Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster

Abstract

Background Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown. Results Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans. Conclusions These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage–host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.

Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family

“…The annotation information generated by different databases was manually checked based on the E -value and bitscore. The tRNAscan-SE ( http://lowelab.ucsc.edu/tRNAscan-SE/ ) was used to identify tRNA ( 51 ). Genome mapping was performed using Rstudio.…”

Characterization and Genomic Analysis of the First Podophage Infecting Shewanella, Representing a Novel Viral Cluster

“…Phage was isolated by the double-layer plate method (Zhang W. et al, 2021). The same seawater sample was filtered through the 0.22 µm pore-size membranes (Millipore) to obtain viral water.…”

“…Then viral culture was passed through a 0.22-µm membrane filter (Millipore) to remove the bacteria. The virus culture was concentrated to 3 ml with an ultrafiltration tube (Millipore Amicon Ultra-15) at 5,000 g (Zhang W. et al, 2021).…”

“…The genome sequence Shewanella phage vB_SInP-X14 has been deposited in GenBank, whose accession number is MK796797. The cumulative GC skew 1 analysis was used to detect the origin and terminus of 1 https://genskew.csb.univie.ac.at/webskew replication of the phage genome (Uchiyama et al, 2008;Zhang W. et al, 2021). The prediction of the putative open reading frames (ORFs) was combined with several different software, including prodigal (Hyatt et al, 2010), GeneMarkS sever (Besemer et al, 2001), and RAST (Brettin et al, 2015).…”

Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae

“…Currently, only eight cultivated phages infecting Oceanospirillaceae strains have been reported, two of which have not yet been classified, and the remaining strains have been classified into Autographiviridae (three phages), Siphoviridae (two phages), and Corticoviridae (one phage) ( 18 – 20 ). However, myoviruses infecting Oceanospirillaceae have not previously been reported ( 25 – 27 ).…”