Genetic Drivers of Plant Root Colonisation by the Biocontrol Agent Pseudomonas protegens Pf-5

Plant growth-promoting bacteria can confer a range of health benefits to plants, and are increasingly being used in agriculture as bioinoculants to enhance crop performance and prevent diseases. However, within complex rhizosphere communities, their success as bioinoculants depends heavily on their capacity to competitively colonise root systems. Here, we uncover genetic determinants of root colonisation by the biocontrol agent Pseudomonas protegens Pf-5, known for its ability to suppress multiple plant diseases. Using Transposon-Directed Insertion Site Sequencing (TraDIS), we systematically assayed the entire P. protegens Pf-5 genome to determine genes involved in colonising the rhizoplane of two key agricultural crops, cotton (n = 153 Pf-5 genes) and wheat (n = 110 Pf-5 genes). We find a large overlap of 80 P. protegens Pf-5 genes which are important for colonisation fitness in both plants, suggesting that these encode core traits linked to root colonisation. In-depth functional annotation of these genes, leveraging both protein sequence and structure, reveals key traits that promote P. protegens Pf-5 rhizoplane fitness, including biofilm formation, surface motility, nucleotide and amino acid biosynthesis, sugar catabolism, iron uptake, low-oxygen growth, and stress response mechanisms. These findings can help guide future design and selection of microbial inoculants with improved capacity for competitive root colonisation.