Characterizing metabolic changes in rice roots induced by Meloidogyne graminicola and modulated by Arthrobotrys oligospora: A pathway-based approach

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. •Metabolite profiling revealed 172 distinct metabolites in rice roots under stress.•Analysis identified 81 significant metabolites, with 47 upregulated and 34 downregulated.•Downregulated compounds like trehalose and N-isovalerylglycine suggest metabolic adjustments under stress.•Key biomarkers like tryptophan and glucuronate showed crucial roles in stress response.•Metabolic pathways, including glutathione metabolism, were significantly altered by nematode infestation.