Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice

Seed-borne microbiota can transmit vertically from generation to generation and be a favour mutualism between the endosymbionts and hosts. The aim of this study was to investigate the rice-associated actinobacterial taxa in roots, stems, and grains and explore vertically transmitted core actinobacteriome of rice plants. Illumina sequencing analyses of samples of rice grains, stems, and roots showed that the roots contained the most diverse actinobacteria among the tissues. The grains contained 78 actinobacterial operational taxonomic units (OTUs), among which 44 were shared with those in the stems, 30 shared with those in the roots. The coexisted OTUs in the three types of samples mainly belong to genera of Pseudonocardia, Dietzia, Nocardioides, Streptomyces, Mycobacterium, Corynebacterium, Citricoccus, Salinibacterium, and Agrococcus, and other unclassified taxa. The dominant actinobacterial genera Pseudonocardia and Dietzia in the stems and roots were still detected in relatively high abundance in the grains. The Streptomyces isolated from surface sterilized grains could improve nitrogen use efficiency of rice seedlings and the resistance to rice blast fungus. The results suggested that the rice grains contained diverse actinobacterial taxa deriving from stems and roots and showed intimate correlation with the host plants.