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

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.

Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum

“…Significant variations in the number of beneficial bacterial communities have been observed in this study. Current findings are consistent with our previous report on whole metagenome studies of infected samples 30 and other reports from literature. The results suggest that abiotic factors, such as an acidic pH and the availability of Fe and Mn, may be contributing to the growth of Fusarium oxysporum , as previously observed.…”

“…The sample was collected from the same orchard under identical conditions 29 . Whole metagenome analysis of the samples ISI and ASI has been performed and published in a separate study and the presence of Fusarium oxysporum has been ascertained followed by further assessment of its adaptations 30 . All the necessary permissions to carry out this study have been obtained in accordance with the local state regulations.…”

“…Physicochemical characterization and total microbial count estimation of the samples were carried out similar to the protocol outlined in our previous study employing whole metagenomics 30 .…”

New Traits of Agriculture/Food Quality Interface

“…It is worth mentioning that the preliminary study of Das et al [13] evidenced how microbiome analysis of the rhizosphere from wilt-infected pomegranate reveals complex adaptations in Fusarium by demonstrating the capabilities of the whole metagenome sequencing approach for rapid identification of potential key players of wilt disease pathogenesis wherein the symptomatology is complex.…”