Compositional and functional characteristics of the rice leaf microbiome

Leaf microbial communities, termed as the phyllomicrobiome, are usually characterized as highly varied in structure because of their dynamic exposure to environmental factors. Yet despite the variations, there have been growing evidences eclucidating the symbioses between phyllomicrobiome and host for processing like growth support and resistance from disease or abiotic stresses. For agricultural products like rice, understanding the phyllomicrobiome is crucial for its implications to effective rice production. Authors captured the phyllomicrobiome information of 3,024 rice varieties through modified metagenomics and found numerous microorganisms, with Proteobacteria and Euryarchaeota as the most abundant groups. Network analyses revealed complex interactions among members of the phyllomicrobiome, pointing out Clostridium, Bacillus, Acidovorax, and Mycoplasma, along with other genera, as microbial hubs. The phyllomicrobiome was also found to have generally two interacting clusters: the beneficial group of Alphaproteobacteria, Betaproteobacteria, and Actinobacteria; and the remaining commensal or potentially pathogenic groups. This suggests that the phyllomicrobiome in rice has a nonrandom structure. As for its community function, predictive analyses revealed that rice phyllomicrobiome may aid its host by functioning as possible source of vitamins, extended defense system through biosynthesis of antibiotics, and degradation of toxic substances like selenium. In addition, multivariate statistics revealed significant difference (P = 0.001) between Indica and Japonica based on their phyllomicrobiome structures, suggesting that microbial communities reflected the phylogenetic relationship of the two major rice varieties despite the high variations across samples. With these findings, we were able to support linkage between the phyllomicrobiome and rice plant.