Genome-wide interrogation of genetic requirements for root colonization by CRISPRi-seq in Bacillus subtilis

Genome-wide CRISPRi-seq in Bacillus subtilis NCIB3610 identified 249 genes that impact early colonization of Arabidopsis thaliana roots.

• Why it matters: The genetic requirements for effective root colonization by this plant growth–promoting rhizobacterium are still unclear, limiting mechanistic understanding for sustainable agriculture.
• What they did: The authors performed genome-wide CRISPR interference sequencing (CRISPRi-seq) to screen gene requirements during early root colonization, and paired it with bacterial RNA-seq under the same conditions.
• The result: Root-associated cells show a distinct transcriptional state, including biofilm-independent cell envelope remodeling via wall teichoic acid synthesis and D-alanylation, plus shifts toward TCA-cycle-driven aerobic growth and fructose utilization while repressing sporulation, competence, and prophage programs.

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