Characterization and genomic analysis of a novel halovirus infecting Chromohalobacter beijerinckii

Abstract

Bacteriophages function as a regulator of host communities and metabolism. Many phages have been isolated and sequenced in environments such as the ocean, but very little is known about hypersaline environments. Phages infecting members of the genus Chromohalobacter remain poorly understood, and no Chromohalobacter phage genome has been reported. In this study, a halovirus infecting Chromohalobacter sp. F3, YPCBV-1, was isolated from Yipinglang salt mine. YPCBV-1 could only infect host strain F3 with burst size of 6.3 PFU/cell. It could produce progeny in 5%–20% (w/v) NaCl with an optimal concentration of 10% (w/v), but the optimal adsorption NaCl concentration was 5%–8% (w/v). YPCBV-1 is sensitive to pure water and depends on NaCl or KCl solutions to survive. YPCBV-1 stability increased with increasing salinity but decreased in NaCl saturated solutions, and it has a broader salinity adaptation than the host. YPCBV-1 has a double-stranded DNA of 36,002 bp with a G + C content of 67.09% and contains a total of 55 predicted ORFs and no tRNA genes. Phylogenetic analysis and genomic network analysis suggested that YPCBV-1 is a novel Mu-like phage under the class Caudoviricetes. Auxiliary metabolic gene, SUMF1/EgtB/PvdO family non-heme iron enzyme, with possible roles in antioxidant was found in YPCBV-1. Moreover, DGR-associated genes were predicted in YPCBV-1 genome, which potentially produce hypervariable phage tail fiber. These findings shed light on the halovirus-host interaction in hypersaline environments.

Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae

“…A droplet of phage suspension (10 9 PFU/ml) was applied onto a carbon-coated copper grid for 10 min. The grids were negatively stained with 2% (w/v) phosphotungstic acid (pH 6.8) for 5 min, air-dried, then observed with an HT7800 transmission electron microscope (HITACHI, Tokyo, Japan) at an accelerating voltage of 100 kV ( Yi et al, 2022 ).…”

Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster

“…The phage DNA was extracted using a TIANamp Virus DNA/RNA Kit (TIANGEN, Beijing, China) according to the manufacturer’s instructions. The DNA library was constructed as previously described [ 27 ] and was sent to Sangon Bioengineering Co., Ltd., for sequencing using Illumina HiSeq. After sequencing, the original data were evaluated and quality controlled.…”

“…Over 100 haloviruses have been isolated to date, most of which infect extreme halophilic archaea. Among these 100 haloviruses, only ~30 phages infect halophilic bacteria [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 ]. Currently, the research on culturable bacterial haloviruses mainly focuses on their morphological, physiological, and biochemical characteristics; research on the viral genome is still relatively scarce.…”

“…Currently, the research on culturable bacterial haloviruses mainly focuses on their morphological, physiological, and biochemical characteristics; research on the viral genome is still relatively scarce. Due to the small number of isolates, the genomes of only 16 bacterial haloviruses have been analyzed in detail [ 17 , 21 , 22 , 24 , 25 , 26 , 27 ], hindering our understanding of virus–host interactions. Four Marseille viruses and one Mimivirus isolated from a hypersaline environment in Tunisia using the halophilic amoeba as the host are the only known eukaryotic haloviruses [ 28 ].…”