Rhizobium determinants of rhizosphere persistence and root colonisation

Bacterial persistence in the rhizosphere and colonisation of root niches are critical for the establishment of many beneficial plant-bacteria interactions including those between Rhizobium leguminosarum and its host legumes. Despite this, most studies on R. leguminosarum have focused on its symbiotic lifestyle as an endosymbiont in root nodules. Here, we use random barcode transposon sequencing (RB-TnSeq) to assay gene contributions of R. leguminosarum during competitive growth in the rhizosphere and colonisation of various plant species. This facilitated the identification of 189 genes commonly required for growth in diverse plant rhizospheres, mutation of 111 of which also affected subsequent root colonisation (rhizosphere progressive), and a further 119 genes necessary for colonisation. Common determinants reveal a need to synthesise essential compounds (amino acids, ribonucleotides, and cofactors), adapt metabolic function, respond to external stimuli, and withstand various stresses (such as changes in osmolarity). Additionally, chemotaxis and flagella-mediated motility are prerequisites for root colonisation. Many genes showed plant-specific dependencies highlighting significant adaptation to different plant species. This work provides a greater understanding of factors promoting rhizosphere fitness and root colonisation in plant-beneficial bacteria, facilitating their exploitation for agricultural benefit.