First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

Lingting Pan; Dengfeng Li; Zhitong Sun; Wei Lin; Binxin Hong; Weinan Qin; Lihua Xu; Wencai Liu; Qin Zhou; Fei Wang; Ruqian Cai; Minhua Qian; Yigang Tong

doi:10.3389/fmicb.2021.754331

First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

Front Microbiol. 2022 Feb 8:12:754331. doi: 10.3389/fmicb.2021.754331. eCollection 2021.

Authors

Lingting Pan^{1

2}, Dengfeng Li¹, Zhitong Sun¹, Wei Lin^{1

2}, Binxin Hong¹, Weinan Qin¹, Lihua Xu¹, Wencai Liu¹, Qin Zhou¹, Fei Wang¹, Ruqian Cai¹, Minhua Qian¹, Yigang Tong²

Affiliations

¹ Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.
² College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.

Abstract

A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35-45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.

Keywords: HNH homing endonuclease; Hafnia phage; big burst size; genome; polymorphism.