Genomic Characterization of a Prophage, Smhb1, That Infects Salinivibrio kushneri BNH Isolated from a Namib Desert Saline Spring.

Israel Olonade,Marla Trindade,Leonardo Joaquim Van Zyl

doi:10.3390/microorganisms9102043

Abstract

Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2. Here, we report the identification of a prophage (Smhb1) that infects Salinivibrio kushneri BNH isolated from a Namib Desert salt pan (playa). Analysis of the genome revealed that it showed the greatest similarity to P2-like phages that infect Vibrio species and showed no relation to any of the previously described Salinivibrio-infecting phages. Despite being distantly related to these Vibrio infecting phages and sharing the same modular gene arrangement as seen in most P2-like viruses, the nucleotide identity to its closest relatives suggest that, for now, Smhb1 is the lone member of the Peduovirus genus Playavirus. Although host range testing was not extensive and no secondary host could be identified for Smhb1, genomic evidence suggests that the phage is capable of infecting other Salinivibrio species, including Salinivibrio proteolyticus DV isolated from the same playa. Taken together, the analysis presented here demonstrates how adaptable the P2 phage model can be.

Highlights

Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2
Fifty milliliters of the microbial mat suspended in spring water from the playa was shaken at 50 rpm for 2 h to encourage the dissociation of bacterial cells from biofilm debris
We further investigated the relation of Smhb1 to other Peduovirinae using VIRIDIC, which showed that, of the viruses on the NCBI virus database, Smhb1 was the most similar to the recently sequenced Vibrio alginolyticus prophage Valm-yong1 (MN56393)

Summary

Introduction

Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2. Host range testing was not extensive and no secondary host could be identified for Smhb, genomic evidence suggests that the phage is capable of infecting other Salinivibrio species, including Salinivibrio proteolyticus DV isolated from the same playa. The range of interactions phages can have with their hosts suggests that they can play an important role in shaping microbial diversity and ecology [6,7,8] Such roles include significant contributions to nutrient cycling in the ocean by being major predators of bacteria and archaea [9] and as major contributors to genetic exchange in the environment with phages estimated to transduce 1025 to 1028 base pairs of DNA per year in the marine environment alone [10]. The impact phages can have on trophic levels was demonstrated in the East African Rift Valley lakes where a short food chain, involving cyanophages, the cyanobacterium Arthrospira fusiformis, and the Lesser

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Results

Conclusion