Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine

Abstract

Bacteria of the genus Serratia inhabit a variety of ecological niches like water, soil, and the bodies of animals, and have a wide range of lifestyles. Currently, the complete genome sequences of 25 Serratia phages are available in the NCBI database. All of them were isolated from nutrient-rich environments like sewage, with the use of clinical Serratia strains as hosts. In this study, we identified a novel Serratia myovirus named vB_SspM_BZS1. Both the phage and its host Serratia sp. OS31 were isolated from the same oligotrophic environment, namely, an abandoned gold mine (Zloty Stok, Poland). The BZS1 phage was thoroughly characterized here in terms of its genomics, morphology, and infection kinetics. We also demonstrated that Serratia sp. OS31 was lysogenized by mitomycin-inducible siphovirus vB_SspS_OS31. Comparative analyses revealed that vB_SspM_BZS1 and vB_SspS_OS31 were remote from the known Serratia phages. Moreover, vB_SspM_BZS1 was only distantly related to other viruses. However, we discovered similar prophage sequences in genomes of various bacteria here. Additionally, a protein-based similarity network showed a high diversity of Serratia phages in general, as they were scattered across nineteen different clusters. In summary, this work broadened our knowledge on the diverse relationships of Serratia phages.

Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of Shewanella sp. M16 Provides Insights into the Genetic Diversity of the Shewanella Virome

“…The virus was sensitive to temperatures ≥ 40 • C, with an immediate loss of infectivity at 50 • C (Figure 5). A similarly limited tolerance to higher temperatures was previously demonstrated for the temperate Serratia phage BZS1 isolated from the same environment, but from rock biofilms [16]. However, the stable low temperature in this gold mine (10-11 • C) [9,10] is probably sufficient for the propagation and survival of these viruses.…”

“…(MBQ3883869.1) and Snodgrassella alvi (RZA00671.1), with 34% sequence identity (Figure S4). By following a previously described procedure [16], we confirmed that GATC sequences are, in fact, substrates for the KASIA_p114 modification protein (Figure S5). Bacterial Dam-like MTases are responsible for a variety of functional roles, including the regulation of DNA replication and segregation, mismatch repair, and the con-trol of gene expression [62].…”

“…O23S [15], vB_SspS_OS31 of Serratia sp. OS31, and the Serratia phage vB_SspM_BZS1 [16]. In the present study, we report on the isolation and characterization of the first virulent phage originating from the microbial mats of the Zloty Stok gold and arsenic mine, i.e., the vB_SspS_KASIA phage, which was obtained using the indigenous bacteria Shewanella sp.…”

“…The TEM analysis was conducted as described previously [16]. The visualization of the phages was performed at the Core Facility of the International Institute of Molecular and Cell Biology (IIMCB, Warsaw, Poland).…”

“…The SDS-PAGE and mass spectrometry protein analysis were conducted as described previously [16]. The mass spectrometry analysis was performed in the Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences (IBB PAS) (Warsaw, Poland).…”