Widespread and Abundant CRISPR-Cas Systems in the Deep Ocean

CRISPR-Cas systems have revolutionized modern biology. Most CRISPR-Cas systems in use for biotechnological applications derive from cultivated bacteria, but evidence suggests that environmental microbiomes harbor a large untapped diversity of these systems. Yet, our understanding of which environmental and biological factors drive the prevalence of CRISPR-Cas systems in the oceans remains limited. A search for CRISPR-Cas systems was conducted among 176 globally-distributed marine microbial metagenomes from the Malaspina expedition, which sampled both free-living and particle-attached microbiomes with emphasis on the deep ocean. We show that CRISPR-Cas systems are proportionally more abundant among microbiomes from the deep ocean than in the photic layers and among free-living microbes compared to those attached to particles, reflecting the higher concentrations of archaea and their viruses in these habitats. We identified 1,146 CRISPR-cas loci, some of which displayed unique loci architectures. From these loci, a total of 48 Cas9 proteins were identified, many of which are potentially novel. These discoveries expand the scope of CRISPR-Cas diversity and point at the deep-sea as a rich reservoir of these resources, which helps guide future bioprospecting efforts.