Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp.

Abstract

A temperate phage (termed AmM-1) was identified from the psychrotolerant Rhizobiales bacterium Aurantimonas sp. C5-1, which was isolated from bathypelagic water (water depth = 1,500 m) in the northwest Pacific. The AmM-1 genome is 47,800 bp in length and contains 67 coding sequences. Although phage AmM-1 morphologically belongs to the family Myoviridae, its genomic structure, particularly modular genome organization, is similar to that of lambda-type phages of Siphoviridae. Genetic and phylogenetic analyses of the structural core genes also revealed that AmM-1 has a mosaic genomic structure that includes a lambda-like head (Siphoviridae) and P2-like tail (Myoviridae). The sequences of the structural core genes of AmM-1 are distinct from those of previously characterized phage groups but similar to those of recently identified one prophage element and one phage of marine Rhizobiales bacteria: a potential prophage element in the marine psychrotolerant Aureimonas ureilytica DSM 18598 genome and the temperate phage RR-1A infecting Rhizobium radiobacter P007 isolated from deep subseafloor sediment. The mosaic genome structure of AmM-1 suggests the occurrence of genetic exchange between distinct temperate phages in marine Rhizobiales populations.

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

“…A similar arrangement has been noted in other Siphoviridae phages [67], such as the well-characterized lambda-like Pseudomonas phage D3 [68], the Burkholderia phage phi644-2 [69], the Antarctic soil Psychrobacter phage Psymv2 [70], the bathyal psychrotolerant alphaproteobacterial phage AmM-1 [29], the deep-sea vent thermophilic phage NrS-1 [30] and several phages that infect low G þ C Gram-positive bacteria [71]. The colors indicate the different functional groups of the gene products as follows: red, integration; purple, restriction-modification system; yellow, auxiliary metabolism; light blue, DNA replication/recombination/regulation; blue, genetic switch; green, DNA packaging; orange, structural protein; pink, cell lysis; and gray, unknown.…”

“…It is known that many tailed phages exhibit a mosaic genomic structure as a result of genetic exchange among the environmental phage pool and their interactions [65]. Indeed, the genomic organization of the deep-sea alphaproteobacterial temperate phage AmM-1 revealed the occurrence of genetic exchange between phages infecting marine Rhizobiales populations [29]. In contrast to AmM-1, the newly identified PstS-1 phage genome displayed characteristics that suggest the occurrence of phage-mediated gene transfer between P. stutzeri and its relatives prior to the early divergence of these lineages, thus indicating that this gene transfer may play an important role in the genetic coevolution of hosts and phages.…”

“…However, phages that infect psychrophilic or psychrotolerant bacteria in deep-sea waters have remained largely unexplored, and at present, only two genomes corresponding to temperate phages are available [29,31]. Among them, the unique genomic properties of the alphaproteobacterial phage AmM-1 suggest the occurrence of genetic exchange between distinct phages and their marine relatives and the potential of gene transfer in deep-sea water habitats [29].…”

“…Although viral ecology in deep-sea ecosystems has been poorly studied and has focused primarily on viral abundance and distribution [e.g., [18e22]], recent metagenomic studies and the isolation of environmental viruses have increasingly been attempted in deep-sea planktonic and benthic environments, including deep waters, hydrothermal areas and subseafloor sediments [e.g., [23e30]]. However, phages that infect psychrophilic or psychrotolerant bacteria in deep-sea waters have remained largely unexplored, and at present, only two genomes corresponding to temperate phages are available [29,31]. Among them, the unique genomic properties of the alphaproteobacterial phage AmM-1 suggest the occurrence of genetic exchange between distinct phages and their marine relatives and the potential of gene transfer in deep-sea water habitats [29].…”

Genomic Comparison of Agrobacterium pusense Strains Isolated from Bean Nodules

“…H41, isolated from eroding rocks (Xi et al, 2014). Plasmid B, which is absent from strain CCGM11, is an intact temperate prophage of about 37 kb, harboring 47 genes, some shared with a prophage present in the circular chromosome of A. tumefaciens C58 and related to phage AmM-1 from Aurantimonas sp., a psychrotolerant bacterium belonging to the order Rhizobiales found in the deep ocean (Goldstein et al, 1982; Yoshida et al, 2015). Some genes assigned to plasmid A had homologs in Rhizobium sp.…”