Ubiquitous, B₁₂-dependent virioplankton utilizing ribonucleotide triphosphate reductase demonstrate interseasonal dynamics and associate with a diverse range of bacterial hosts in the pelagic ocean

Abstract

Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B12 dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide triphosphate reductase (RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling downwelling events. Defining RTPR carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from RTPR sequences mirrored ecological patterns in virio and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene.

Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes

“…Despite the fact that there is no universal marker gene carried by all viruses, studies of specific hallmark genes have revealed large-scale viral diversity of certain viral groups from marine and host associated biomes [23][24][25][26][27][28] . For example, Sakowski et al 2014 and Wu et al 2023 found great novel dsDNA bacteriophage diversity from marine samples using ribonucleotide reductase 23,28 while Wolf et al 2020, Zayed et al 2022 andEdgar et al 2022 expanded the known RNA viruses using RNA-dependent RNA polymerase as a marker [25][26][27] . Complementary to marker gene approaches, shotgun metagenomic sequencing is suitable for discovering viruses without targeted marker genes 29,30 .…”