A Novel Phage Infecting the Marine Photoheterotrophic Bacterium Citromicrobium bathyomarinum.

Ruijie Ma,Shuzhen Wei,Rui Zhang,Yahui Yang,Nianzhi Jiao,Shuai Shao,Junlei Ye

doi:10.3390/v14030512

Abstract

This study isolated and characterized a new phage infecting the marine photoheterotrophic bacterium Citromicrobium bathyomarinum, which fills the gap in research on phages targeting this ecologically important species. The phage vB_CbaS-RXM (RXM) has a dsDNA genome with a length of 104,206 bp and G+C content of 61.64%. The taxonomic analysis found a close evolutionary relationship between RXM, Erythrobacter phage vB_EliS-L02, and Sphingobium phage Lacusarx, and we propose that RXM represents a new species of the Lacusarxvirus genus. A one-step growth curve revealed a burst size of 75 plaque-forming units (PFUs) per cell in a 3-hour infection cycle. The lysis profile of RXM showed an intraspecific lethal rate of 26.3% against 38 citromicrobial strains. RXM contains 15 auxiliary metabolic genes (AMGs) related to diverse cellular processes, such as putative metabolic innovation and hijacking of host nucleotide metabolism to enhance its biosynthetic capacity. An in-depth analysis showed that phage functional genes strongly rely on the host for translation, while the translation of unique phage genes with less host dependency may be complemented by phage tRNA. Overall, our study investigated the infection kinetics, genetic traits, taxonomy, and predicted roles of AMGs and tRNA genes of this new phage, which contributes to a better understanding of phage diversity and phage–bacterium interactions.

Highlights

IntroductionAs the most abundant organisms in the ocean, marine viruses have attracted extensive attention
We isolated a new phage, RXM, from sewage collected at a seafood market in Zhangzhou city, China (23.70◦ N, 117.43◦ E)
Transmission Electron Microscopy (TEM) inspection revealed that RXM displays a unique Siphoviridae B3 morphotype [25], with a prolate capsid (111.50 ± 1.48 nm long and 56.02 ± 3.06 nm wide) and a long flexible tail (220.57 ± 3.88 nm long)

Summary

Introduction

As the most abundant organisms in the ocean, marine viruses have attracted extensive attention. Virus-mediated lysis is considered important in the mortality of organisms and cycles of biogenic elements in marine ecosystems [1]. Despite progress in high-throughput techniques, the isolation and characterization of new viruses are still an important method to continually decode viral dark matter from metagenomic data and understand novel information on specific virus–host interactions. Citromicrobium bathyomarinum is a Gram-negative marine species in the family Sphingomonadaceae and the class Alphaproteobacteria. As it benefits from its good adaptability to dynamic environmental conditions [2], the species has been commonly found from various depths in seawater [3,4]. C. bathyomarinum is an aerobic anoxygenic photoheterotroph that plays an important role in oceanic carbon cycling and energy flow [5]

Methods

Results

Conclusion