Research Article

Oxygen minimum zones harbour novel viral communities with low diversity

  1. Noriko Cassman1,3,†,
  2. Alejandra Prieto-Davó1,†,
  3. Kevin Walsh1,
  4. Genivaldo G. Z. Silva2,
  5. Florent Angly1,4,
  6. Sajia Akhter2,
  7. Katie Barott1,
  8. Julia Busch1,
  9. Tracey McDole1,
  10. J. Matthew Haggerty1,
  11. Dana Willner1,4,5,
  12. Gadiel Alarcón6,
  13. Osvaldo Ulloa6,
  14. Edward F. DeLong7,
  15. Bas E. Dutilh8,
  16. Forest Rohwer1,
  17. Elizabeth A. Dinsdale1,*

Article first published online: 5 OCT 2012

DOI: 10.1111/j.1462-2920.2012.02891.x

Issue

Environmental Microbiology

Environmental Microbiology

Volume 14, Issue 11, pages 3043–3065, November 2012

Additional Information

How to Cite

Cassman, N., Prieto-Davó, A., Walsh, K., Silva, G. G. Z., Angly, F., Akhter, S., Barott, K., Busch, J., McDole, T., Haggerty, J. M., Willner, D., Alarcón, G., Ulloa, O., DeLong, E. F., Dutilh, B. E., Rohwer, F. and Dinsdale, E. A. (2012), Oxygen minimum zones harbour novel viral communities with low diversity. Environmental Microbiology, 14: 3043–3065. doi: 10.1111/j.1462-2920.2012.02891.x

Author Information

  1. 1

    Department of Biology, San Diego State University, San Diego, CA, USA

  2. 2

    Department of Computational Science Research Center, San Diego State University, San Diego, CA, USA

  3. 3

    Facultad de Química, Unidad Sisal, Universidad Nacional Autónoma de México Sisal, Yucatán, México

  4. 4

    Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, Australia

  5. 5

    Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia

  6. 6

    Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile

  7. 7

    Department of Biological Engineering & Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, MA, USA

  8. 8

    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, GA, Nijmegen, The Netherlands

  1. †

    Both authors contributed equally to the manuscript.

*For correspondence. E-mail elizabeth_dinsdale@hotmail.com; Tel. 619 5945623; Fax 619 5745676.

  1. †

    Both authors contributed equally to the manuscript.

Publication History

  1. Issue published online: 24 OCT 2012
  2. Article first published online: 5 OCT 2012
  3. Accepted manuscript online: 11 SEP 2012 04:52AM EST
  4. Manuscript Accepted: 2 SEP 2012
  5. Manuscript Revised: 23 AUG 2012
  6. Manuscript Received: 5 SEP 2011

Funded by

  • Agouron Research Institute
  • Gordon and Betty Moore Fund
  • NSF. Grant Number: #1044453
  • CONACyT. Grant Number: #120512
  • Chilean National Commission for Scientific and Technological Research (CONICYT). Grant Number: 15010007

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Summary

Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodiversity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral-to-microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral diversity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences sampled within the altered oxygen conditions of the ETSP OMZ, more than 97.8% were novel. Of the average 3.2% of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and diversity across the oxygen gradient. The ecological significance of these changes was difficult to predict; however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.

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