CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography.

Matthias Wietz,Paul R Jensen,Natalie Millán-Aguiñaga

doi:10.1186/1471-2164-15-936

Abstract

BackgroundProkaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus.ResultsCRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense.ConclusionsThis study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-936) contains supplementary material, which is available to authorized users.

Highlights

Prokaryotic CRISPR-Cas systems confer resistance to viral infection and mediate bacteria-phage interactions
CRISPR content in 75 Salinispora strains Genome sequences from 75 Salinispora strains derived from seven global collection sites were analyzed for CRISPR-Cas content (Additional file 1)
Salinispora CRISPR content exceeded the average reported for mesophilic bacteria [1] and marine bacterial metagenomes [41] and accounted for up to 0.3% of some genomes, which is approximately a third of the reported ‘prokaryotic maximum’ [2]

Summary

Introduction

Prokaryotic CRISPR-Cas systems confer resistance to viral infection and mediate bacteria-phage interactions. Comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus. CRISPRs (clustered regularly interspaced short palindromic repeats) have been detected in approximately 85% of archaeal and 50% of bacterial genomes [1]. They are considered a means of prokaryotic adaptive immunity against bacteriophages [2], which are major determinants of prokaryotic abundance, diversity and community structure [3]. In the case of environmental bacteria, it has been shown that CRISPRs are widespread in Cyanobacteria except for the major marine lineages Prochlorococcus and Synechococcus [15]. CRISPRs have been linked to host-phage co-evolution, community structuring and biogeographic patterns in microbial mats [21], acidophilic biofilms [22], and hot spring microbiota [23]

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Conclusion