A predicted CRISPR-mediated symbiosis between uncultivated archaea

Sarah P Esser, Janina Rahlff, Weishu Zhao, Michael Predl, Julia Plewka, Katharina Sures, Franziska Wimmer, Janey Lee, Panagiotis S Adam, Julia McGonigle, Victoria Turzynski, Indra Banas, Katrin Schwank, Mart Krupovic, Till L V Bornemann, Perla Abigail Figueroa-Gonzalez, Jessica Jarett, Thomas Rattei, Yuki Amano, Ian K BlabyJan-Fang Cheng, William J Brazelton, Chase L Beisel, Tanja Woyke, Ying Zhang, Alexander J Probst (Corresponding author)

Publications: Contribution to journalArticlePeer Reviewed


CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.

Original languageEnglish
Pages (from-to)1619-1633
Number of pages15
JournalNature Microbiology
Issue number9
Early online dateSep 2023
Publication statusPublished - 1 Sep 2023

Austrian Fields of Science 2012

  • 106026 Ecosystem research
  • 106022 Microbiology


  • Archaea/genetics
  • Symbiosis/genetics
  • Genomics
  • Plasmids
  • DNA/metabolism

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