Abstract

Understanding the bacterial communities associated with rice seeds is crucial for evaluating both beneficial microbiota and potential pathogens. In this study, 16S rRNA gene amplicon sequencing and species-specific PCR assays were employed to investigate the bacterial communities associated with Thai fragrant rice seeds of Khao Dawk Mali 105 (KDML105, susceptible to bacterial leaf blight, BLB) and Pathum Thani 1 (PTT1, moderately resistant), collected from paddy fields. The impact of Xanthomonas oryzae pv. oryzae (Xoo) infection on the seed-associated bacterial community in KDML105 was also analyzed. The core bacterial genera included Pantoea, Pseudomonas, Methylobacterium-Methylorubrum, Xanthomonas, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. While Pantoea predominated in seed samples of both rice cultivars and among culturable epiphytes in PTT1, Pseudomonas was the most abundant culturable bacterium in the endosymbiont communities of both cultivars. Alpha and beta diversity analyses revealed that BLB infection influenced bacterial community composition, with species richness being higher in KDML105 than in PTT1. Kosakonia, Paenibacillus, and Deinococcus were enriched in non-infected seeds, whereas Acidovorax, Mycobacterium, and Williamsia were more abundant in BLB-infected seeds. Species-specific assays confirmed the presence of Xoo in BLB-infected KDML105 seeds, while multiple Pantoea species were detected in all samples. Importantly, 16S rRNA amplicon sequencing identified Burkholderia glumae at the species level, which was further validated using species-specific primers. These findings demonstrate the effectiveness of integrating 16S rRNA gene amplicon sequencing with species-specific PCR for comprehensive profiling of seed-associated microbiota in BLB-susceptible and moderately resistant cultivars, while revealing the coexistence of pathogenic and potentially beneficial bacteria that warrant further investigation into their roles in rice health and disease resistance.