Isolation and genomic characterization of Psychrobacillus isolate L3 and bacteriophage Spoks: a new phage-host pair...

Most habitats on Earth house unfathomable microbial diversity, yet much of it remains uncultured. The same applies to temperate phages, most of which documented to date are predicted purely in silico from the prophage-like genomic regions of the bacteria, lacking any experimental evidence of their functional integrity (e.g., the ability to undergo lytic replication). Hard-to-access parts of our planet with unique environments serve as especially promising places to collect samples for the isolation of novel microbes highly divergent from those isolated thus far. Antarctica, a continent mostly covered by a thick ice sheet, is one such area of our planet rife with novel microbiological entities. In this study, we aimed to isolate and characterize a novel culturable phage-host pair from Antarctic soils.

Psychrobacillus phage Spoks was retrieved alongside its host bacterial strain designated as "L3" from an ice-free soil sample collected at Waddington Bay, Graham Coast, Antarctica. Whole-genome sequencing of both the phage and the host revealed that they are divergent from, respectively, viruses and bacteria cultured and characterized thus far, and the intergenomic differences suggest that both might represent novel taxa. The genome of siphophage Spoks is a 36,472 bp long linear double-stranded DNA molecule with 11 base long 3' cohesive overhangs. Spoks can integrate into the chromosome of its isolation host strain in a site-specific fashion. Integration takes place in the genomic region of the host chromosome between the ORFs predicted to encode a DNA topoisomerase III and a BlaI/MecI/CopY family transcriptional regulator via recombination between attP and attB, which share a 19 bp "core" overlap sequence. L3 lysogens containing Spoks are not stable, with regular spontaneous induction occurring. Although the attachment site overlap sequence was found in the publicly available genomic sequences of several other Psychrobacillus spp. strains isolated from different habitats, none were found to contain a Spoks-like prophage.

The isolation and characterization of Psychrobacillus temperate phage Spoks and its host strain L3 from Antarctica highlight the potential for discovering novel biological entities divergent from their closest cultured relatives with relative ease, given access to such difficult-to-access undersampled environments, and are expected to encourage similar studies.