Characterization and Genomic Analysis of the First Podophage Infecting Shewanella, Representing a Novel Viral Cluster

Abstract

Shewanella is a common bacterial genus in marine sediments and deep seas, with a variety of metabolic abilities, suggesting its important roles in the marine biogeochemical cycles. In this study, a novel lytic Shewanella phage, vB_SInP-X14, was isolated from the surface coastal waters of Qingdao, China. The vB_SInP-X14 contains a linear, double-strand 36,396-bp with the G + C content of 44.1% and harbors 40 predicted open reading frames. Morphological, growth, and genomic analysis showed that it is the first isolated podovirus infecting Shewanella, with a short propagation time (40 min), which might be resulted from three lytic-related genes. Phylogenetic analysis suggested that vB_SInP-X14 could represent a novel viral genus, named Bocovirus, with four isolated but not classified phages. In addition, 14 uncultured viral genomes assembled from the marine metagenomes could provide additional support to establish this novel viral genus. This study reports the first podovirus infecting Shewanella, establishes a new interaction system for the study of virus–host interactions, and also provides new reference genomes for the marine viral metagenomic analysis.

Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus

“…At the same time, a whole-genome-based phylogenetic tree was constructed with vB_PstS_ZQG1 and its homologous sequences by VICTOR, which was an effective tool for viral classification ( Dong et al., 2022 ). Based on whole-genome phylogeny and OPTSIL taxon results, it was determined that vB_PstS_ZQG1 and the other 13 viruses cannot be classified into the same genus.…”

Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m

“…At the same time, all of the protein sequences of vB_HmeY_H4907 were queried against the whole IMG/VR protein database using BLASTp with an E -value of 1 × 10 −5 to recruit as many homologous sequences as possible. Finally, 10 uncultivated viral genomes that had at least 22 proteins (40% of the ORFs) that were homologous with vB_HmeY_H4907 were selected ( 60 , 61 ).…”

Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus

“…The genome completeness assessment of vB_PstM_ZRG1 used CheckV ( Nayfach et al., 2021 ). ORF functions were annotated by several pathways, including BLASTp against the Non-redundant protein sequences (nr) database of the GenBank ( https://blast.ncbi.nlm.nih.gov/ ) and searching for the conserved domain in the Pfam database ( http://pfam-legacy.xfam.org/ ) ( Dong et al., 2022 ; Guo et al., 2022 ; Wang et al., 2021 ). The GC skew analysis was performed using Genskew ( https://genskew.csb.univie.ac.at/webskew ) ( Lu and Salzberg, 2020 ).…”