundant than cellular microorganisms in the marine ecosystem. However, very few viruses have so far been isolated from marine sediments, especially hydrothermal vent sediments, hindering the understanding of the biology and ecological functions of these tiny organisms. Here, we report the isolation and characterization of a temperate bacteriophage, named PVJ1, which infects Psychrobacillus from a hydrothermal vent field in Okinawa Trough. PVJ1 belongs to the Myoviridae family of the order Caudovirales. The tailed phage possesses a 53,187 bp linear dsDNA genome, with 84 ORFs encoding structural proteins, genome replication, host lysis, etc. in a modular pattern. The phage genome is integrated into the host chromosome near the 3′-end of deoD, a gene encoding purine nucleoside phosphorylase (PNP). The phage integration does not appear to disrupt the function of PNP. The phage DNA is packaged by the headful mechanism. Release of PVJ1 from the host cell was drastically enhanced by treatment with mitomycin C. Phages encoding an MCP sharing significant similarity (≥70% identical amino acids) with that of PVJ1 are widespread in diverse environments, including marine and freshwater sediments, soils, artificial ecosystems, and animal intestines, and primarily infect Firmicutes. These results are valuable to the understanding of the lifestyle and host interactions of bacterial viruses at the bottom of the ocean.

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

“…Unlike Ascomycota and Basidiomycota reported in sea sediments of the Antarctic Ocean, in the present samples, Mucormycota was the most common fungal phyla [ 21 ]. The T4 virus of Myoviridae is a bacteriophage and most probably infects the inherent bacterial communities [ 75 , 76 ].…”

Polysaccharides and Their Derivatives as Potential Antiviral Molecules

“…Viruses are considered not only one of the most abundant biological entities on Earth [3] but also one of the major causes of mortality, and, at the same time, they are the driver of genetic diversity on our planet [4]. These parasites can be found everywhere in our surroundings (including in water and soil) and can infect all life forms [5][6][7][8][9][10][11].…”

PVJ1 Is Not the First Tailed Temperate Phage Infecting Bacteria from Genus Psychrobacillus. Comment on Liu et al. Isolation and Characterization of the First Temperate Virus Infecting Psychrobacillus from Marine Sediments. Viruses 2022, 14, 108

“…In a recent study published in Viruses [ 1 ], the authors claim to have isolated and characterized the first tailed temperate phage able to infect a bacterium from the genus Psychrobacillus — Psychrobacillus phage PVJ1 (GenBank accession number: MZ983385). These claims, however, are misleading, as at least two tailed temperate siphophages infecting a Psychrobacillus sp.…”

“…GC2J1 came from marine sediments. However, overall, the phage PVJ1 still remains the third temperate tailed virus infecting a member of this bacterial genus following the temperate Psychrobacillus siphophages Perkons and Spoks, despite the fact the authors claim that “… there were no reports of bacteriophages infecting the genus Psychrobacillus …”, “… PVJ1 is the first bacteriophage isolated from Psychrobacillus ” and “… PVJ1, the first-tailed temperate phage-infecting Psychrobacillus ” within the paper [ 1 ]. Interestingly, although the host of phages Perkons and Spoks was initially classified by us based on 16S rRNA gene near-full-length sequencing as a strain of Psychrobacillus psychrodurans (on the basis of the closest 16S rRNA gene sequence match from cultured bacteria), the genus seems to have expanded shortly after with the addition of species that are more closely related to Psychrobacillus isolate L4— Psychrobacillus vulpis [ 3 ] and Psychrobacillus glaciei [ 4 ]—with the latter being isolated from an Antarctic iceberg and having the closest 16S rRNA gene sequence match to isolate L4 as of now ( Figure 1 ).…”