CRISPR–Cas systems in Microcoleus cyanobacteria show a dynamic history of gene flow

CRISPR–Cas immune systems are widespread across the filamentous cyanobacterial genus Microcoleus, but their distribution does not follow the species-level phylogeny of these bacteria, according to a new open-access study published in Biology Direct on 21 October 2026.

The research, led by Barbora Hájková and including Aleksandar Stanojković, Svatopluk Skoupý and Petr Dvořák, integrated CRISPR–Cas locus identification, phylogenetic analyses, genome and environmental association analyses, and spacer target searches across 14 Microcoleus species.

Microcoleus is globally distributed and plays an important role in biological soil crusts, the study’s background notes. CRISPR–Cas immunity is a prokaryotic defense mechanism that mediates interactions with mobile genetic elements and may thereby contribute to genome evolution, yet its diversity and evolutionary significance in cyanobacteria had remained poorly understood.

Instead of tracking species relationships, the analysis found that locus heterogeneity and module-specific evolutionary histories indicate repeated gain, loss and exchange of CRISPR–Cas components. The authors suggest that gene flow has contributed to the diversification of these systems.

Spacer composition and sharing patterns indicated dynamic exposure to mobile genetic elements, potentially linked to environmental context.

Although a large proportion of spacer targets remained unidentified, expanded protospacer searches revealed plasmid-like elements as prominent targets among the identifiable sequences, the researchers report.

Together, the authors conclude, the results suggest that CRISPR–Cas systems in Microcoleus are highly dynamic and reflect interactions between gene flow, mobile genetic elements and environmental context, highlighting their potential role as variable components of cyanobacterial genome evolution.

The findings are based on computational analyses of bacterial genomes rather than experiments testing immune function, and the article is being shared early as a peer-reviewed, accepted manuscript that is citable and carries a permanent DOI, subject to further edits before the final version of record.

Subject of Research: Diversity and evolution of CRISPR–Cas systems in Microcoleus cyanobacteria

Article Title: CRISPR–Cas diversity in Microcoleus genomes reveals a dynamic history of gene flow and mobile genetic element interactions

Article References: Hájková, B., Stanojković, A., Skoupý, S., & Dvořák, P. (2026). CRISPR–Cas diversity in Microcoleus genomes reveals a dynamic history of gene flow and mobile genetic element interactions. Biology Direct. https://doi.org/10.1186/s13062-026-01031-8

Image Credits: AI Generated

DOI: 10.1186/s13062-026-01031-8

Keywords: CRISPR-Cas, Microcoleus, cyanobacteria, gene flow, mobile genetic elements, biological soil crusts, spacers, plasmids, genome evolution, phylogenetics, CRISPR, diversity