title: Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems.
abstract: Current understanding of microorganism-virus interactions, which shape the evolution and functioning of Earth's ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. We correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: David
authors.initials: D
authors.lastname: Burstein
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.|Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: Christine L
authors.initials: CL
authors.lastname: Sun
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Christopher T
authors.identifier: http://orcid.org/0000-0002-7758-6447
authors.initials: CT
authors.lastname: Brown
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Itai
authors.initials: I
authors.lastname: Sharon
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Karthik
authors.initials: K
authors.lastname: Anantharaman
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Probst
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Thomas
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.|Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D001419:Bacteria; D064113:CRISPR-Cas Systems / Q000235:genetics*; D005227:Fatty Acids / Q000096:biosynthesis; D016680:Genome, Bacterial / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D054892:Metagenome / Q000235:genetics; D009711:Nucleotides / Q000096:biosynthesis; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D013559:Symbiosis / Q000235:genetics*; D014780:Viruses
chemical_list: D005227:Fatty Acids; D009711:Nucleotides
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