• Garriga-Canut M, Cannon N, Benton M, Zanon A, Horsfield ST, Scheurich J, Remans K, Lees J, Paix A, van Gestel J. 2026. Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species. Mol Syst Biol. doi: 10.1038/s44320-025-00180-8. Online ahead of print.

Dictyostelids are a species-rich clade of cellular slime molds that are widely found in soils and have been studied for over a century. Due to a lack of genome editing methods, most molecular research in Dictyostelids has focused on only a single species, Dictyostelium discoideum, which has severely limited broad-scale comparative analyses. Here, we introduce the first CRISPR-Cas9 editing approach that is cloning-free, selection-free, highly efficient, and effective across Dictyostelid species that diverged millions of years ago. Depending on the CRISPR-Cas9 target site, our editing approach generates knock-out efficiencies of up to 90% and knock-in efficiencies of up to 50% without a selective marker. We show that mutants can be isolated as soon as one day post-transfection, vastly outpacing existing methods for generating knock-outs, fusion proteins, and expression reporters. Leveraging single-cell sorting and fluorescent microscopy, we could readily apply our CRISPR-Cas9 editing approach to phylogenetically distant Dictyostelid species, including those that have never been genome edited before. Our methods therefore open the door to performing broad-scale genetic interrogations across the Dictyostelids.

  • Garriga-Canut M, Cannon N, Benton M, Zanon A, Horsfield ST, Scheurich J, Remans K, Lees J, Paix A, van Gestel J. 2025. Selection-free CRISPR-Cas9 editing protocol for distant Dictyostelid species. bioRxiv. 10.1101/2025.03.23.644600

  • Koo BM, Todor H, Sun J, van Gestel J, Hawkins JS, Hearne CC, Banta AB, Huang KC, Peters JM, Gross CA. 2025.
    Comprehensive genetic interaction analysis of the Bacillus subtilis envelope using double-CRISPRi. Cell Syst. 16(11):101406.

  • van Gestel J, Koo BM, Stürmer VS, Garriga-Canut M, Wagner J, Zanon A, Gross CA. 2025. Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation. Proc Natl Acad Sci U S A. 122(39):e2518989122.

Soils host complex multi-trophic communities with diverse, mostly microbial, predator and prey species, including numerous bacterivorous protists and bacterial prey. The molecular mechanisms underlying microbial predator-prey interactions have thus far mainly been explored using reductionist methods, outside the soil environment and independent from the broader life history strategies that microbes display in soils. In this Comment, we advocate for an integrative research approach, combining molecular systems biology and microbial ecology, to investigate how predator-prey interactions shape microbial life history strategies and thereby population dynamics in natural soil communities.