Endophytic bacteria in different tissue compartments of African wild rice (Oryza longistaminata) promote perennial rice growth

Oryza longistaminata is an African wild rice species with valuable agronomic traits and the donor parent of perennial rice. Endophytic bacteria play an important role in host health, adaptive evolution and stress tolerance. However, endophytic bacterial communities in O. longistaminata and their plant growth-promoting (PGP) effects on the perennial rice of O. longistaminata offspring are poorly understood. In this study, the endophytic bacterial diversity, composition and network structures in the root, stem, and leaf tissues of O. longistaminata were characterized using Illumina sequencing of the 16S rRNA gene. The results suggested that O. longistaminata contains a multitude of niches for different endophytic bacteria, among which the root endosphere is more complex and functionally diverse than the stem and leaf endospheres. Tissue-specific biomarkers were identified, including Paludibaculum, Pseudactinotalea and Roseimarinus and others, for roots, Blautia for stems and Lachnospiraceae NK4A136 for leaves. The endophytic bacterial network of O. longistaminata was reassembled for various functions, including degradation/utilization/assimilation, detoxification, generation of precursor metabolites and energy, glycan pathways, macromolecule modification and metabolism. A total of 163 endophytic bacterial strains with PGP traits of potassium release, phosphate solubilization, nitrogen fixation, siderophore activity, indole-3-acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity were isolated from O. longistaminata. Eleven strains identified as Enterobacter cloacae, Enterobacter ludwigii, Stenotrophomonas maltophilia, Serratia fonticola, and Bacillus velezensis showed stable colonization abilities and PGP effects on perennial rice seedlings. Inoculated plants generally exhibited an enhanced root system and greater photosynthesis, biomass accumulation and nutrient uptake. Interestingly, two strains of E. cloacae have host genotype-dependent effects on perennial rice growth. The results of this study provide insights into the endophytic bacterial ecosystems of O. longistaminata, which can potentially be used as biofertilizers for sustainable perennial rice productivity.