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

Abstract

Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.

Keywords: Biogeographic analysis; Fuevirus; Genomic and phylogenetic analysis; Stutzerimonas stutzeri; Vb_psts_zqg1.

Fig. 1

Morphology and biological properties of phage vB_PstS_ZQG1. (A) Transmission electron microscopy (TEM) morphology of phage vB_PstS_ZQG1. Scale bar, 100nm. (B) The curve of pH stability of vB_PstS_ZQG1. (C) The curve of thermal stability of vB_PstS_ZQG1.

Fig. 2

Genome map of phage vB_PstS_ZQG1. Putative functional categories were classified into five parts according to annotation and are represented by different colors. The length of each arrow represents the length of each gene.

Fig. 3

Phylogenetic and comparative genomic analysis of phage vB_PstS_ZQG1. (A) Phylogenetic tree of two isolated S. stutzeri phages and vB_PstS_ZQG1 by ViPTree. The red star is vB_PstS_ZQG1, yellow stars are other two S. stutzeri phages. (B) Phylogenetic tree of phage vB_PstS_ZQG1 and the 20 closest virus genomes, and the heatmap showing the percentage of shared genes among 20 genome sequences. The ratio of shared genes was based on all-vs-all BLASTp analysis using OrthoFinder with E-value < 1e-10. (C) Genomic comparisons between phage vB_PstS_ZQG1 and four closely related viruses in the phylogenetic tree.

Fig. 4

(A) Gene content-based viral network of phage vB_PstS_ZQG1 with related isolated viruses from NCBI virus database and related UViGs from IMG/VR dataset. The nodes represent the viral genomic sequences. The edges represent the hosts. The isolated viral sequences are indicated by filled circles, and UViGs are indicated by regular hexagons. Among those, the star represents phage vB_PstS_ZQG1. (B) Phylogenetic tree of phage vB_PstS_ZQG1 and other related viruses. The members in VC 23_3 are shown in red. (C) The heat map shows nucleotide-based intergenomic similarities of the phage vB_PstS_ZQG1 and other 13 related phages in VC 23_3 calculated by VIRIDIC. These values represent Average Nucleotide Identity (ANI) of each genome pair.

Fig. 5

The heat map shows AAI (A) and shared genes (B) among phage vB_PstS_ZQG1 and other 13 related phages in VC 23_3. The ratio of AAI was calculated using an AAI calculator. The ratio of shared genes was based on all-vs-all BLASTp analysis using OrthoFinder with E-value < 1e-10. (C) Phylogenetic analysis of the vB_PstS_ZQG1 TerL domain. The maximum-likelihood tree was constructed based on TerL domain sequences using IQtree according to the results of vConTACT. Shading indicates the four TerL domains. The colored rings represent the viral families (inner ring) and length (outer ring), respectively. The shape of nodes of the circle represents uncultured viral genomes from the IMG/VR database, the rectangle represents the isolated phages, and the star represents the phage vB_PstS_ZQG1.

Fig. 6

The relative abundance of phage vB_PstS_ZQG1 in 154 viromes of the Global Ocean Viromes (GOV 2.0) data set. The relative abundance is calculated by CoverM and express by RPKM (reads per kilobase per million mapped reads). Values are normalized based on the number of databases of each viral ecological zone (VEZ) for the right bar chart, and the results are log10 transformed for the left heatmap. ARC, Arctic; ANT, Antarctic; BATHY, bathypelagic; EPI, temperate and tropical epipelagic; MES, temperate and tropical mesopelagic.