Comparative Genomic Understanding of Gram-Positive Plant Growth-Promoting Leifsonia

Abstract

Root-associated bacteria play critical roles in shaping plant health for abiotic and biotic stress tolerance. The Leifsonia genus includes pathogenic and beneficial bacteria but limited research is available comparatively across species regarding their association with plants. We recently identified the plant growth-promoting Leifsonia sp. C5G2 isolated from the rhizosphere of Plectranthus scutellarioides (coleus) that increased stress tolerance and quality of water-stressed greenhouse ornamentals. Using this beneficial strain as a model, we performed comparative genomics with beneficial, commensal, and pathogenic Leifsonia spp. to better understand plant association and growth promotion under abiotic stress. Comparative phylogenetic analyses showed that beneficial and commensal Leifsonia spp. clustered separately from pathogenic Leifsonia xyli subsp. xyli. In addition, the beneficial or commensal strains share biosynthetic gene and orthologous protein clusters that are not shared with known phytopathogens in our analysis. The phytopathogenic Leifsonia strains also share noticeably higher percent homology with plant-associated virulence factors in closely related Clavibacter spp. than the beneficial or commensal strains. Genome analysis supplemented with in vitro assays validated the findings that our model growth-promoting Leifsonia sp. strain C5G2 was highly prolific on diverse carbon sources. This is unlike known fastidious growth behaviors of phytopathogenic Leifsonia spp. Beneficial Leifsonia sp. C5G2 imparts water stress tolerance in plants, and multiple genes were identified in the genomes of beneficial Leifsonia strains that are potentially involved in bacterial osmotic stress and the production of osmoprotectants and vitamin B9. This work sheds light on the diversity of the genus Leifsonia, with a better understanding of potential mechanisms employed by poorly understood beneficial bacteria.