Browsing by Author "Vedant Gautam"

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“Characterizing metabolic changes in rice roots induced by Meloidogyne graminicola and modulated by Arthrobotrys oligospora: A pathway-based approach”
(Academic Press, 2025) Vedant Gautam; Vibhootee Garg; Ravi Nagar; Nitesh K. Meena; Sunidhi Kumari; Hivre Anand Dashrath; Shreyashi Singh; Shubham Patel; Mukesh; Himanshu Singh; Prahlad Masurkar; Rajendra K. Singh
Root-knot nematodes (Meloidogyne graminicola) are significant agricultural pests that adversely affect rice yield and quality. Understanding the metabolic responses of rice to these pathogens, and the potential modulation by beneficial microorganisms like nematophagous fungi, is crucial for developing effective disease management strategies. This study explores the metabolic responses of rice roots to Meloidogyne graminicola infection and its modulation by the nematophagous fungus Arthrobotrys oligospora. Utilizing NMR-MS in negative ion mode, we identified 172 metabolite features, with 81 showing significant differences (p ≤ 0.1) between pathogen-challenged and non-challenged conditions. Among these, 47 metabolites were upregulated and 34 were downregulated. Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) effectively differentiated between treatment groups, revealing key biomarkers such as tryptophan, 4-hydroxyphenylacetate, isopropanol, and glucuronate. Notably, acetone and ribose were upregulated, suggesting their role in stress responses and metabolic adaptation. Conversely, downregulated metabolites included N-isovaleroylglycine and 2-hydroxy-3-methylvalerate, reflecting reduced levels in pathogen-challenged roots. Pathway enrichment analysis highlighted significant metabolic pathways involved in plant defense, including glutathione metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, and amino sugar metabolism. These findings enhance our understanding of the metabolic adjustments in rice roots during pathogen attack and underscore potential biomarkers and pathways for improving crop resistance. The results provide a foundation for future research aimed at developing effective disease management strategies and enhancing plant resilience through targeted metabolic interventions. © 2024 Elsevier Ltd
Corrigendum to “ExploringUstilaginoidea virens, the causal agent of false smut of rice disease: A comprehensive study of infection dynamics, effectors, and genetic structure” [Microb. Pathogenes. 208 (2025) 107987]
(Academic Press, 2025) Prahlad Masurkar; Jhumishree Meher; Sukram Thapa; Rakesh Kumar Singh; Manas Kumar Bag; Vedant Gautam; Shivam Maurya
The authors regret that the affiliation of author Vedant Gautam was incorrectly mentioned as b Department of Plant Pathology, School of Agriculture, Lovely Professional University, Punjab, 144411, India.The correct affiliation is a Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India. The authors would like to apologise for any inconvenience caused. © 2025 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.
Evaluation of Resistance in Indian Rice to Root-Knot Nematode (Meloidogyne graminicola): Insights from Field and Histopathological Studies
(Springer, 2025) Vedant Gautam; Vibhootee Garg; Hivre Anand Dashrath; Nitesh K. Meena; Nikhil Kumar Singh; Ashish Kumar; Nethi Somasekhar; Rajendra K. Singh
Rice (Oryza sativa L.) is a staple crop for over half of the global population, yet its cultivation faces significant threats from biotic stresses, particularly root-knot nematodes (Meloidogyne spp.). Among these, M. graminicola poses a major challenge in rice-growing regions, leading to substantial yield losses. This study evaluated the resistance of 348 rice varieties to M. graminicola through controlled pot and field experiments over two years (2023 and 2024). Varieties were classified based on gall index, revealing a spectrum of susceptibility from highly susceptible to highly resistant. Notably, varieties such as JR-1124 and JR-403 exhibited high gall index, while others like RP-5219-9-7-3-2-1-1, NPT-10, MTU 1390 (IR17M1172), Kushiari, RP 6750-RMS-2-23-67-91, Sonkharchi, Sugandha-3, HRT-183, and HR-12 demonstrated significant resistance. Resistant rice genotypes exhibited significantly higher PAL, POX, and total phenolic content at all intervals, indicating a strong biochemical defense response against Meloidogyne graminicola. Advanced techniques, including confocal microscopy, revealed distinct histopathological responses to M. graminicola infection, with susceptible rice varieties exhibiting extensive giant cell formation and root tissue degradation, while a resistant variety displayed restricted giant cell development, enhanced callose deposition, and maintained vascular integrity—highlighting robust defense mechanisms against nematode invasion. The findings underscore the potential for breeding programs to enhance resistance traits in rice, contributing to sustainable agricultural practices and improved food security. As nematode populations evolve, ongoing research is essential to adapt breeding strategies and maintain effective management of this significant pest in rice production systems. © The Author(s) 2025.
Exploring the rice root metabolome to unveil key biomarkers under the stress of Meloidogyne graminicola
(Elsevier B.V., 2024) Vedant Gautam; Ravi Nagar; Pradeep Barai; Vibhootee Garg; Shreyashi Singh; Himanshu Singh; Shubham Patel; Mukesh; Ashish Kumar; R.K. Singh
Rice (Oryza sativa) is a highly significant cereal crop on a global scale. Crop plants usually respond to the biotic challenges with altered metabolic composition and physiological perturbations. We have deciphered altered metabolite composition, modulated metabolic pathways and identified metabolite biomarkers in M. graminicola-challenged susceptible rice variety HUR-917 using NMR (Nuclear magnetic resonance) mass spectrophotometry-based metabolomics. In this study, we conducted a comprehensive analysis of the metabolome of susceptible rice plants challenged with the pathogen M. graminicola to unravel complex metabolic changes, identify key biosynthetic pathways, and pinpoint metabolite biomarkers. Through statistical analysis, we identified 100 significant metabolites, with 48 upregulated and 52 downregulated metabolites at a fold change threshold of ≥ 2.0. Multivariate analyses, including Partial Least Squares Discriminant Analysis (PLS-DA) and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), revealed clear discrimination between control and treated samples, with high predictive ability for annotated discriminant metabolites. Pathway enrichment analysis unveiled prominent involvement of metabolic pathways such as nicotine and nicotinamide metabolism and valine, leucine, and isoleucine degradation. Furthermore, putatively annotated biomarkers identified through multivariate ROC curve analysis included metabolites like Thymol, Glycylproline, N-acetylglutamate, and Betaine, among others. These biomarkers, along with pathway enrichment results, underscored the intricate defense mechanisms employed by rice plants in response to M. graminicola infection. Notably, upregulated metabolites such as betaines, histamine, and 5-hydroxytryptophan were implicated in plant defense responses, while downregulated metabolites like thymol and N-acetylglutamate may contribute to increased susceptibility to nematode infection. Nicotinic acid downregulation is crucial in enhanced susceptibility of rice against M. graminicola. Pathway mapping highlighted the enrichment of crucial metabolic pathways involved in primary and secondary metabolism, emphasizing the shift from growth-related processes to defense-related responses like nicotine and nicotinamide metabolism under stress conditions. Overall, our findings provide valuable insights into the metabolic dynamics of rice plants during pathogen invasion, identifying potential biomarkers and elucidating key metabolic pathways involved in plant defense mechanisms. This research contributes to a deeper understanding of plant-nematode interactions and holds implications for the development of effective strategies for root knot management in rice cultivation. © 2024
Exploring Ustilaginoidea virens, the causal agent of false smut of rice disease: A comprehensive study of infection dynamics, effectors, and genetic structure
(Academic Press, 2025) Prahlad Masurkar; Jhumishree Meher; Sukram Thapa; Rajendra K. Singh; Manas Kumar Bag; Vedant Gautam; Shivam Maurya
Villosiclava virens (Anamorph: Ustilaginoidea virens) is an important and enigmatic pathogen that causes rice false smut. Some similarities between Claviceps and Ustilaginoidea genera have been found, but according to recent genomic sequence comparison research, they have different sequences. U. virens secretes mycotoxins, which make the infected grains unfavorable for human consumption. The transcriptomic analysis and genome sequencing of U. virens showed 52,554,142 clean reads assembled into 36,496 transcripts, representing 18,534 unigenes. U. virens also contains the UvNLP protein as an NLP-specific NPP1 domain that belongs to a MAMPs class protein that acts as an elicitor for defence responses in resistant plants. Unique proteins, UvCGBP1, UvPRO1, and UvBI-1, are associated with the virulence, growth, and sporulation of U. virens. Several host QTLs-qFsr1, qFsr2, qFsr4, qFsr8, qFsr10, qFsr11 and qFsr12 have been validated in diverse background (IR28, Tequing NILs, MR183-2), and are crucial for resistance breeding. The genetic diversity of U. virens was measured using molecular markers, including RAPD, AFLP, SSR, ISSR, and, more recently, SNPs. The genetic diversity of U. virens isolates was higher among the isolates than in the geographical population. This review integrates advances in molecular biology, genomics, and host-pathogen interactions to inform sustainable management strategies. Further research is needed in early detection, chlamydospore germination, targeted fungicides, and resistant hybrid rice development. © 2025 Elsevier Ltd
Fungal-derived ZnO nanoparticles functionalized with riboflavin and UDP-GlcNAc exhibit potent nematicidal activity against M. incognita
(Nature Research, 2025) Vedant Gautam; Vibhootee Garg; Nitesh K. Meena; Hivre Anand Dashrath; Kaminee Singh; A. Kumar; Ashish Ashwin Kumar; Rajendra K. Singh
This study reports the green synthesis of zinc oxide nanoparticles (ZnO NPs) using the nematophagous fungus Arthrobotrys oligospora and their evaluation as nematicidal agents against Meloidogyne incognita. The ZnO NPs were synthesized from fungal culture filtrate and characterized by UV–Vis, FTIR, XRD, Raman spectroscopy, SEM, TEM and EDAX confirming nanoscale particles (29.45–71.30 nm) with hexagonal wurtzite crystallinity. ^1H NMR-based metabolomics revealed functionalization of the nanoparticle surface with fungal metabolites, notably riboflavin and UDP-N-acetylglucosamine. In vitro bioassays demonstrated strong, dose-dependent nematicidal activity, achieving 94.8% juvenile mortality at 200 µg/mL after 72 h, significantly higher than the fungal extract alone (p < 0.05). Molecular docking showed that ZnO–riboflavin bound effectively to acetylcholinesterase and ZnO–UDP-GlcNAc to chitin synthase, suggesting dual disruption of neural signaling and cuticle biosynthesis. Collectively, these findings establish A. oligospora-mediated ZnO NPs as a metabolite-enriched nano-biocomposite with enhanced nematicidal efficacy, offering a novel and eco-friendly strategy for sustainable crop protection. © The Author(s) 2025.
Harnessing NMR technology for enhancing field crop improvement: applications, challenges, and future perspectives
(Springer, 2025) Vedant Gautam; Vibhootee Garg; Nitesh K. Meena; Sunidhi Kumari; Shubham Patel; Mukesh; Himanshu Singh; Shreyashi Singh; Rajendra K. Singh
Introduction: Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as a transformative technology in agricultural research, offering powerful analytical capabilities for field crop improvement. With global challenges such as food security and climate change intensifying, there is an urgent need for innovative methodologies to enhance our understanding of plant health, metabolic pathways, and crop-environment interactions. NMR’s ability to provide nondestructive, real-time analysis of plant metabolites and soil chemistry positions it as a critical tool for addressing these pressing concerns. Objective: This review aims to elucidate the potential of NMR spectroscopy in advancing field crop improvement by highlighting its applications, challenges, and future perspectives in agricultural methodologies. The focus is on the evolution and application of NMR in agricultural research, particularly in metabolomics, phenotyping, and quality assessment. Method: A comprehensive literature review was conducted to analyze recent advancements in NMR applications in agriculture. Particular emphasis was given to high-resolution magic angle spinning (HR-MAS) and time-domain NMR techniques, which have been instrumental in elucidating plant metabolites and soil chemistry. Studies showcasing the integration of NMR with complementary technologies for enhanced metabolic profiling and genetic marker identification were reviewed. Results: Findings indicate that NMR spectroscopy is an indispensable tool in agriculture due to its ability to identify biomarkers indicative of crop resilience, monitor soil composition, and contribute to food safety and quality assessments. The integration of NMR with other technologies has accelerated metabolic profiling, aiding in the breeding of high-yielding and stress-resistant crop varieties. However, challenges such as sensitivity limitations and the need for standardization remain. Conclusion: NMR spectroscopy holds immense potential for revolutionizing agricultural research and crop improvement. Overcoming existing challenges, such as sensitivity and standardization, is crucial for its broader application in practical agricultural settings. Collaborative efforts among researchers, agronomists, and policymakers will be essential for leveraging NMR technology to address global food security challenges and promote sustainable agricultural practices. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2025.
Retraction Note: Harnessing NMR technology for enhancing field crop improvement: applications, challenges, and future perspectives (Metabolomics, (2025), 21, 2, (27), 10.1007/s11306-025-02229-z)
(Springer, 2025) Vedant Gautam; Vibhootee Garg; Nitesh K. Meena; Sunidhi Kumari; Shubham Patel; Mukesh; Himanshu Singh; Shreyashi Singh; Rajendra K. Singh
The Editor in Chief has retracted this article because of numerous incorrect references, including mismatched references, nonexistent references, and inadequate references. Authors R. K. Singh, Vedant Gautam, Shubham Patel and Mukesh agree with this retraction. Authors Vibhootee Garg, Nitesh Meena, Sunidhi Kumari, Himanshu Singh and Shreyashi Singh have not responded to any correspondence from the publisher about this retraction. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2025.