Culturing novel and abundant pelagiphages in the ocean

Abstract

Summary Viruses play a key role in biogeochemical cycling and host mortality, metabolism, physiology and evolution in the ocean. Viruses that infect the globally abundant SAR11 bacteria (pelagiphages) were reported to be an important component of the marine viral communities. Our current knowledge of pelagiphages is based on a few studies and therefore is limited. In this study, 10 new pelagiphages were isolated and genomically characterized. These pelagiphages represent the first cultivated representatives of four viral lineages only found in metagenomic sequencing datasets previously. Many abundant environmental viral sequences, i.e., single‐virus vSAG 37‐F6 and several Global Ocean Viromes (GOV) viral populations, are now further confirmed with these pelagiphages. Viromic read mapping reveals that these new pelagiphages are globally distributed in the ocean and can be detected throughout the water column. Remarkably, isolation of these pelagiphages contributed up to 12% of all viromic reads annotated in the analysed viromes. Altogether, this study has greatly broadened our understanding of pelagiphages regarding their morphology, genetic diversity, infection strategies, and distribution pattern. The availability of these newly isolated pelagiphages and their genome sequences will allow us to further explore their infectivities and ecological strategies.

Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria

“…ICTV-recognised genera based on shared-gene content were assigned with VConTACT2 [19]. The relative abundance of novel phages in the Western English Channel [12] and Global Ocean viromes [11] was estimated (RPKM) by competitive read recruitment of five million randomly subsampled reads against pelagiphage and methylophage genomes from this study and others [38,52,64,82].…”

Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria

“…ICTV-recognised genera based on shared gene content were assigned with VConTACT2 [19]. The relative abundance of novel phages in the Western English Channel [12] and Global Ocean viromes [11] was estimated (RPKM) by competitive read recruitment of five million randomly subsampled reads against pelagiphage and methylophage genomes from this study and others [38, 52, 64, 82].…”

“…The Global Ocean Virome (GOV2) [37] and a virome from the Western English Channel [38] were screened for contigs that belonged to the same population (95% ANI over 80% length using ClusterGenomes.pl - https://github.com/simroux/ClusterGenomes) or the same genus (clustered by VConTACT2 [39] into the same viral cluster, using default parameters) as isolate genomes. Additionally, all available genomes from Pelagibacter phage isolates were included, as well as selected fosmid derived contigs from Mediterranean metagenomes and 26 sequences from metagenomic mining that were identified as putative Pelagimyophages [33–35, 40, 41]. All sequences were subjected to gene calling using Prodigal v2.6.3.…”

“…Metagenomic reads were downloaded from the European Nucleotide Archive ERR2625613 and subsampled to 5 million reads using bbmap’s reformat.sh command. A bowtie2 [13] index of dereplicated contigs was created from 25 known pelagiphage genomes from isolates [33, 34, 41], LD28 phage P19250A [46] and from this study six viral population representative genomes isolated on SAR11 hosts and one Methylophilales phage Venkman isolated on OM43 host. Reads were mapped against the genomes for each metagenome sample using bowtie2 using these commands: .…”

Draft Genome Sequences of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P, Isolated from Devil’s Hole, Bermuda

“…Viruses infecting the heterotrophic bacterial clade of Pelagibacterales are an important component of marine microbial communities throughout global oceans ( 1 ). Since the discovery and first isolation of four pelagiphages in 2013 ( 2 ), 38 more have been isolated and sequenced ( 3 – 5 ). Out of the 38 isolated pelagiphages, 36 belong to the Podoviridae family, with only one species each of Myoviridae and Siphoviridae .…”