Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection

Authors: LUNEAU, JULIEN - Inrae; BAUDIN, MAEL - University Of California; MONNENS, THOMAS QUIRROZ - Inrae; CARRERE, SEBASTIEN - Inrae; BOUCHEZ, OLIVIER - Lawrence Berkeley National Laboratory; JARDINAUD, MARIE-FRANCOISE - Inrae; GRIS, CARINE - Inrae; FRANCOIS, JONAS - Inrae; RAY, JAYASHREE - Lawrence Berkeley National Laboratory; TORRALBA, BABIL - Inrae; ARLAT, MATTHIEU - Inrae; Lewis, Jennifer; LAUBER, EMMANUELLE - Inrae; DEUTSCHBAUER, ADAM - Lawrence Berkeley National Laboratory; NOEL, LAURENT - Inrae; BOULANGER, ALICE - Inrae

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2022
Publication Date: 6/15/2022
Citation: Luneau, J.S., Baudin, M., Monnens, T., Carrere, S., Bouchez, O., Jardinaud, M., Gris, C., Francois, J., Ray, J., Torralba, B., Arlat, M., Lewis, J.D., Lauber, E., Deutschbauer, A.M., Noel, L.D., Boulanger, A. 2022. Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection. New Phytologist. https://doi.org/10.1111/nph.18313.
DOI: https://doi.org/10.1111/nph.18313

Interpretive Summary: Plant diseases cause significant crop losses. Xanthomonas campestris is a bacterial pathogen that causes a destructive disease named black rot, in cauliflower, cabbage and broccoli. Once plants are infected, the bacteria can spread rapidly and cause disease, which leads to high yield losses. Bacteria must overcome many hurdles in order to cause disease, including entering the plant, colonizing host tissue and manipulating plant defense responses. We found that X. campestris readily enters the plant through natural pores called hydathodes, and that 365 genes are required for the bacteria to live. In addition, more than 180 genes are important for optimal growth of the bacteria in the host. This work identifies a suite of responses that contribute to the bacteria’s ability to colonize and cause disease in the host, as well as potential strategies to protect plants from infection.

Technical Abstract: Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization, especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) to perform a genome-wide screen and identify key bacterial fitness determinants of the vascular pathogen Xanthomonas campestris pv. campestris (Xcc) during infection of the cauliflower host plant (Brassica oleracea). This high-throughput analysis was conducted in hydathodes, the natural entry site of Xcc, in xylem sap and in synthetic media. Xcc did not face a strong bottleneck during hydathode infection. 181 genes important for fitness were identified in plant-associated environments with functional enrichment in genes involved in metabolism when only few genes known to be involved in virulence were found to be affected. The biological relevance of 12 genes was independently confirmed by phenotyping single mutants. Notably, we show that XC_3388, a protein with no known function (DUF1631), plays a key role in the adaptation and virulence of Xcc possibly through c-di-GMP-mediated regulation. This study revealed yet unsuspected social behaviors adopted by Xcc individuals when confined inside hydathodes at early infection stages.