The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments

Abstract

CRISPR-Cas systems are considered as barriers to horizontal gene transfer (HGT). However, the influence of such systems on HGT within species is unclear. Also, little is known about the impact of CRISPR-Cas systems on bacterial evolution at the population level. Here, using Bacillus cereus sensu lato as model, we investigate the interplay between CRISPR-Cas systems and HGT at the population scale. We found that only a small fraction of the strains have CRISPR-Cas systems (13.9% of 1871), and most of such systems are defective based on their gene content analysis. Comparative genomic analysis revealed that the CRISPR-Cas systems are barriers to HGT within this group, since strains harboring active systems contain less mobile genetic elements (MGEs), have lower fraction of unique genes and also display limited environmental distributions than strains without active CRISPR-Cas systems. The introduction of a functional CRISPR-Cas system into a strain lacking the system resulted in reduced adaptability to various stresses and decreased pathogenicity of the transformant strain, indicating that B. cereus group strains could benefit from inactivating such systems. Our work provides a large-scale case to support that the CRISPR-Cas systems are barriers to HGT within species, and that in the B. cereus group the inactivation of CRISPR-Cas systems correlated with acquisition of MGEs that could result in better adaptation to diverse environments.

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

“…euphylliae H1 genome, most Thalassotalea genomes (n = 11) have a few CRISPR and spacers. This suggests that members of the genus Thalassotalea might be less subject to evolutionary (i.e., it is genomically stable) or phage infection stresses in their ecological niches [ 93 , 94 , 95 ].…”

Isolation and Characterization of Bacillus cereus Phage vB_BceP-DLc1 Reveals the Largest Member of the Φ29-Like Phages

“…Interestingly, in the four sensitive strains, only 1608-3C showed blurry plaques when spotted with less diluted DLc1 suspension, and the plaques disappeared in high dilutions (Figure 7). Since B. cereus 1608-3C can be also largely adsorbed by DLc1, as with other sensitive strains (Figure 9D), the resistance of this strain to DLc1 could be due to some other reasons, such as the CRISPR-Cas defense system [62], rather than the adsorption inhibition. The occurrence of blurry plaques in 1608-3C under high-titer phage spotting and the absence of individual plaques under higher dilutions could be the situation of "lysis from without" [63], in which the bacterial lysis is induced by phage adsorption at high multiplicity and no progeny is produced.…”

Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato

“…Previous studies have shown that the number of MGEs is higher in C. botulinum BoNT C/D (lineage Ia) than in BoNT D/C (lineage Ib) containing several different CRISPR types ( Woudstra et al, 2016 , 2017 ). In B. cereus , strains with active CRISPR-Cas systems have fewer MGEs than strains with partial CRISPR-Cas systems or without any CRISPR-Cas systems ( Zheng et al, 2020 ). Likewise, CRISPR-Cas systems may play a barrier role against horizontal gene transfer by preventing the acquisition of MGEs, resulting in a lower occurrence of plasmids and phages in strains from lineage Ib, and the opposite in lineage Ia strains.…”