Genomic and experimental characterization of unique Antarctic temperate phage Perkons reveals multiple integrases and complex lysogenic dynamics in Psychrobacillus sp. L4

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BACKGROUND: Advances in culture-free microbial research have considerably expanded the known genomic diversity of prokaryotes and viruses associated with any imaginable environment. However, only a tiny fraction of this diversity has been obtained in culture, locking most of it to merely biological sequences of various contiguities, regardless of the environment. Yet, many environments are housing relatively easily culturable biological entities sufficiently distinct from those cultures so far, allowing for a better understanding of at least some of their manifestations and impacts in the said environment by virtue of culture-based studies. Expectedly, undersampled and understudied environments serve as a low-hanging fruit for uncovering novel culturable microbiological entities with exciting biology, given access to the samples. RESULTS: Attempts to culture novel phage-host pairs from ice-free soil samples collected at Waddington Bay, Graham Coast, Antarctica, during the First Latvian Antarctic Expedition have resulted in the recovery of a unique Psychrobacillus siphophage Perkons that infects a Psychrobacillus isolate designated as "L4" originating from the same source material. Results of the whole genome sequencing revealed phage Perkons to be unique in terms of its overall genomic nucleotide sequence similarity, whereas isolate L4 was found to be most closely related to Psychrobacillus glaciei strain PB01 and Psychrobacillus sp. L3 (latter of which originated from the same source material, but was not susceptible to infection by Perkons), yet demonstrated sufficient differences from both. The unexpected presence of several integrase genes in the genome of Perkons has prompted lysogenization experiments of the host strain, revealing site-specific integration into the chromosome of Psychrobacillus sp. L4 resulting in the disruption of an ORF encoding a flotillin-like protein floA. While the temperate nature of phage Perkons hindered replicability of the classical microbiological assays, ddPCR-based investigations have given a hint at the Perkons-L4 interaction dynamics and verified spontaneous Perkons induction from the lysogenized host. CONCLUSIONS: Isolation and characterization of Psychrobacillus sp. L4 and unique temperate bacteriophage Perkons expand the known culturable microbial diversity. Characterization of bacteriophage Perkons presented in this work is expected to provide baseline knowledge of the Perkons-like phages, more of which are anticipated to be uncovered in the future owing to both culture-independent and culture-dependent experimental efforts.

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