AimsCotton seeds are frequently treated with acid to remove fibres and reduce seed-transmitted diseases. This process also eliminates beneficial bacteria on the seed surface. The goal of this research was to seek and apply beneficial bacteria to acid delinted cotton seeds to evaluate their growth-promoting and salt stress alleviating effects in seedlings. Methods and ResultsBacteria were isolated from non-cultivated plants in the Malvaceae. Seeds were collected from Portia tree (Thespesia populnea) and wild cotton (Gossypium hirsutum) from coastal and arid areas of Puerto Rico. Bacillus amyloliquefaciens, Curtobacterium oceanosedimentum and Pseudomonas oryzihabitans were inoculated onto acid delinted cotton seeds. Bacteria increased cotton seed germination and length of emerging seedling radicles. Cotton seeds were inoculated with B. amyloliquefaciens to evaluate growth and root architecture of non-stressed and salt stressed seedlings. Inoculating cotton seeds with B. amyloliquefaciens led to a greater percentage of seedlings with expanded cotyledons after 8days, enhanced primary and lateral root growth, and altered root architecture. Similar results were obtained when okra seeds were inoculated with B. amyloliquefaciens. ConclusionThe data supported the hypothesis that non-cultivated plants in the Malvaceae growing in stressful environments possess bacteria that promote growth, alter root architecture and alleviate salt stress of cotton and okra seedlings. Significance and Impact of the StudyThis study demonstrated the effects of applying beneficial bacteria on acid delinted cotton seeds. Inoculating seeds with salt stress alleviating bacteria could improve the growth of crop seedlings that are vulnerable to soil salinization.