Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation

Israela Turgeman-Grott, Shirley Joseph, Sam Marton, Kim Eizenshtein, Adit Naor, Shannon M. Soucy, Aris Edda Stachler, Yarden Shalev, Mor Zarkor, Leah Reshef, Neta Altman-Price, Anita Marchfelder, Uri Gophna*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)177-186
Number of pages10
JournalNature Microbiology
Issue number1
StatePublished - 1 Jan 2019


FundersFunder number
Constantiner Institute
Horizon 2020 Framework Programme787514
European Research Council
Deutsche ForschungsgemeinschaftMA1538/16-2
United States-Israel Binational Science Foundation2013061
Israel Science Foundation535/15


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