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ABSTRACT CRISPR–Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids based on DNA acquired from these invaders, known as spacers. Surprisingly, many

archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a

single site, we demonstrate that inter-species spacers are common. We show experimentally, by mating _Haloferax volcanii_ and _Haloferax mediterranei_, that spacers are indeed acquired

chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in

interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those

originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be

targeted by the other’s CRISPR–Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role

for CRISPR–Cas systems in microbial speciation. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access

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Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS CRISPR-CAS SYSTEMS RESTRICT HORIZONTAL GENE TRANSFER IN _PSEUDOMONAS AERUGINOSA_ Article Open access 21 December 2020

PERVASIVE PROPHAGE RECOMBINATION OCCURS DURING EVOLUTION OF SPORE-FORMING _BACILLI_ Article 20 December 2020 TYPE III-A CRISPR IMMUNITY PROMOTES MUTAGENESIS OF STAPHYLOCOCCI Article 07 April

2021 DATA AVAILABILITY Haloarchaeal environmental isolates genomes are available at GenBank under accession numbers PSYS00000000, PSYT00000000, PSYU00000000, PSYV00000000, PSYW00000000,

PSYX00000000, PSYY00000000, QEQI00000000, QEQJ00000000, QPLN00000000, QPLO00000000, QPLP00000000, QPLQ00000000, QPLR00000000, QPLS00000000, QPLT00000000, QPLU00000000, QXIJ00000000,

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Central  Google Scholar  Download references ACKNOWLEDGEMENTS The authors thank R. Sorek and A. Herskovits for their helpful comments and insights, and H. Xiang for providing sequence data

and provirus annotations. The authors thank S. Green of the University of Illinois at Chicago for his continued expert help in challenging sequencing projects and E. Koonin (NIH) for helpful

discussions. Funding was provided by Deutsche Forschungsgemeinschaft (MA1538/16-2), the Israel Science Foundation (535/15), the Binational Science Foundation (2013061) with partial support

by the Constantiner Institute, European Research Council (grant ERC-AdG 787514). AUTHOR INFORMATION Author notes * Adit Naor Present address: Department of Microbiology and Immunology,

Stanford University School of Medicine, Stanford, CA, USA AUTHORS AND AFFILIATIONS * Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv

University, Tel Aviv, Israel Israela Turgeman-Grott, Shirley Joseph, Sam Marton, Kim Eizenshtein, Adit Naor, Yarden Shalev, Mor Zarkor, Leah Reshef, Neta Altman-Price & Uri Gophna *

Department of Biological Sciences, Dartmouth College, Hanover, NH, USA Shannon M. Soucy * Department of Biology II, Ulm University, Ulm, Germany Aris-Edda Stachler & Anita Marchfelder

Authors * Israela Turgeman-Grott View author publications You can also search for this author inPubMed Google Scholar * Shirley Joseph View author publications You can also search for this

author inPubMed Google Scholar * Sam Marton View author publications You can also search for this author inPubMed Google Scholar * Kim Eizenshtein View author publications You can also

search for this author inPubMed Google Scholar * Adit Naor View author publications You can also search for this author inPubMed Google Scholar * Shannon M. Soucy View author publications

You can also search for this author inPubMed Google Scholar * Aris-Edda Stachler View author publications You can also search for this author inPubMed Google Scholar * Yarden Shalev View

author publications You can also search for this author inPubMed Google Scholar * Mor Zarkor View author publications You can also search for this author inPubMed Google Scholar * Leah

Reshef View author publications You can also search for this author inPubMed Google Scholar * Neta Altman-Price View author publications You can also search for this author inPubMed Google

Scholar * Anita Marchfelder View author publications You can also search for this author inPubMed Google Scholar * Uri Gophna View author publications You can also search for this author

inPubMed Google Scholar CONTRIBUTIONS U.G. and I.T.-G. conceived the study. U.G., I.T.-G. and A.M. designed the experiments. S.S. assembled and annotated genome sequences. I.T.-G., A.N. and

N.A.-P. designed and constructed strains. I.T.-G., S.J., K.E., Y.S., A.-E.S. and M.Z. performed experiments. L.R., S.M., I.T.G. and U.G. analysed data. U.G. and I.T.-G. wrote the manuscript.

L.R., S.S. and A.M. commented and made critical revisions to the manuscript. CORRESPONDING AUTHOR Correspondence to Uri Gophna. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare

no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Figures 1–10, Supplementary Tables 1–12, Supplementary References. REPORTING SUMMARY SUPPLEMENTARY TABLE 13 Complete spacer

acquisition data from H. volcanii arrays obtained following three independent inter-species mating experiments. SUPPLEMENTARY TABLE 14 Complete spacer acquisition data from H. mediterranei

arrays obtained following three independent inter-species mating experiments. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Turgeman-Grott, I., Joseph,

S., Marton, S. _et al._ Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. _Nat Microbiol_ 4, 177–186 (2019).

https://doi.org/10.1038/s41564-018-0302-8 Download citation * Received: 29 March 2018 * Accepted: 23 October 2018 * Published: 26 November 2018 * Issue Date: January 2019 * DOI:

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