Abstract
Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.
Highlights
In marine environments, phages influence global biogeochemical cycles by lysing bacterial cells which alters nutrient and organic matter fluxes, as well as the dynamics and diversity of microbial communities [1,2,3,4,5,6,7,8,9]
Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event
Viral community diversity has been analyzed by culture-independent approaches including (i) Pulse-Field Gel Electrophoresis (PFGE) which discriminates viruses by genome size [15, 16], (ii) Randomly Amplified Polymorphic DNA PCR (RAPD) which provides a genetic fingerprint for the whole viral community [17,18,19] and most recently (iii) viral metagenomics which, currently, provides fragmented sequence data for the whole double-stranded DNA viral community [20,21,22,23,24,25,26,27,28]
Summary
Phages influence global biogeochemical cycles by lysing bacterial cells which alters nutrient and organic matter fluxes, as well as the dynamics and diversity of microbial communities [1,2,3,4,5,6,7,8,9]. Even when it is possible to grow the host organism in the lab, not all phages produce identifiable plaques [6, 14] To circumvent these limitations, viral community diversity has been analyzed by culture-independent approaches including (i) Pulse-Field Gel Electrophoresis (PFGE) which discriminates viruses by genome size [15, 16], (ii) Randomly Amplified Polymorphic DNA PCR (RAPD) which provides a genetic fingerprint for the whole viral community [17,18,19] and most recently (iii) viral metagenomics (viromics) which, currently, provides fragmented sequence data for the whole double-stranded DNA (dsDNA) viral community [20,21,22,23,24,25,26,27,28]. New methods are needed to capture RNA and ssDNA viral sequence space, and relevant and representative isolate-based genomes are essential to better map dsDNA viral sequence space and virus–host interactions in nature
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