BACKGROUND: Microorganisms play important ecological roles during interactions with plants, with some strains promoting plant performance. However, the molecular basis of bacterial adaptation to the plant environment remains poorly understood. Microbial plant growth promotion is a complex process that likely involves numerous bacterial genes, many of which remain uncharacterized. In this study, we aimed to identify genes tightly associated with the bacterial adaptation to plant hosts by integrating transcriptomic data from bacteria colonizing roots with comparative genomic and metagenomic analyses. RESULTS: Here, we identified a set of bacterial genes that were significantly upregulated during root colonization and are more abundant in rhizosphere communities than in bulk soils. Many of these genes had not been previously linked to plant-bacteria interactions. Comparative genomic analyses revealed some of these genes as more prevalent in plant-associated Pseudomonas genomes than in genomes from other environments. We argue that these genes may play relevant biological roles in this host, although only a few have been previously associated with plant colonization. Among them, we focused on a gene homologous to yafL, which encodes a cysteine peptidase of the NlpC/P60 family, known for its role in peptidoglycan remodelling. This gene is more abundant in rhizosphere microbiomes than in bulk soils, and it showed induced expression on the root surface, supporting its ecological relevance in root-associated environments. Functional validation using a knockout mutant confirmed its contribution to plant-bacteria interactions by affecting root architecture and plant growth. CONCLUSIONS: This study provides new insights into the genetic basis of bacterial adaptation to the plant root environment. By integrating transcriptomic and comparative genomic analyses, we identified numerous genes upregulated during root colonization that are enriched in plant-associated Pseudomonas genomes. Our findings highlight previously overlooked bacterial functions with potential roles in plant-microbe interactions. The functional validation of a protein of the NlpC/P60 family supports its involvement in plant-bacteria interactions and underscores the importance of uncharacterized genes in shaping beneficial associations in the rhizosphere. Video Abstract.

Associated Research Unit of Plant Microorganism Interaction USAL CSIC Salamanca 37008 Spain

Biological Institute of São Paulo Vila Mariana Av Conselheiro Rodrigues Alves 1252 São Paulo SP 04014 002 Brazil

College of Life Sciences Sichuan Normal University Chengdu 610101 China

Departamento de Microbiología y Genética Universidad de Salamanca Salamanca 37007 Spain

Huzhou Center of Industrial Biotechnology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Huzhou 313000 China

Institute for Agribiotechnology Research Villamayor Salamanca 37185 Spain

Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai 200032 China

Laboratory of Environmental Microbiology Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague Czech Republic

Laboratory of Fungal Genetics and Metabolism Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague Czech Republic

Laboratory of Molecular Structure Characterization Institute of Microbiology of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague Czech Republic

Norwegian College of Fishery Science UiT the Arctic University of Norway Muninbakken 21 Tromsø 9019 Norway

Unidad de Excelencia Producción Agrícola y Medioambiente Universidad de Salamanca Salamanca 37185 Spain

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