Defining seasonal patterns of SAR11 viruses in the Western English Channel via long-read sequencing and viral isolation
Ben Temperton1, Joanna Louisa Warwick-Dugdale2, Holger Buchholz1, Michelle Michelsen1, Natalie Solonenko3, Ann C Gregory4, Mike Allen2 and Matthew B Sullivan5, (1)University of Exeter, Exeter, United Kingdom, (2)Plymouth Marine Laboratory, Plymouth, United Kingdom, (3)Ohio State University Main Campus, Columbus, OH, United States, (4)Ohio State University, Microbiology, Columbus, OH, United States, (5)Ohio State University Main Campus, Microbiology, Columbus, United States
Abstract:
Members of the SAR11 clade comprise up to 50% of surface marine microbial communities, and are estimated to be responsible for converting up to 20% of global primary production back to atmospheric CO
2. Of similar importance to carbon biogeochemistry, predation of microbial communities by viruses modulates the largest carbon fluxes in the oceans (150Gt/yr), with recent advances in viral metagenomics providing insight into predicted mechanisms of metabolic reprogramming and genes-to-ecosystem modelling of carbon flux from surface to deep water. Recruitment of short-read metagenomic data to genomes of viral isolates revealed that viruses infecting members of the SAR11 clade (pelagiphages) dominate marine viral communities across the global oceans. However, due to computational challenges associated with high abundance and high microdiversity, reconstructed pelagiphage genomes from such datasets are highly fragmented and thus almost entirely absent from metagenomic assemblies, posing a significant challenge for accurate ecosystem modelling of pelagiphage influences on global carbon biogeochemistry. Poor accuracy of
in silico host prediction for pelagiphages further exacerbates the problem.
We developed two complementary methods developed to address this issue. First, long-read sequencing of viral metagenomes performed exceptionally well at capturing genomes that fragmented using short-read-only approaches, including 19 of the 50 most globally abundant and ubiquitous marine viruses; captured niche-defining viral genomic islands and identified a putatively novel role for ribonuclease in antagonistic evolution. Second, high-throughput culturing that couples sequential enrichment with dilution-to-extinction has yielded >100 novel phages for SAR11, revealing inter- and intra-population structure in the Western English Channel and improving in silico host prediction from metagenomes. Coupled with monthly long-read viral metagenomes that can capture near-complete viral genomes on single reads, we show how pelagiphage populations wax and wane over seasonal timescales
