Microbiome Analysis of the Rhizosphere from Wilt Infected Pomegranate Reveals Complex Adaptations in Fusarium—A Preliminary Study

Anupam J. Das, Renuka Ravinath, Talambedu Usha, Biligi Sampgod Rohith, Hemavathy Ekambaram, Mothukapalli Krishnareddy Prasannakumar, Nijalingappa Ramesh and Sushil Kumar Middha
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Anupam J. Das: School of Applied Sciences, Reva University, Rukmini Knowledge Park, Bangalore 562149, Karnataka, India
Renuka Ravinath: School of Applied Sciences, Reva University, Rukmini Knowledge Park, Bangalore 562149, Karnataka, India
Talambedu Usha: Department of Biochemistry, Maharani Lakshmi Ammanni College for Women, Bangalore 560012, Karnataka, India
Biligi Sampgod Rohith: Molsys Pvt. Ltd., Yelahanka, Bangalore 561249, Karnataka, India
Hemavathy Ekambaram: DBT-BIF Facility, Department of Biotechnology, Maharani Lakshmi Ammanni College for Women, Bangalore 560012, Karnataka, India
Mothukapalli Krishnareddy Prasannakumar: Department of Plant Pathology, University of Agricultural Sciences, Bangalore 560065, Karnataka, India
Nijalingappa Ramesh: School of Applied Sciences, Reva University, Rukmini Knowledge Park, Bangalore 562149, Karnataka, India
Sushil Kumar Middha: DBT-BIF Facility, Department of Biotechnology, Maharani Lakshmi Ammanni College for Women, Bangalore 560012, Karnataka, India

Agriculture, 2021, vol. 11, issue 9, 1-17

Abstract: Wilt disease affecting pomegranate crops results in rapid soil-nutrient depletion, reduced or complete loss in yield, and crop destruction. There are limited studies on the phytopathogen Fusarium oxysporum prevalence and associated genomic information with respect to Fusarium wilt in pomegranate. In this study, soil samples from the rhizosphere of different pomegranate plants showing early stage symptoms of wilt infection to an advanced stage were collected from an orchard situated in Karnataka, India. A whole metagenome sequencing approach was employed to gain insights into the adaptations of the causative pathogen F. oxysporum . Physicochemical results showed a drop in the pH levels, N, Fe, and Mn, and increase in electrical conductivity, B, Zn, Cl, Cu was observed in the early and intermediate stage samples. Comparative abundance analysis of the experimental samples ESI and ISI revealed an abundance of Proteobacteria phyla Achromobacter sp. 2789STDY5608625, Achromobacter sp. K91, and Achromobacter aegrifaciens and Eukaryota namely Aspergillus arachidicola , Aspergillus candidus, and Aspergillus campestris. Functional pathway predictions implied carbohydrate binding to be significant ( p < 0.05) among the three experimental samples. Microbiological examination and whole microbiome analysis confirmed the prevalence of F. oxysporum in the soil samples. Variant analysis of F. oxysporum revealed multiple mutations in the 3IPD gene with high impact effects. 3-Isopropylmalate dehydratase and carbohydrate-active enzymes could be good targets for the development of antifungals that could aid in biocontrol of F. oxysporum . The present study demonstrates the capabilities of the whole metagenome sequencing approach for rapid identification of potential key players of wilt disease pathogenesis wherein the symptomatology is complex.

Keywords: microbiomics; soil metagenomics; DNA sequencing; wilt; rot; Punica granatum (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2021
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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