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

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)...

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Autores principales:	Kuleshwar Prasad Sahu, Asharani Patel, Mukesh Kumar, Neelam Sheoran, Sahil Mehta, Bhaskar Reddy, Pierre Eke, Narayanasamy Prabhakaran, Aundy Kumar
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	antibiosis blast defense genes Magnaporthe oryzae microbiome phyllosphere Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/525c28479e4c4e2887e4e429783a89a1
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spelling	oai:doaj.org-article:525c28479e4c4e2887e4e429783a89a12021-12-01T18:41:45ZIntegrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression1664-302X10.3389/fmicb.2021.780458https://doaj.org/article/525c28479e4c4e2887e4e429783a89a12021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.780458/fullhttps://doaj.org/toc/1664-302XPhyllosphere—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 Pantoea, Enterobacter, Pseudomonas, and Erwinia 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 Pantoea. The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, Magnaporthe oryzae, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as Enterobacter sacchari, Microbacterium testaceum, Pantoea ananatis, Pantoea dispersa, Pantoea vagans, Pseudomonas oryzihabitans, Rhizobium sp., and Sphingomonas 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 OsCEBiP, OsCERK1, and phytohormone-associated genes such as OsPAD4, OsEDS1, OsPR1.1, OsNPR1, OsPDF2.2, and OsFMO 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.Kuleshwar Prasad SahuAsharani PatelMukesh KumarNeelam SheoranSahil MehtaBhaskar ReddyPierre EkeNarayanasamy PrabhakaranAundy KumarFrontiers Media S.A.articleantibiosisblastdefense genesMagnaporthe oryzaemicrobiomephyllosphereMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	antibiosis blast defense genes Magnaporthe oryzae microbiome phyllosphere Microbiology QR1-502
spellingShingle	antibiosis blast defense genes Magnaporthe oryzae microbiome phyllosphere Microbiology QR1-502 Kuleshwar Prasad Sahu Asharani Patel Mukesh Kumar Neelam Sheoran Sahil Mehta Bhaskar Reddy Pierre Eke Narayanasamy Prabhakaran Aundy Kumar Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression
description	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 Pantoea, Enterobacter, Pseudomonas, and Erwinia 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 Pantoea. The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, Magnaporthe oryzae, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as Enterobacter sacchari, Microbacterium testaceum, Pantoea ananatis, Pantoea dispersa, Pantoea vagans, Pseudomonas oryzihabitans, Rhizobium sp., and Sphingomonas 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 OsCEBiP, OsCERK1, and phytohormone-associated genes such as OsPAD4, OsEDS1, OsPR1.1, OsNPR1, OsPDF2.2, and OsFMO 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.
format	article
author	Kuleshwar Prasad Sahu Asharani Patel Mukesh Kumar Neelam Sheoran Sahil Mehta Bhaskar Reddy Pierre Eke Narayanasamy Prabhakaran Aundy Kumar
author_facet	Kuleshwar Prasad Sahu Asharani Patel Mukesh Kumar Neelam Sheoran Sahil Mehta Bhaskar Reddy Pierre Eke Narayanasamy Prabhakaran Aundy Kumar
author_sort	Kuleshwar Prasad Sahu
title	Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression
title_short	Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression
title_full	Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression
title_fullStr	Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression
title_full_unstemmed	Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression
title_sort	integrated metabarcoding and culturomic-based microbiome profiling of rice phyllosphere reveal diverse and functional bacterial communities for blast disease suppression
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/525c28479e4c4e2887e4e429783a89a1
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Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression

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