Comparative metagenomic analysis of rice phyllosphere bacterial communities under semi-organic and non-organic farming systems

In the global cultivation of rice (Oryza sativa L.), synthetic fertilizers and pesticides are used to increase yield and manage pests and diseases. Intensive agriculture disrupts native microbial populations including those in the phyllosphere. This study used metagenomic analysis to compare the diversity and composition of phyllosphere bacterial communities in rice cultivated in semi-organic and non-organic systems. The analysis identified 38 phyla, 76 classes, 166 orders, 343 families, 732 genera, and 1094 bacterial species. Although both systems shared a similar taxonomic composition from the phylum to genus level, the semi-organic samples showed slightly higher microbial diversity and evenness. The most dominant phylum in both cultivation systems was Cyanobacteriota. Bacilliota, Pseudomonadota, and Fusobacteriota were more abundant in the semi-organic system. The dominant species in both systems Thalassoporum komareki, Holzapfeliella floricola, Cyanothece aeruginosa, and Idiomarina baltica, are associated with ecological functions such as photosynthesis, nitrogen fixation, and organic matter decomposition. Semi-organic farming also resulted in a lower relative abundance of putative pathogens, including Xanthomonas oryzae, Burkholderia glumae, Pseudomonas fuscovaginae, and Pantoea ananatis, suggesting that a more balanced microbial community may help suppress pathogens. These findings suggest that semi-organic farming practices have the potential to support a more ecologically stable phyllosphere microbiome, which may, in turn, contribute to improved plant health. Further research is needed to explore the ecological functions and interactions of phyllosphere microorganisms in sustainable rice-cultivation systems.