@article{8e946546fc9a4f0391a2cb40050d68cd,
title = "High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems",
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.",
keywords = "CRISPR-Cas, bacteriophages, metagenomics, microbial ecology",
author = "Sean Meaden and Ambarish Biswas and Ksenia Arkhipova and Morales, {Sergio E} and Dutilh, {Bas E} and Westra, {Edze R} and Fineran, {Peter C}",
note = "Funding Information: This work was funded by a grant from the European Research Council under the European Union's Horizon 2020 research and innovation programme (ERC-STG-2016-714478 to E.R.W.). E.R.W. was further supported by a NERC Independent Research Fellowship (NE/M018350/1). S.M. received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie grant agreement no. 842656. B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 and European Research Council (ERC) Consolidator grant 865694: DiversiPHI. P.C.F. was supported by the former Bio-Protection Research Centre and Bioprotection Aotearoa (Tertiary Education Commission [TEC]), New Zealand. Conceptualization, B.E.D. E.R.W. P.C.F. and S.E.M.; methodology, A.B. B.E.D. E.R.W. K.A. P.C.F. S.E.M. and S.M.; software, A.B. B.E.D. and K.A.; formal analysis, A.B. B.E.D. K.A. and S.M.; investigation, A.B. B.E.D. K.A. and S.M.; data curation, A.B. B.E.D. K.A. and S.M.; writing – original draft, E.R.W. P.C.F. and S.M.; writing – review & editing, A.B. B.E.D. E.R.W. K.A. P.C.F. S.E.M. and S.M.; visualization, S.M.; supervision, B.E.D. E.R.W. P.C.F. and S.E.M.; project administration, B.E.D. E.R.W. S.E.M. and P.C.F.; funding acquisition, B.E.D. E.R.W. S.E.M. S.M. and P.C.F. The authors declare no competing interests. Funding Information: This work was funded by a grant from the European Research Council under the European Union{\textquoteright}s Horizon 2020 research and innovation programme ( ERC-STG-2016-714478 to E.R.W.). E.R.W. was further supported by a NERC Independent Research Fellowship ( NE/M018350/1 ). S.M. received funding from the European Union {\textquoteright}s Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie grant agreement no. 842656 . B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 and European Research Council (ERC) Consolidator grant 865694 : DiversiPHI. P.C.F. was supported by the former Bio-Protection Research Centre and Bioprotection Aotearoa (Tertiary Education Commission [TEC]), New Zealand. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2022",
month = jan,
day = "10",
doi = "10.1016/j.cub.2021.10.038",
language = "English",
volume = "32",
pages = "220--227.e5",
journal = "Current Biology",
issn = "0960-9822",
publisher = "Cell Press",
number = "1",
}