Putative archaeal viruses from the mesopelagic ocean

Dean R. Vik, Simon Roux, Jennifer R. Brum, Ben Bolduc, Joanne B. Emerson, Cory C. Padilla, Frank J. Stewart, Matthew Sullivan

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Oceanic viruses that infect bacteria, or phages, are known to modulate host diversity, metabolisms, and biogeochemical cycling, while the viruses that infect marine Archaea remain understudied despite the critical ecosystem roles played by their hosts. Here we introduce ``MArVD'', for Metagenomic Archaeal Virus Detector, an annotation tool designed to identify putative archaeal virus contigs in metagenomic datasets. MArVD is made publicly available through the online iVirus analytical platform. Benchmarking analysis of MArVD showed it to be >99% accurate and 100% sensitive in identifying the 127 known archaeal viruses among the 12,499 viruses in the VirSorter curated dataset. Application of MArVD to 10 viral metagenomes from two depth profiles in the Eastern Tropical North Pacific (ETNP) oxygen minimum zone revealed 43 new putative archaeal virus genomes and large genome fragments ranging in size from 10 to 31 kb. Network-based classifications, which were consistent with marker gene phylogenies where available, suggested that these putative archaeal virus contigs represented six novel candidate genera. Ecological analyses, via fragment recruitment and ordination, revealed that the diversity and relative abundances of these putative archaeal viruses were correlated with oxygen concentration and temperature along two OMZ-spanning depth profiles, presumably due to structuring of the host Archaea community. Peak viral diversity and abundances were found in surface waters, where Thermoplasmata 16S rRNA genes are prevalent, suggesting these archaea as hosts in the surface habitats. Together these findings provide a baseline for identifying archaeal viruses in sequence datasets, and an initial picture of the ecology of such viruses in non-extreme environments.

Original languageEnglish (US)
Article number3428
JournalPeerJ
Volume2017
Issue number6
DOIs
StatePublished - 2017
Externally publishedYes

Fingerprint

Archaeal Viruses
Viruses
Oceans and Seas
oceans
viruses
Archaea
Metagenomics
Genes
Ecosystem
Archaeal Genome
Euryarchaeota
Metagenome
Oxygen
Benchmarking
Phylogeny
Ecology
rRNA Genes
Bacteriophages
oxygen
genome

Keywords

  • Archaea
  • Archaeal virus
  • Oxygen
  • Oxygen minimum zone
  • Temperature
  • Thermoplasmata

ASJC Scopus subject areas

  • Neuroscience(all)
  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Vik, D. R., Roux, S., Brum, J. R., Bolduc, B., Emerson, J. B., Padilla, C. C., ... Sullivan, M. (2017). Putative archaeal viruses from the mesopelagic ocean. PeerJ, 2017(6), [3428]. https://doi.org/10.7717/peerj.3428

Putative archaeal viruses from the mesopelagic ocean. / Vik, Dean R.; Roux, Simon; Brum, Jennifer R.; Bolduc, Ben; Emerson, Joanne B.; Padilla, Cory C.; Stewart, Frank J.; Sullivan, Matthew.

In: PeerJ, Vol. 2017, No. 6, 3428, 2017.

Research output: Contribution to journalArticle

Vik, DR, Roux, S, Brum, JR, Bolduc, B, Emerson, JB, Padilla, CC, Stewart, FJ & Sullivan, M 2017, 'Putative archaeal viruses from the mesopelagic ocean', PeerJ, vol. 2017, no. 6, 3428. https://doi.org/10.7717/peerj.3428
Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC et al. Putative archaeal viruses from the mesopelagic ocean. PeerJ. 2017;2017(6). 3428. https://doi.org/10.7717/peerj.3428
Vik, Dean R. ; Roux, Simon ; Brum, Jennifer R. ; Bolduc, Ben ; Emerson, Joanne B. ; Padilla, Cory C. ; Stewart, Frank J. ; Sullivan, Matthew. / Putative archaeal viruses from the mesopelagic ocean. In: PeerJ. 2017 ; Vol. 2017, No. 6.
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