CaltechAUTHORS
  A Caltech Library Service

Seasonal and diel patterns of abundance and activity of viruses in the Red Sea

Hevroni, Gur and Flores-Uribe, José and Béjà, Oded and Philosof, Alon (2020) Seasonal and diel patterns of abundance and activity of viruses in the Red Sea. Proceedings of the National Academy of Sciences of the United States of America, 117 (47). pp. 29738-29747. ISSN 0027-8424. https://resolver.caltech.edu/CaltechAUTHORS:20200511-091357802

[img]
Preview
PDF - Published Version
See Usage Policy.

1918Kb
[img] PDF - Submitted Version
Creative Commons Attribution Non-commercial No Derivatives.

16Mb
[img] PDF - Supplemental Material
See Usage Policy.

5Mb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20200511-091357802

Abstract

Virus–microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, methods such as cooccurrence, nucleotide composition, and other statistical frameworks have been widely used to infer virus–microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable as cooccurrence does not necessarily mean interaction. Here we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus–host pairs. By size fractionating water samples into free viruses and microbes (i.e., also viruses inside or attached to their hosts) and looking at how viral group abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral clusters, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1073/pnas.2010783117DOIArticle
https://www.pnas.org/content/suppl/2020/11/09/2010783117.DCSupplementalRelated ItemSupporting Information
https://doi.org/10.1101/2020.05.07.082883DOIDiscussion Paper
https://doi.org/10.17605/osf.io/b74mtDOICode
ORCID:
AuthorORCID
Hevroni, Gur0000-0002-2066-0466
Flores-Uribe, José0000-0002-6229-365X
Béjà, Oded0000-0001-6629-0192
Philosof, Alon0000-0003-2684-8678
Alternate Title:Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses
Additional Information:© 2020 National Academy of Sciences. Published under the PNAS license. Edited by David M. Karl, University of Hawaii at Manoa, Honolulu, HI, and approved October 9, 2020 (received for review May 27, 2020). PNAS first published November 10, 2020. We thank IUI in Eilat, Israel, for providing access to their pier as well as work space and the Genomics Centers at the Biomedical Core Facility and Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering at the Technion for library preparation and sequencing. We also thank Dan Fishman for sample preparation, Itai Sharon for help with metagenome assemblies, Sheila Roitman and Faris Salama for their help with sampling, David Cohen of the Physics Department at the Technion for his help with the HPC ATLAS cluster used for the analyses, and Michael McLaren for invaluable comments on our manuscript. This work was funded by a European Commission European Research Council Advanced grant 321647, Israel Science Foundation grant 143/18, the Technion’s Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering and the Russell Berrie Nanotechnology Institute, and the Louis and Lyra Richmond Memorial Chair in Life Sciences (to O.B.). Data Availability: The assembled viral contigs, along with raw sequence data, are available from the European Nucleotide Archive under accession no. PRJEB35627. SI Appendix, Tables S1–S5, can be downloaded from https://doi.org/10.17605/osf.io/b74mt. Code Availability: Scripts and notebooks for reproducing the rank state analysis are available at https://doi.org/10.17605/osf.io/b74mt. Author contributions: G.H., O.B., and A.P. designed research; G.H. and A.P. performed research; G.H., J.F.-U., and A.P. analyzed data; and G.H. and A.P. wrote the paper. The authors declare no competing interest. This article is a PNAS Direct Submission. This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2010783117/-/DCSupplemental.
Funders:
Funding AgencyGrant Number
European Research Council (ERC)321647
Israel Science Foundation143/18
TechnionUNSPECIFIED
Russell Berrie Nanotechnology InstituteUNSPECIFIED
Louis and Lyra Richmond Memorial ChairUNSPECIFIED
Subject Keywords:marine viruses; seasonal succession; virus–host interaction; diel oscillation
Issue or Number:47
Record Number:CaltechAUTHORS:20200511-091357802
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200511-091357802
Official Citation:Seasonal and diel patterns of abundance and activity of viruses in the Red Sea. Gur Hevroni, José Flores-Uribe, Oded Béjà, Alon Philosof. Proceedings of the National Academy of Sciences Nov 2020, 117 (47) 29738-29747; DOI: 10.1073/pnas.2010783117
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:103093
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:11 May 2020 18:16
Last Modified:25 Nov 2020 17:05

Repository Staff Only: item control page