Comparative analysis of spermosphere and phyllosphere bacteriome of rice and their effect on foliar pathogens, Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae
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Date
2019
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DIVISION OF PLANT PATHOLOGY ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI
Abstract
Rice is an important cereal crop which feeds billions of people predominantly in Asia. With the current estimation of increase in human population, the yield has to be doubled or tripled to meet the growing demand. The major constraints to rice production are its biotic stresses such as blast disease caused by Magnaporthe oryzae and bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae. Current method of disease management exploits host resistance and agrochemicals. While host resistance is short lived, the agrochemicals are not acceptable in international trade due to chemical residues on the product of commerce. In order to develop an alternative or supplementary ecofriendly option for disease management, bacterial flora naturally occurring on the phyllosphere and spermosphere of rice was explored. The phyllopshere and spermosphere bacteriome of basmati and non basmati rice cultivars, namely PB1 and VLD85 were analysed using metagenomic and traditional cultivation based methods. While the culturable bacteriome was analysed on nutrient agar and M9 media, the total bacteriome was estimated by sequencing ribosomal V3-V4 conserved region using Illumina HiSeq Platform. Bacteriome of adaxial and abaxial surface of phyllosphere as well as bacteriome of blast lesion were also studied. Bacterial species like Pseudomonas fulva and Pantoea agglomerans were found dominating in cultured bacteriome of both the surfaces and Methylobacterium platani were found in high numbers in native bacteriome of phyllosphere of two cultivars. On blast lesion, two species were exclusively found namely Paenibacillus lautus and Pantoea septica. Pseudomonas oryzihabitans and Flavobacterium acidificum were found dominant in cultured and native spermosphere of basmati cultivar whereas Pantoea ananatis and Flavobacterium acidificum were found in non basmati cultivar in high numbers. A total of 189 bacterial isolates were obtained from the two surfaces of the phyllosphere and spermosphere. BOX PCR based DNA fingerprinting of isolates revealed 104 distinct bacterial isolates among the collection that was glycerol preserved for long term storage. The isolates were further species identified by comparing 16S rDNA sequences with four public databases like NCBI, SILVA, RDP and EMBL. Among the 104 species, 36 different species of bacteria were evaluated for their potential to suppress
two important foliar pathogens of rice, Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae. Nineteen isolates were found highly antagonistic against blast fungus by showing up more than 50% inhibition, several isolates displayed antagonism against bacterial blight pathogen. Pantoea dispersa, Pantoea agglomerans, Pseudomonas parafulva, Pantoea ananatis, Acinetobacter baumannii, Enterobacter cloacae, Pantoea vagans, Pantoea deleyi were found effective against Magnaporthe oryzae. Pseudomonas parafulva BG1, Chryseobacterium cucilis, Pantoea anthophila, Enterobacter cloacae, Pantoea ananatis, Pseudomonas psychrotolerans, Pseudomonas monteilii, Acinetobacter bayliyi, Pantoea vagans, Pseudomonas stutzeri were found effective against Xanthomonas oryzae pv. oryzae.
Key words: Adaxial, abaxial, phyllosphere, spermosphere, bacteriome, PB1, VLD85,
Magnaporthe oryzae, Xanthomonas oryzae pv. oryzae
Description
T-10155
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