High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems
dc.contributor.author | Meaden, S | |
dc.contributor.author | Biswas, A | |
dc.contributor.author | Arkhipova, K | |
dc.contributor.author | Morales, SE | |
dc.contributor.author | Dutilh, BE | |
dc.contributor.author | Westra, ER | |
dc.contributor.author | Fineran, PC | |
dc.date.accessioned | 2021-11-16T15:04:22Z | |
dc.date.issued | 2021-11-09 | |
dc.date.updated | 2021-11-16T14:42:05Z | |
dc.description.abstract | CRISPR-Cas are adaptive immune systems that protect their hosts against viruses and other parasitic mobile genetic elements.1 Although widely distributed among prokaryotic taxa, CRISPR-Cas systems are not ubiquitous.2-4 Like most defense-system genes, CRISPR-Cas are frequently lost and gained, suggesting advantages are specific to particular environmental conditions.5 Selection from viruses is assumed to drive the acquisition and maintenance of these immune systems in nature, and both theory6-8 and experiments have identified phage density and diversity as key fitness determinants.9,10 However, these approaches lack the biological complexity inherent in nature. Here, we exploit metagenomic data from 324 samples across diverse ecosystems to analyze CRISPR abundance in natural environments. For each metagenome, we quantified viral abundance and diversity to test whether these contribute to CRISPR-Cas abundance across ecosystems. We find a strong positive association between CRISPR-Cas abundance and viral abundance. In addition, when controlling for differences in viral abundance, CRISPR-Cas systems are more abundant when viral diversity is low, suggesting that such adaptive immune systems may offer limited protection when required to target a diverse viral community. CRISPR-Cas abundance also differed among environments, with environmental classification explaining roughly a quarter of the variation in CRISPR-Cas relative abundance. The relationships between CRISPR-Cas abundance, viral abundance, and viral diversity are broadly consistent across environments, providing robust evidence from natural ecosystems that supports predictions of when CRISPR is beneficial. These results indicate that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems. | en_GB |
dc.description.sponsorship | European Union Horizon 2020 | en_GB |
dc.description.sponsorship | Natural Environment Research Council (NERC) | en_GB |
dc.description.sponsorship | Netherlands Organization for Scientific Research (NWO) | en_GB |
dc.description.sponsorship | European Research Council (ERC) | en_GB |
dc.identifier.citation | Published online 9 November 2021 | en_GB |
dc.identifier.doi | https://doi.org/10.1016/j.cub.2021.10.038 | |
dc.identifier.grantnumber | ERC-STG-2016-714478 | en_GB |
dc.identifier.grantnumber | NE/M018350/1 | en_GB |
dc.identifier.grantnumber | 842656 | en_GB |
dc.identifier.grantnumber | 864.14.004 | en_GB |
dc.identifier.grantnumber | 865694 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/127827 | |
dc.identifier | ORCID: 0000-0003-4396-0354 (Westra, Edze R) | |
dc.language.iso | en | en_GB |
dc.publisher | Elsevier | en_GB |
dc.relation.url | https://www.ncbi.nlm.nih.gov/pubmed/34758284 | en_GB |
dc.relation.url | https://github.com/s-meaden/Meaden_CB_2021 | en_GB |
dc.rights | © 2021 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) | en_GB |
dc.subject | CRISPR-Cas | en_GB |
dc.subject | bacteriophages | en_GB |
dc.subject | metagenomics | en_GB |
dc.subject | microbial ecology | en_GB |
dc.title | High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2021-11-16T15:04:22Z | |
dc.identifier.issn | 0960-9822 | |
exeter.place-of-publication | England | |
dc.description | This is the final version. Available on open access from Elsevier via the DOI in this record | en_GB |
dc.description | Data and code availability: DNA sequence data are publicly available from the SRA database. Accession numbers are listed in Data S1F. No new sequence data was generated for this study. Original code is deposited in the github repositories listed in the Key resources table and statistical analysis scripts are available at https://github.com/s-meaden/Meaden_CB_2021. Code is publicly available at the time of publication. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. | en_GB |
dc.identifier.eissn | 1879-0445 | |
dc.identifier.journal | Current Biology | en_GB |
dc.relation.ispartof | Curr Biol | |
dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0/ | en_GB |
dcterms.dateAccepted | 2021-10-19 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2021-11-09 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2021-11-16T14:58:01Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2021-11-16T15:04:25Z | |
refterms.panel | A | en_GB |
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Except where otherwise noted, this item's licence is described as © 2021 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)