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Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars

  • Environmental Microbiology - Research Paper
  • Published:
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Abstract

Highly varied bacterial communities inhabiting the soybean rhizosphere perform important roles in its growth and production; nevertheless, little is known about the changes that occur in these communities under disease-stress conditions. The present study investigated the bacterial diversity and their metabolic profile in the rhizosphere of disease-resistant (JS-20–34) and disease-susceptible (JS-335) soybean (Glycine max (L.) Merr.) cultivars using 16S rRNA amplicon sequencing and community-level physiological profiling (CLPP). In disease-resistant soybean (AKADR) samples, the most dominating phyla were Actinobacteria (40%) followed by Chloroflexi (24%), Proteobacteria (20%), and Firmicutes (12%), while in the disease-susceptible (AKADS) sample, the most dominating phyla were Proteobacteria (35%) followed by Actinobacteria (27%) and Bacteroidetes (17%). Functional profiling of bacterial communities was done using the METAGENassist, and PICRUSt2 software, which shows that AKADR samples have more ammonifying, chitin degrading, nitrogen-fixing, and nitrite reducing bacteria compared to AKADS rhizosphere samples. The bacterial communities present in disease-resistant samples were significantly enriched with genes involved in nitrogen fixation, carbon fixation, ammonification, denitrification, and antibiotic production. Furthermore, the CLPP results show that carbohydrates and carboxylic acids were the most frequently utilized nutrients by the microbes. The principal component analysis (PCA) revealed that the AKADR soils had higher functional activity (strong association with the Shannon–Wiener index, richness index, and hydrocarbon consumption) than AKADS rhizospheric soils. Overall, our findings suggested that the rhizosphere of resistant varieties of soybean comprises of beneficial bacterial population over susceptible varieties.

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Data availability

The sequence data of Illumina MiSeq Sequencer has been deposited at SRA under the bio project PRJNA589888 disease-resistant (SAMN13293567) and disease-susceptible (SAMN13293568).

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Acknowledgements

The authors would like to thank Dr. Devendra Pyasi, Plant Breeder at Krishi Vigyan Kendra, Bamhori Seed Farm Bhopal Road, Sagar (M.P.), India, for his assistance in sample collection.

Funding

AD received grants through the DST Inspire PhD. Fellowship (IF160797) from the department of science and technology, New Delhi, India. AK gratefully acknowledge DST-SERB for financial support obtained through project grant of (CRG/2021/003696), New Delhi, Govt of India.

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Authors and Affiliations

  1. Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India

    Anamika Dubey, Muneer Ahmad Malla & Ashwani Kumar

  2. Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India

    Muneer Ahmad Malla

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  1. Anamika Dubey
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  2. Muneer Ahmad Malla
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  3. Ashwani Kumar
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Contributions

AD conducted the experiments and prepared the manuscript. AD and MM performed the data analysis under the guidance and supervision of AK.

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Correspondence to Ashwani Kumar.

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Dubey, A., Malla, M.A. & Kumar, A. Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars. Braz J Microbiol 53, 1355–1370 (2022). https://doi.org/10.1007/s42770-022-00746-w

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