Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations

Beta-proteobacteria belonging to the genus Acidovorax have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study, we investigated the genomic properties of 52 bacterial strains of the genus Acidovorax, isolated from healthy roots of Lotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with L. japonicus, performed in a gnotobiotic system, we distinguished seven robust plant-growth promoting strains from strains with no significant effects on plant-growth. We showed that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus Acidovorax sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We showed that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living Acidovorax strains did not harbour any secretion-systems. Overall, our data indicate that Acidovorax strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.

Automated summary

This study investigated the genomic properties of 52 bacterial strains of the genus Acidovorax isolated from healthy roots of Lotus japonicus, identifying traits important for effective plant-growth promotion. Seven robust plant-growth promoting strains were distinguished based on bioassays, showing differences in protein families related to sensing and transport of organic acids, phytohormone production, resistance, and antimicrobial compound production. Comparing the genomes with plant pathogens and free-living strains of Acidovorax revealed features correlated with commensal and pathogenic lifestyle, with differences mainly in the use of plant-derived lipids and presence of secretion systems. Overall, Acidovorax strains undergo extensive adaptations in their particular lifestyle through genetic changes.