Isolation and Genome Sequencing of a Novel Pseudoalteromonas Phage PH1

Abstract

The family Pseudoalteromonas is highly adaptable to dissimilar ecological habitats and plays an important ecological role in the marine environment. In this study, a new Pseudoalteromonas phage PH1 was isolated from the Yellow Sea. To better understand the bacteriophage, its biological properties, including morphology, host range, growth phenotype, thermal and pH stability, and nucleic acid composition, were investigated in detail. The result showed that the phage PH1 is a Podoviridae-phage with an icosahedral head (60 nm of diameter) and a short tail (26 nm in length). The phage PH1 genome consists of 42,685 bp length double-stranded DNA with a G+C content of 42.24% and is predicted to have 55 open reading frames (ORFs) with an average length of 740 bp nucleotides each. The phage PH1 genome adds a new Podoviridae-phage genome to marine bacteriophage dataset, which will provide useful basic information for further molecular research on interaction mechanisms between bacteriophages and their hosts.

Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses

“…(Table S3 and S4). Functional annotation of predicted ORFs in the NCBI non-redundant protein database showed that only 72 (29.15%) were assigned to specific functions in S-N03 (E-value < 10 −5 ), while the rest 175 (70.85%) were predicted to encode hypothetical proteins, due to incomplete genomic information of the cyanophage in database [69]. Similarly, 70 (28.46%) predicted ORFs were assigned to specific functions in S-H34, while the rest 176 (71.54%) were predicted to encode hypothetical proteins.…”

A Novel Wide-Range Freshwater Cyanophage MinS1 Infecting the Harmful Cyanobacterium Microcystis aeruginosa

“…Next, 1 µL of the ultra-purified phage (remaining samples could be stored directly at 4 • C) was dropped onto a grid surface, 2% uranyl acetate negative staining was undertaken, and then the excess staining solution was immediately removed. Phage morphology was then examined under a 100 kV transmission electron microscope (Hitachi H-7650, Tokyo, Japan) [18].…”

“…The supernatant was discarded, and the precipitate was washed twice using PBS and then suspended in 30 mL of BG11 medium; this was then incubated in a lighted incubator. Samples were collected at 0, 6,12,18,24,30,36,42,48,54,60,66, and 72 h. All of the 1 mL samples were centrifuged (6000 g, 10 min) and filtered (using 0.45 µm and 0.22 µm filters), and titration was undertaken using the double-layer agar plate method. The burst size was calculated as the ratio of the number of free phages at the end of the logarithmic period to the number of infected host cyanobacteria cells at the beginning of the latent period.…”

“…A total of 75 ORFs of MinS1 were predicted using RAST [18], averaging 203 amino acid (aa) long, the smallest of which had only 24 aa and the largest as many as 1155 aa (Table 3). Contrary to evidence from cyanophage SH-68 (107 positive strands and 10 negative strands), MinS1 had just 5 positive strands but 70 negative strands, but MinS1 had the same coding density (91.8%) as that of M. elabens vB_MelS-Me-ZS1.…”

“…Contrary to evidence from cyanophage SH-68 (107 positive strands and 10 negative strands), MinS1 had just 5 positive strands but 70 negative strands, but MinS1 had the same coding density (91.8%) as that of M. elabens vB_MelS-Me-ZS1. Homology align- A total of 75 ORFs of MinS1 were predicted using RAST [18], averaging 203 amino acid (aa) long, the smallest of which had only 24 aa and the largest as many as 1155 aa (Table 3). Contrary to evidence from cyanophage SH-68 (107 positive strands and 10 negative strands), MinS1 had just 5 positive strands but 70 negative strands, but MinS1 had the same coding density (91.8%) as that of M. elabens vB_MelS-Me-ZS1.…”