# Phenylpropanoid- and Flavonoid-Centered Metabolic Adaptation to Continuous Cropping Stress in Ornamental Gourd

## TL;DR

This study shows how ornamental gourd plants adapt metabolically to continuous cropping stress through a coordinated cascade from soil to roots to leaves, with phenylpropanoids and flavonoids playing a central role.

## Contribution

The study introduces a multi-compartment untargeted metabolomics framework to identify spatially resolved metabolic biomarkers for continuous cropping stress in ornamental gourd.

## Key findings

- Continuous cropping causes a hierarchical metabolic cascade with suppressed rhizosphere metabolism, activated root defense, and enriched leaf signaling.
- Phenylpropanoid and flavonoid pathways are central to stress adaptation, showing tissue-specific accumulation patterns.
- Metabolite-based targets for stress diagnosis and crop management were identified through pathway reprogramming in multiple compartments.

## Abstract

Untargeted metabolomics revealed a spatially organized rhizosphere–root–leaf metabolic cascade in ornamental gourd plants under continuous cropping stress, characterized by suppressed rhizosphere metabolism, reinforced root defense metabolism, and coordinated leaf-level signaling responses. Phenylpropanoid, flavonoid, amino acid, lipid, and hormone-related pathways were identified as key biochemical drivers of replanting stress adaptation, providing quantitative tissue-specific metabolite patterns that can be used as metabolic markers for continuous cropping disorders.

What are the main findings?
Continuous cropping induces a clear, quantitative metabolic hierarchy across plant–soil compartments, with strong suppression of rhizosphere metabolites, pronounced activation of root-centered defense metabolism, and coordinated enrichment of signaling-related metabolites in leaves, demonstrating a rhizosphere–root–leaf metabolic cascade under replanting stress.Phenylpropanoid and flavonoid biosynthesis pathways emerged as central drivers of stress adaptation, showing tissue-specific accumulation patterns that link reinforced root defense with leaf-level metabolic signaling while revealing conserved core metabolites shared across the rhizosphere, roots, and leaves.

Continuous cropping induces a clear, quantitative metabolic hierarchy across plant–soil compartments, with strong suppression of rhizosphere metabolites, pronounced activation of root-centered defense metabolism, and coordinated enrichment of signaling-related metabolites in leaves, demonstrating a rhizosphere–root–leaf metabolic cascade under replanting stress.

Phenylpropanoid and flavonoid biosynthesis pathways emerged as central drivers of stress adaptation, showing tissue-specific accumulation patterns that link reinforced root defense with leaf-level metabolic signaling while revealing conserved core metabolites shared across the rhizosphere, roots, and leaves.

What are the implications of the main findings?
The multi-compartment untargeted metabolomics framework demonstrates how environmental perturbations reorganize metabolic pathways at the system level, providing a transferable strategy for identifying spatially resolved metabolic biomarkers, pathway signatures, and metabolite networks relevant to metabolomics, systems biology, and agricultural research.The identification of phenylpropanoid-, flavonoid-, amino acid-, lipid-, and hormone-associated pathway reprogramming under continuous cropping stress offers metabolite-based targets for stress diagnosis and crop management, supporting the use of metabolomics to link environmental stressors with functional metabolic adaptation in plant–soil systems.

The multi-compartment untargeted metabolomics framework demonstrates how environmental perturbations reorganize metabolic pathways at the system level, providing a transferable strategy for identifying spatially resolved metabolic biomarkers, pathway signatures, and metabolite networks relevant to metabolomics, systems biology, and agricultural research.

The identification of phenylpropanoid-, flavonoid-, amino acid-, lipid-, and hormone-associated pathway reprogramming under continuous cropping stress offers metabolite-based targets for stress diagnosis and crop management, supporting the use of metabolomics to link environmental stressors with functional metabolic adaptation in plant–soil systems.

Background: Continuous cropping severely restricts ornamental gourd productivity through yield decline, microbial dysbiosis, and rhizosphere autotoxin production. This study characterized rhizosphere–root–leaf metabolic reorganization under three-year monoculture, identifying key metabolites, pathways, and a hierarchical cascade for stress adaptation. Methods: Ornamental gourd seedlings were potted in three-year monoculture soil exhibiting replanting disorders. At the seven-leaf stage, rhizosphere soil, roots, and leaves were sampled for untargeted UHPLC-MS/MS metabolomics, followed by PCA, OPLS-DA, differential analysis (VIP > 1, p < 0.05), and KEGG pathway enrichment analysis. Results: A total of 10,792 metabolic features were detected in positive mode and 8992 in negative mode. PCA explained 83.84% of the variance, with PC1 at 56.35% and PC2 at 27.49%, clearly separating the compartments of the study. A total of 1132 shared metabolites were suppressed, with log2 fold changes exceeding −1. Roots displayed activation, with upregulated metabolites outnumbering downregulated ones, and log2 fold changes frequently exceeding +3. Leaves exhibited mean log2 fold changes of approximately +1 for phenylpropanoid intermediates, indole, and terpenoid biosynthesis. The enriched pathways included amino acid metabolism, phenylpropanoid and flavonoid biosynthesis, lipid metabolism, and hormone signaling. Conclusions: Continuous cropping induces a hierarchical rhizosphere–root–leaf metabolic cascade, linking suppressed soil activity with reinforced root defense and coordinated leaf signaling, centered on the phenylpropanoid and flavonoid pathways as key drivers of adaptation.