{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "University of Lausanne"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "name": "V. Minhas"
    },
    {
      "name": "W. Abidi"
    },
    {
      "name": "J. C. Almiron"
    },
    {
      "name": "H.-H. M. Tsai"
    },
    {
      "name": "V. D. Tendon"
    },
    {
      "name": "D. Synefiaridou"
    },
    {
      "name": "J.-W. Veening"
    },
    {
      "affs": [
        0
      ],
      "name": "N. Geldner"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/evtrpsk1ebxhf.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.10.750580",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750580v1.full",
  "id": "evtrpsk1ebxhf",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750580v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "microbiology"
    ],
    [
      "openalex",
      "1110|Plant-Microbe Interactions and Immunity"
    ]
  ],
  "openalex": "W7212373912",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750580v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-10",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/evtrpsk1ebxhf.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:34Z",
      "native_id": "10.64898/2026.09.10.750580",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750580v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "Genome-wide interrogation of genetic requirements for root colonization by CRISPRi-seq in Bacillus subtilis",
  "title_text": "Genome-wide interrogation of genetic requirements for root colonization by CRISPRi-seq in Bacillus subtilis",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:34Z",
  "url": "https://research.draconitic.com/paper/evtrpsk1ebxhf",
  "venue": "bioRxiv",
  "versions": []
}