Niche and Geographic Drivers Shape the Diversity and Composition of Endophytic Bacteria in Salt-Tolerant Peanut

Endophytic bacteria play an important role in the growth, stress tolerance, and metabolic function of salt-tolerant peanuts, yet their community assembly across different saline-alkali soils and plant organs remains poorly characterized. In this study, the V3-V4 variable region of the endophytic bacteria 16S rRNA gene in three organs (roots, leaves, and pods) of high-oleic-acid peanut variety Huayu9118 from three saline-alkali locations (Xinjiang, Jilin, and Shandong, China) was analyzed by high-throughput sequencing. A total of 1,360,313 effective sequences yielded 19,449 amplicon sequence variants (ASVs), with <i>Proteobacteria</i> (45.86-84.62%), <i>Bacteroidota</i> (6.52-13.90%), and <i>Actinobacteriota</i> (3.97-10.87%) dominating all samples. Niche strongly influenced microbial diversity: the roots exhibited the highest level of richness (Chao 1/ACE indices), while the leaves showed the greatest diversity (Shannon/Simpson indices) in XJ samples. Significant compositional differences were observed between aerial (leaves) and underground (roots/pods) organs. Geographic location also markedly shaped endophytic communities, with stronger effects in roots and pods than in leaves-a pattern supported by PCoA combined with ANOSIM (R (roots) = 1, R (pods) = 0.874, R (leaves) = 0.336, respectively, <i>p</i> < 0.001). Saline-alkali adaptation led to a marked enrichment of <i>Novosphingobium</i> in roots and pods and of <i>Halomonas</i> in leaves compared to non-saline-alkali-grown peanuts. Furthermore, the endophytic communities within the same organ type varied significantly across the three saline-alkali sites. Redundancy analysis (RDA) identified the key environmental factors shaping bacterial community composition in the root samples from each location: available phosphorus (AP) and sulfate (SO₄^2-) were the strongest predictors in XJ; available potassium (AK) and chloride (Cl^-) in DY; and hydrolyzed nitrogen (HN), pH, soil organic matter (SOM), and bicarbonate (HCO₃^-) in JL. These findings demonstrate that niches and geographical conditions determined the composition and relative abundance of endophytic bacteria in salt-tolerant peanuts, providing new insights into microbial ecological adaptation in saline-alkali ecosystems.