Cold‐active bacteriophages from the Baltic Sea ice have diverse genomes and virus–host interactions

Abstract

Heterotrophic bacteria are the major prokaryotic component of the Baltic Sea ice microbiome, and it is postulated that phages are among their major parasites. In this study, we sequenced the complete genomes of six earlier reported phage isolates from the Baltic Sea ice infecting Shewanella sp. and Flavobacterium sp. hosts as well as characterized the phage-host interactions. Based on the genome sequences, the six phages were classified into five new genera. Only two phages, 1/4 and 1/40, both infecting Shewanella sp. strains, showed significant nucleotide sequence similarity to each other and could be grouped into the same genus. These two phages are also related to Vibrio-specific phages sharing approximately 25% of the predicted gene products. Nevertheless, cross-titrations showed that the cold-active phages studied are host specific: none of the seven additionally tested, closely related Shewanella strains served as hosts for the phages. Adsorption experiments of two Shewanella phages, 1/4 and 3/49, conducted at 4 °C and at 15 °C revealed relatively fast adsorption rates that are, for example, comparable with those of phages infective in mesophilic conditions. Despite the small number of Shewanella phages characterized here, we could already find different types of phage-host interactions including a putative abortive infection.

Viruses of microorganisms in the Baltic Sea: current state of research and perspectives

“…These phages were assigned to the viral families Siphoviridae and Myoviridae and showed great specificity to the host strain . Again, like the study of Holmfeldt et al (2013), genomic analysis of six of these bacteriophages showed that they belong to five different and newly proposed genera (Senčilo et al 2014).…”

“…Variability in environmental conditions might also help to explain the high diversity of viruses that infect the same host that have been isolated at different places and/or time points (Holmfeldt et al 2007;Martínez et al 2015). The genome analyses revealed that most of the Baltic Sea viruses are unique and belong to previously unknown genera or even form new families (Attoui et al 2006;Holmfeldt et al 2013;Senčilo et al 2014). Comparative (meta)genomics in parallel with experimental studies can help further elucidation of links between phage specificity, infection strategy (lysis vs. lysogeny) and environmental gradients in the Baltic Sea.…”

Isolation and Complete Genome Sequence of a Novel Pseudoalteromonas Phage PH357 from the Yangtze River Estuary

“…Among the enzymes directly involved in DNA replication, ORF104 encodes a DNA ligase containing Adenylation_kDNA_ligase_like domain (cd07896), shows homology to DNA ligase in Shewanella sp. phage 1/4 (YP_009100328.1) [24]. ORF118 encodes a DNA helicase containing a PIF1 domain (pfam05970), shows [28].…”

“…Putative portal protein encoded by ORF141 with a length of 505 amino acids shows 57% identity with portal protein in Shewanella sp. phage 1/4 (YP_009100417.1) [24]. The portal protein is a key functional component of the capsid for DNA packaging and genome encapsidation [22].…”

“…Most of the structural proteins (ORF176, ORF180, ORF187, and ORF189) were found to share high similarity with structural proteins from Pseudoalteromonas phage PH101 (NC_029094) [26], except for major capsid protein (ORF145), which shows 57% identity with major capsid protein in Shewanella sp. phage 1/4 (YP_009100422.1) [24]. TMP is the only one viral tail protein detected in the genome, it plays an important role in phage tails assembling, and is involved in tail-length determination [14,30].…”