Species-level bacterial community shift in rice growth stages

The phyllosphere is a major microbial habitat, where resident communities promote plant growth, suppress pathogens, and induce disease resistance. Here we examined how rice growth stages influence microbial colonization by analyzing bacterial communities in the phyllospheres of three growth stages (panicle initiation, heading, harvesting) across three genotypes: 'Koshihikari' and two introgression lines. Bacterial communities were similar among genotypes in both leaves and stems at heading but became distinct at harvesting, indicating that growth stages and plant organ play primary roles in shaping community structure. Full-length 16S rRNA gene amplicon sequencing further revealed significant shifts in species composition, with Pseudomonas species, such as Pseudomonas brenneri and Pseudomonas helmanticensis, were consistently present across organs and stages, while Enterobacter species showed stage-specific colonization. These findings highlight the dynamic nature of phyllosphere microbial communities throughout plant development and underscore the importance of organ- and stage-specific factors in shaping plant-microbe interactions.