Genome-wide interrogation of genetic requirements for root colonization by CRISPRi-seq in Bacillus subtilis
- 1University of Lausanne
Abstract
Bacillus subtilis is a known plant growth promoting rhizobacterium, yet, the genetic basis of effective root colonization remains understudied. Here, we applied genome-wide CRISPR interference sequencing (CRISPRi-seq) to systematically identify genes required for early Arabidopsis thaliana root colonization by the B. subtilis strain 3610 . Our genome-wide inducible CRISPRi library was used to screen for bacterial fitness during hydroponic root colonization. A complementary RNA-seq in the same conditions further revealed a distinct transcriptional state of root-associated cells. We identified 249 genes impacting root colonization. We reveal a critical role of cell envelope remodeling during early root association, specifically wall teichoic acid synthesis and D-alanylation. Moreover, we observed a metabolic shift toward TCA-cycle-driven aerobic growth with uptake of fructose, active repression of sporulation, competence and prophage programs, as well as induction of secondary metabolite biosynthesis. Our work establishes CRISPRi-seq as a powerful tool for dissecting bacterial-plant interactions relevant to sustainable agriculture.
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BibTeX
@misc{minhas2026genomewide,
title = {{Genome-wide interrogation of genetic requirements for root colonization by CRISPRi-seq in Bacillus subtilis}},
author = {V. Minhas and W. Abidi and J. C. Almiron and H.-H. M. Tsai and V. D. Tendon and D. Synefiaridou and J.-W. Veening and N. Geldner},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.10.750580},
url = {https://www.biorxiv.org/content/10.64898/2026.09.10.750580v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Genome-wide interrogation of genetic requirements for root colonization by CRISPRi-seq in Bacillus subtilis
AU - V. Minhas
AU - W. Abidi
AU - J. C. Almiron
AU - H.-H. M. Tsai
AU - V. D. Tendon
AU - D. Synefiaridou
AU - J.-W. Veening
AU - N. Geldner
PY - 2026
DA - 2026/09/10
PB - bioRxiv
DO - 10.64898/2026.09.10.750580
UR - https://www.biorxiv.org/content/10.64898/2026.09.10.750580v1
AB - Bacillus subtilis is a known plant growth promoting rhizobacterium, yet, the genetic basis of effective root colonization remains understudied. Here, we applied genome-wide CRISPR interference sequencing (CRISPRi-seq) to systematically identify genes required for early Arabidopsis thaliana root colonization by the B. subtilis strain 3610 . Our genome-wide inducible CRISPRi library was used to screen for bacterial fitness during hydroponic root colonization. A complementary RNA-seq in the same conditions further revealed a distinct transcriptional state of root-associated cells. We identified 249 genes impacting root colonization. We reveal a critical role of cell envelope remodeling during early root association, specifically wall teichoic acid synthesis and D-alanylation. Moreover, we observed a metabolic shift toward TCA-cycle-driven aerobic growth with uptake of fructose, active repression of sporulation, competence and prophage programs, as well as induction of secondary metabolite biosynthesis. Our work establishes CRISPRi-seq as a powerful tool for dissecting bacterial-plant interactions relevant to sustainable agriculture.
ER -