CRISPR-Cas Systems to Probe Ecological Diversity and Host–Viral Interactions

  • Nicole L. Held
  • Lauren M. Childs
  • Michelle Davison
  • Joshua S. Weitz
  • Rachel J. Whitaker
  • Devaki BhayaEmail author


A key feature of the CRISPR-Cas defense system is the ability of the host to rapidly acquire novel spacers from invasive foreign genetic elements such as plasmids, viruses, or transposons. Consequently, host CRISPR loci have the potential to provide time-resolved information about exposure to foreign genetic elements as well as fine-scale ecological diversity. Furthermore, viral genomes can mutate rapidly, allowing viruses to circumvent the host CRISPR-encoded immunity system, which relies on close matches between spacers and incoming nucleic acids. Thus, CRISPR-Cas systems may drive complex, coevolving relationships between bacteria or archaea and viruses. We discuss how ecologically based approaches, in both natural and experimental systems, provide unique insights into host and viral diversity and horizontal gene transfer of CRISPR loci. We critically review recent attempts to model host–viral coevolutionary dynamics in the context of CRISPR loci. Finally, we highlight the future directions in which experimental analyses of host–viral coevolution can be fruitfully combined with theoretical approaches.


strain-specific spacers 



NLH and RJW acknowledge support from NSF DEB-0816885. DB and MD acknowledge support from the NSF, The Carnegie Institution of Science and Stanford University. JSW acknowledges the support of a grant from the James S. McDonnell Foundation. JSW holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Nicole L. Held
    • 1
  • Lauren M. Childs
    • 2
  • Michelle Davison
    • 3
    • 5
  • Joshua S. Weitz
    • 4
  • Rachel J. Whitaker
    • 1
  • Devaki Bhaya
    • 3
    Email author
  1. 1.Department of MicrobiologyUniversity of IllinoisUrbanaUSA
  2. 2.School of Biology and School of MathematicsGeorgia Institute of TechnologyAtlantaUSA
  3. 3.Department of Plant BiologyCarnegie Institution for ScienceStanfordUSA
  4. 4.School of Biology and School of PhysicsGeorgia Institute of TechnologyAtlantaUSA
  5. 5.Department of BiologyStanford UniversityStanfordUSA

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