AUTHOR=Sahu Kuleshwar Prasad , Patel Asharani , Kumar Mukesh , Sheoran Neelam , Mehta Sahil , Reddy Bhaskar , Eke Pierre , Prabhakaran Narayanasamy , Kumar Aundy 

TITLE=Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.780458

DOI=10.3389/fmicb.2021.780458

ISSN=1664-302X

ABSTRACT=<p>Phyllosphere—the harsh foliar plant part exposed to vagaries of environmental and climatic variables is a unique habitat for microbial communities. In the present work, we profiled the phyllosphere microbiome of the rice plants using 16S rRNA gene amplicon sequencing (hereafter termed metabarcoding) and the conventional microbiological methods (culturomics) to decipher the microbiome assemblage, composition, and their functions such as antibiosis and defense induction against rice blast disease. The blast susceptible rice genotype (PRR78) harbored far more diverse bacterial species (294 species) than the resistant genotype (Pusa1602) that showed 193 species. Our metabarcoding of bacterial communities in phyllomicrobiome revealed the predominance of the phylum, Proteobacteria, and its members <italic>Pantoea</italic>, <italic>Enterobacter</italic>, <italic>Pseudomonas</italic>, and <italic>Erwinia</italic> on the phyllosphere of both rice genotypes. The microbiological culturomic validation of metabarcoding-taxonomic annotation further confirmed the prevalence of 31 bacterial isolates representing 11 genera and 16 species with the maximum abundance of <italic>Pantoea.</italic> The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, <italic>Magnaporthe oryzae</italic>, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as <italic>Enterobacter sacchari</italic>, <italic>Microbacterium testaceum</italic>, <italic>Pantoea ananatis</italic>, <italic>Pantoea dispersa</italic>, <italic>Pantoea vagans</italic>, <italic>Pseudomonas oryzihabitans</italic>, <italic>Rhizobium</italic> sp., and <italic>Sphingomonas</italic> sp. elicited a defense response and contributed to the suppression of blast disease. qRT-PCR-based gene expression analysis indicated over expression of defense-associated genes such as <italic>OsCEBiP</italic>, <italic>OsCERK1</italic>, and phytohormone-associated genes such as <italic>OsPAD4</italic>, <italic>OsEDS1</italic>, <italic>OsPR1.1</italic>, <italic>OsNPR1</italic>, <italic>OsPDF2.2</italic>, and <italic>OsFMO</italic> in phyllobacterized rice seedlings. The phyllosphere bacterial species showing blast suppressive activity on rice were found non-plant pathogenic in tobacco infiltration assay. Our comparative microbiome interrogation of the rice phyllosphere culminated in the isolation and identification of agriculturally significant bacterial communities for blast disease management in rice farming through phyllomicrobiome engineering in the future.</p>