Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages

Abstract

Epsilonproteobacteria are among the predominant primary producers in deep-sea hydrothermal vent ecosystems. However, phages infecting deep-sea vent Epsilonproteobacteria have never been isolated and characterized. Here, we successfully isolated a novel temperate phage, NrS-1, that infected a deep-sea vent chemolithoautotrophic isolate of Epsilonproteobacteria, Nitratiruptor sp. SB155-2, and its entire genome sequence was obtained and analyzed. The NrS-1 genome is linear, circularly permuted, and terminally redundant. The NrS-1 genome is 37,159 bp in length and contains 51 coding sequences. Five major structural proteins including major capsid protein and tape measure protein were identified by SDS-PAGE and mass spectrometry analysis. NrS-1 belongs to the family Siphoviridae, but its sequence and genomic organization are distinct from those of any other previously known Siphoviridae phages. Homologues of genes encoded in the NrS-1 genome were widely distributed among the genomes of diverse Epsilonproteobacteria. The distribution patterns had little relation to the evolutionary traits and ecological and physiological differentiation of the host epsilonproteobacterial species. The widespread occurrence of phage genes in diverse Epsilonproteobacteria supports early co-evolution between temperate phages and Epsilonproteobacteria prior to the divergence of their habitats and physiological adaptation.

Identification and genomic analysis of temperate Pseudomonas bacteriophage PstS-1 from the Japan trench at a depth of 7000 m

“…A similar arrangement has been noted in other Siphoviridae phages [67], such as the well-characterized lambda-like Pseudomonas phage D3 [68], the Burkholderia phage phi644-2 [69], the Antarctic soil Psychrobacter phage Psymv2 [70], the bathyal psychrotolerant alphaproteobacterial phage AmM-1 [29], the deep-sea vent thermophilic phage NrS-1 [30] and several phages that infect low G þ C Gram-positive bacteria [71]. The colors indicate the different functional groups of the gene products as follows: red, integration; purple, restriction-modification system; yellow, auxiliary metabolism; light blue, DNA replication/recombination/regulation; blue, genetic switch; green, DNA packaging; orange, structural protein; pink, cell lysis; and gray, unknown.…”

“…The phage particles induced by treatment with MitC for 24 h were filtered from approximately 900 ml of culture medium and concentrated via polyethylene glycol (PEG) precipitation as previously described [30]. Then, the precipitate was resuspended in 10 ml of SM buffer (50 mM TriseHCl, pH 7.5, 100 mM NaCl, 10 mM MgSO 4 $7H 2 O and 0.01% gelatin).…”

High potential for temperate viruses to drive carbon cycling in chemoautotrophy‐dominated shallow‐water hydrothermal vents

“…Accordingly, proviruses are widespread in diverse chemolithoautotrophic epsilonproteobacteria isolated from hydrothermal vents (including the Sulfurovum gen ., dominant in our mat sediments), and they are highly inducible at the low concentrations of MitC used in this study (Nakagawa et al ., ; Yoshida‐Takashima et al ., ). Moreover, the production rates of the temperate viruses in mat sediments (up to ∼2.5 × 10 9 viruses h −1 ) were consistent with those reported for cultured proviruses of epsilonproteobacteria (∼8.3 × 10 9 viruses h −1 , Yoshida‐Takashima et al ., ) providing further support to the evidences based on metagenomics and induction experiments.…”

Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp.

“…Phage particles induced by 33 h of MitC treatment were filtered from approximately 900 mL of culture and concentrated by polyethylene glycol (PEG) precipitation, as described previously (Yoshida-Takashima et al 2013). The precipitate was then resuspended in 10 mL of SM buffer (50 mM TrisHCl, pH 7.5; 100 mM NaCl; 10 mM MgSO 4 Á7H 2 O; 0.01 % gelatin).…”

“…Despite the ecological significance of marine phages in surface environments, the viral ecology of deep-sea ecosystems has focused mainly on viral abundance and distribution (e.g., Danovaro et al 2008;Engelhardt et al 2014;Magiopoulos and Pitta 2012;Yanagawa et al 2014;Yoshida-Takashima et al 2012). Metagenomics-and isolation-based studies have increasingly been applied to viral populations in deep-sea planktonic and benthic environments, including deep-sea hydrothermal environments and subseafloor sediments (e.g., Angly et al 2006;Engelhardt et al 2011;Gorlas et al 2012;Wang and Zhang 2010;Williamson et al 2008;Yoshida-Takashima et al 2013).…”