The CRISPR-Cas system is an adaptive immune mechanism prevalent in most archaea and approximately half of bacteria, enabling specific recognition and targeting of foreign nucleic acids associated with viruses, bacteriophages, and other mobile genetic elements. The current classification comprises two classes, six types and 33 subtypes. Given the diversity of microbial taxonomy and habitats, the phylogenetic relationships and ecological interactions involving CRISPR-Cas systems may vary significantly. To investigate these variations, we constructed a dataset of 75,909 non-redundant metagenome-assembled genomes (MAGs) from 11 ecosystems, which illuminated the distribution and evolutionary trajectories of CRISPR-Cas systems and Cas operons across different habitats and taxa. Our findings indicate that CRISPR-Cas systems and Cas operons are more prevalent in anaerobic and thermophilic ecosystems, such as thermal spring, wastewater anaerobic digestor, terrestrial deep subsurface soil, marine mammal guts, and the human gut. Notably, phyla adapted to these extreme conditions exhibited a higher prevalence of CRISPR-Cas systems and Cas operons. Even among widely distributed phyla, such as Acidobacteriota, Armatimonadota, and Chloroflexota those residing in anaerobic or thermophilic environments showed greater CRISPR-Cas  prevalence than their counterparts in more general ecosystems. These results suggest that environmental factors significantly impact the presence of CRISPR-Cas systems, supporting the hypothesis that these systems evolved in thermophilic Archaea. Furthermore, variations in subtypes across different habitats within certain phyla imply that horizontal gene transfer plays a crucial role in microbial adaptation. This study enhances our understanding of microbial adaptation via CRISPR-Cas systems, which also hold promise for genome editing applications. However, numerous practical limitations still exist. Thus, we interrogated our dataset to identify potential active Cas9 with compact structures and broader applications, aiming to enrich the genome editing toolbox and facilitate the development of innovative genetic engineering technologies.
 

CRISPR-Cas9,microbial,Genome editing