Abstract
Intensive cropping degrades soil quality and disrupts the soil microbiome. To understand the effect of rice monocropping on soil-microbiome, we used a comparative 16S rRNA metagenome sequencing method to analyze the diversity of soil microflora at the genomic level. Soil samples were obtained from five locations viz., Chamarajnagara, Davangere, Gangavathi, Mandya, and Hassan of Karnataka, India. Chemical analysis of soil samples from these locations revealed significant variations in pH (6.00–8.38), electrical conductivity (0.17–0.69 dS m−1), organic carbon (0.51–1.29%), available nitrogen (279–551 kg ha−1), phosphorous (57–715 kg ha−1) and available potassium (121–564 kg ha−1). The 16S metagenome analysis revealed that the microbial diversity in Gangavathi soil samples was lower than in other locations. The soil sample of Gangavathi showed a higher abundance of Proteobacteria (85.78%) than Mandya (27.18%). The Firmicutes were more abundant in Chamarajnagar samples (36.01%). Furthermore, the KEGG pathway study revealed enriched nitrogen, phosphorus, and potassium metabolism pathways in all soil samples. In terms of the distribution of beneficial microflora, the decomposers were more predominant than the nutrient recyclers such as nitrogen fixers, phosphorous mineralizers, and nitrifiers. Furthermore, we isolated culturable soil microbes and tested their antagonistic activity in vitro against a fungal pathogen of rice, Magnaporthe oryzae strain MG01. Six Bacillus sp. and two strains of Trichoderma harzianum showed higher antagonistic activity against MG01. Our findings indicate that metagenome sequencing can be used to investigate the diversity, distribution, and abundance of soil microflora in rice-growing areas. The knowledge gathered can be used to develop strategies for maintaining soil quality and crop conservation to increase crop productivity.
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Funding
This project was funded by Watershed Development Department, Government of Karnataka, India. Also, supported by Directorate of Research, University of Agricultural Sciences, Bangalore under Varietal Development Project ID. DR/VTDP/2017–18. The funding agency had no role in study design, data collection, analysis and interpretation, decision to publish, or preparation of the manuscript.
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Conceptualization- MKP, HBM; Data curation- AJD, BSR; Data analysis- LMN, BP, MEP, DP, AS; Fund acquisition- MKP; Project Supervision- MKP and HBM; Data Validation- MKP, HBM, DP, AJD and AS; Writing manuscript- LMP, HBM, MKP and AJD; Manuscript review and editing: HBM and MKP.
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Prasannakumar, M.K., Netravathi, L.M., Mahesh, H.B. et al. Comparative metagenomic analysis of rice soil samples revealed the diverse microbial population and biocontrol organisms against plant pathogenic fungus Magnaporthe oryzae. 3 Biotech 11, 245 (2021). https://doi.org/10.1007/s13205-021-02783-y
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DOI: https://doi.org/10.1007/s13205-021-02783-y