Active prophages in coral-associated Halomonas capable of lateral transduction.

Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.

Complete genome sequence of Halomonas ventosae virulent halovirus QHHSV-1.

A virulent halovirus QHHSV-1 which lyses Halomonas ventosae QH52-2 originating from the Qiaohou salt mine in Yunnan, Southwest China was characterized. The complete genome of QHHSV-1 is composed of a circular double-stranded DNA of 37,270 base pairs in length, with 66.8% G+C content and 69 putative open reading frames (ORFs), which were classified into five functional groups, including morphogenesis, replication/regulation, packaging, lysis and lysogeny. A putative Cro repressor gene and an integrase gene were found in the genome, showing that QHHSV-1 may utilize a lambda-like repression system under unfavorable conditions. QHHSV-1 is the first report of the whole genome sequence of the virulent Halomonas phage belonging to the family Siphoviridae.

A novel Halomonas ventosae-specific virulent halovirus isolated from the Qiaohou salt mine in Yunnan, Southwest China.

Although Halomonas phages belonging to the families Myoviridae and Siphoviridae have been reported, no virulent Halomonas siphoviruses are known. In this study, a virulent bacteriophage, QHHSV-1, of the family Siphoviridae that specifically infects H. ventosae QH52-2 was isolated from the Qiaohou salt mine. Restriction analysis indicated that QHHSV-1 is a dsDNA virus with a genome size of 33.5-39.5 kb. Transmission electron microscopy showed that QHHSV-1 is a typical representative of the Siphoviridae, with an icosahedral head (47 nm in diameter) and a non-contractile tail (75 nm in length). We also assessed the adsorption rate of QHHSV-1 for the host bacterium and found significant inhibition after the addition of 10 mM CaCl2. Based on a one-step growth curve, we determined a latent period of 30 min and a burst size of 73 PFU/infected cell. At the optimal pH of 8.0, 25.9 and 15.2 % of the phages survived after a 60-min incubation at 50 and 60 °C, respectively. Phage replication was possible at a wide range of salt concentrations, from 2.0 to 20 % (w/v), with an optimum concentration of 5 %. The survival of QHHSV-1 at different salt concentrations decreased with time and 25 % survival after 25 days at 30 % salt concentration.

The temperate marine phage PhiHAP-1 of Halomonas aquamarina possesses a linear plasmid-like prophage genome.

A myovirus-like temperate phage, PhiHAP-1, was induced with mitomycin C from a Halomonas aquamarina strain isolated from surface waters in the Gulf of Mexico. The induced cultures produced significantly more virus-like particles (VLPs) (3.73 x 10(10) VLP ml(-1)) than control cultures (3.83 x 10(7) VLP ml(-1)) when observed with epifluorescence microscopy. The induced phage was sequenced by using linker-amplified shotgun libraries and contained a genome 39,245 nucleotides in length with a G+C content of 59%. The PhiHAP-1 genome contained 46 putative open reading frames (ORFs), with 76% sharing significant similarity (E value of <10(-3)) at the protein level with other sequences in GenBank. Putative functional gene assignments included small and large terminase subunits, capsid and tail genes, an N6-DNA adenine methyltransferase, and lysogeny-related genes. Although no integrase was found, the PhiHAP-1 genome contained ORFs similar to protelomerase and parA genes found in linear plasmid-like phages with telomeric ends. Southern probing and PCR analysis of host genomic, plasmid, and PhiHAP-1 DNA indicated a lack of integration of the prophage with the host chromosome and a difference in genome arrangement between the prophage and virion forms. The linear plasmid prophage form of PhiHAP-1 begins with the protelomerase gene, presumably due to the activity of the protelomerase, while the induced phage particle has a circularly permuted genome that begins with the terminase genes. The PhiHAP-1 genome shares synteny and gene similarity with coliphage N15 and vibriophages VP882 and VHML, suggesting an evolutionary heritage from an N15-like linear plasmid prophage ancestor.

Isolation and characterization of a bacteriophage with an unusually large genome from the Great Salt Plains National Wildlife Refuge, Oklahoma, USA.

In this study we present a bacteriophage isolated from the Great Salt Plains National Wildlife Refuge (GSP) that is shown to have a genome size of 340 kb, unusually large for a bacterial virus. Transmission electron microscopy analysis of the virion showed this to be a Myoviridae, the first reported to infect the genus Halomonas. This temperate phage, PhigspC, exhibits a broad host range, displaying the ability to infect two different Halomonas spp. also isolated from the GSP. The phage infection process demonstrates a high level of tolerance towards temperature, pH and salinity; however, free virions are rapidly inactivated in water unless supplemented with salt. We show that susceptibility to osmotic shock is correlated with the density of the packaged DNA (rho(pack)). Lysogens of Halomonas salina GSP21 were detrimental to host fitness at 10% salinity, but the lysogen was able to grow faster than the wild type at 20% salinity. From these results we propose that the extensive genome of PhigspC may encode environmentally relevant genes (ERGs); genes that are perhaps not essential for the phage life cycle but increase host and phage fitness in some environmental conditions.