Bioprospecting Rice Bacterial Endophytes: Different Phylogenetic Groups in the Microniches of Oryza Species

Rice, one of the most important crops, is inhabited by diverse groups of bacterial endophytes, many of which are still functionally unknown. This chapter summarizes information on the diversity and community structure of bacterial endophytes residing in the rice endosphere. Specifically, it presents an overview of those endophytes inhabiting the rice microniches, including the roots, shoots, and seeds. The bacterial endophyte community structure and diversity across Oryza spp., mainly those from Oryza sativa ssp. indica and ssp. japonica, are presented. A literature survey of 16S rDNA sequences from cultured and uncultured endophytic bacteria is presented. A total of 1047 screened 16S rDNA sequences were collated with complete taxonomic classification. The most abundant and commonly detected endophytic bacterial groups in the phylum level mainly include Proteobacteria (61%), followed by Actinobacteria (20%) and Firmicutes (14%). Class-level identification mostly shows that Gammaproteobacteria (32%), Actinobacteria (19%), and Alphaproteobacteria (19%) are the commonly detected groups, followed by less abundant groups. The most prominent trend observed is the occurrence of the same bacterial genera isolated or detected throughout the rice endosphere. Bacterial genera such as Bacillus, Enterobacter, Herbaspirillum, Methylobacterium, Microbacterium, Pantoea, Pseudomonas, Sphingomonas, and others are commonly detected throughout the rice endosphere. This indicates the potential importance of these groups to the rice plants and could be targeted as plant growth-promoting bacterial bioinoculants. On the other hand, there are also bacterial genera that are more specifically isolated or detected in the major microniches of rice, including Bradyrhizobium, Azospirillum, and Aeromonas (roots), Azorhizobium (leaves), and Kosakonia (seeds). In addition, this chapter encompasses bioprospecting potential bacterial endophytes of rice, focusing on target groups of interest, as classified in terms of their plant growth-promoting (PGP) mechanism or bacterial genera where they are identified. There are diverse bacterial endophytic communities, and some of these bacterial groups are present in all the major microniches of rice, indicating their high association and functional importance.