Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria

Abstract

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from −20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.

Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax

“…Two domains were identified in VG_p48, including Toprim (PF13362; from 227 to 302), which is found in bacterial DnaG-type primases and their viral counterparts [ 45 ], and virulence-associated protein E (PF05272; from 574 to 755). While the segment of VGp_48 spanning the latter domain showed similarity to several putative phage primases (e.g., Marinobacter phage PS3, ATN93361.1 [ 46 ]), VG_p48 was homologous over its entire length only with the protein (DAS38011.1) encoded by a virus assembled from human metagenomes [ 47 ].…”

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

“…The purified phage was expanded and cultured to 500 mL and then filtered using a 0.22 µm membrane filter (microporous). The phage culture was concentrated to 3 mL using an ultrafiltration tube (microporous Amicon Ultra-15) at 5,000 g ( 44 ). The purified phage was preserved in SM buffer at 4°C for further processing.…”

Characterization of a novel genus of jumbo phages and their application in wastewater treatment

“…For pH Sensitivity assay, phages preparation (10 9 PFU/mL) was incubated at pH 2-12 with 1 M NaOH or 1 M HCl for 1 hour at 37°C. 46 The bacteriophage titer was then assessed by double-agar layer method. 47 , 48 All experiments were performed in triplicate.…”