Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

Simon Roux, Alyse K. Hawley, Monica Torres Beltran, Melanie Scofeld, Patrick Schwientek, Ramunas Stepanauskas, Tanja Woyke, Steven J. Hallam, Matthew Sullivan

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specifc virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplifed genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing fve new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-defciency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identifcation of virus-encoded dissimilatory sulfte reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.

Original languageEnglish (US)
Article numbere03125
JournaleLife
Volume2014
Issue number3
DOIs
StatePublished - 2014

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Ecology
Genomics
Viruses
Bacteria
Microviridae
Oxygen
Caudovirales
Metagenome
Infection
Climate
Coinfection
Ecosystems
Energy Metabolism
Ecosystem
Oxidoreductases
Genes
Genome
Recovery

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Medicine(all)
  • Neuroscience(all)

Cite this

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. / Roux, Simon; Hawley, Alyse K.; Beltran, Monica Torres; Scofeld, Melanie; Schwientek, Patrick; Stepanauskas, Ramunas; Woyke, Tanja; Hallam, Steven J.; Sullivan, Matthew.

In: eLife, Vol. 2014, No. 3, e03125, 2014.

Research output: Contribution to journalArticle

Roux, S, Hawley, AK, Beltran, MT, Scofeld, M, Schwientek, P, Stepanauskas, R, Woyke, T, Hallam, SJ & Sullivan, M 2014, 'Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics', eLife, vol. 2014, no. 3, e03125. https://doi.org/10.7554/eLife.03125.001
Roux, Simon ; Hawley, Alyse K. ; Beltran, Monica Torres ; Scofeld, Melanie ; Schwientek, Patrick ; Stepanauskas, Ramunas ; Woyke, Tanja ; Hallam, Steven J. ; Sullivan, Matthew. / Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. In: eLife. 2014 ; Vol. 2014, No. 3.
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