A Novel Broad Host Range Phage Infecting Alteromonas

Abstract

Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin-endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage-host interactions and ecological importance of alterophages.

Keywords: Alteromonas; Autographiviridae; host range; phage.

Figure 1

Biological characteristics of the alterophage vB_AmeP-R8W (R8W). (a) Image of plaques 24 h after infection. (b) TEM of the podovirus alterophage R8W. (c) One-step growth curve of R8W in the host, Alteromonas mediterranea strain DE. Error bars indicate standard deviation.

Figure 2

(a) Genome organization and comparison of the phage R8W to vB_AspP-H4/4 (H4) (GenBank accession no. MF278336) and prokaryotic dsDNA virus TS (GenBank accession no. MK892710, isolated from the Tara Oceans expedition Tp1_25_SUR_0-0d2_C3569776_1). Arrows indicate the direction of transcription of each gene. Each color indicates a putative function. The color gradients represent the amino acid sequence identity obtained from BLASTP matching. (b) The network diagram shows the similarity between three phage genomes. The nodes represent genes, and the other end is a phage connected by lines. Genes from different phages that are in the same loop indicate that the similarity between the two genes is greater than 70%.

Figure 3

(a) Phylogenetic analysis of thymidylate synthase amino acid sequences of 22 Alteromonas and 14 phages. (b) Phylogenetic analysis of TerL amino acid sequences of 60 phages. (c) The genome-wide tree based on the average nucleotide identity (ANI) from 10 phages. Numbers at the nodes indicate bootstrap values (1000 replications and values >50%).

Figure 4

The predicted structures of putative receptor binding proteins in vB_AmeP-R8W (R8W). (a) Gp45, putative long tail fibers. (b) Gp34, putative short tail fibers. N-terminal is colored blue, and C-terminal is colored red. The C-score of two proterins are −1.85 and −0.86, respectively.

Figure 5

(a) Genome BLAST distance phylogeny (GBDP) tree of 57 virus genomes. Based on nucleotide sequences, the GBDP tree is reconstructed by VICTOR, which used the D6 formula and yielded an average support of 71%. Numbers at the nodes are GBDP pseudo-bootstrap values (100 replications and values >50%). (b) ICTV and OPTSIL clusters at the genus and family levels. Each genus is indicated by a unique shape and color. Background colors indicate the 8 OPTSIL clusters at the family level. (c) G + C content and genome sizes.