Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

Abstract

Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12–20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

“…The genes provided by the phage might induce a change in the structures responsible for phage recognition and act as a serotype conversion mechanism to avoid superinfection by other phages (87). Similar mechanisms have been described for other marine and nonmarine podoviruses (88)(89)(90).…”

Phage-specific metabolic reprogramming of virocells

“…Growth and infection were conducted as described previously [24,[43][44][45]. Briefly, Pseudoalteromonas sp 13-15 cells were grown in an orbital shaker shaking at 150 rpm at 21°C in 1%Z + CNP medium (26 g/L sea salts, 1 g/L yeast extract, 5 g/L proteose, 8.3 mM ammonium sulfate, 0.15 mM phosphoric acid, and 11 mM glucose added after autoclaving).…”

“…Metagenomics has enabled us to resolve population-level viral biodiversity globally [11][12][13][14][15][16][17][18][19][20][21], where "population" has been resolved from extensive genetics-grounded studies in cyanophages [22,23], Pseudoalteromonas phages [24], reference-database phages [25], and from viromics-enabled studies [21]. Metagenomics answers "who is there?".…”

“…str. 13-15 [24] (herein "host") by a podophage (PSA-HP1, herein "HP1") and a siphophage (PSA-HS2, herein "HS2") [24] independently via timeresolved transcriptomics and proteomics. We assessed phage and host response to one another, and aggregated the findings into a new conceptual model as a baseline for quantifying potential ecosystem footprints and incorporating these processes into virus-explicit ecosystem models.…”

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

“…Until recently, the bulk of the research on marine viruses focused on phages that infect cyanobacteria (cyanophages) that include T4-like myoviruses, T7-like podoviruses, and siphoviruses [13][14][15][16][17][18][19] . However, cultivation of hosts and mining of metagenomic and metaviromic datasets revealed abundant phages infecting heterotrophic hosts [20][21][22][23][24][25] , some of which even have demonstrated diel cycles 26 .…”