Linking CRISPR-Cas to ecology and evolution of the fish pathogenic Moritella viscosa

Background: Moritella viscosa is the causative agent of winter-ulcer disease affecting farmed Atlantic salmon (Salmo salar L.). To gain further insight into the traits that cause the phenotypic and genotypic clades within this bacterium we analyzed the genome sequences of twelve M.viscosa strains. Horizontal gene transfer may cause genome variations and effect evolution and adaptation of microorganisms. In this study, we used genome structure characteristics to investigate if clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) correlates with adaptive immunity against mobile genetic elements (MGEs).Results: The comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages, where the major genomic variations between the isolates resulted from MGEs. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follows the phylogenetic lineages. A subset of the spacer content was revealed to match essential prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid distribution were reflected in the content of the CRISPR-spacer profiles.Conclusions: Our data describe that CRISPR-Cas interactions in M. viscosa may impact genome evolution by prophage and plasmid diversity, and that patterns in spacer and MGE distributions, linked to strain relationship, point to a lineage-specific contact with microenvironments.