Browsing by Author "Shreyashi Singh"

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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
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
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.