Plant Metabolomics: An Overview of the Role of Primary and Secondary Metabolites against Different Environmental Stress Factors

**Background:** Biotic and abiotic stresses negatively affect crop production, causing marked decreases in annual crop yield both qualitatively and quantitatively. It is estimated that these stresses are responsible for more than 50% of crop losses worldwide, with abiotic stressors causing significantly higher losses than biotic factors. Salinity affects more than 800 million hectares of land—nearly 50% of the total irrigated area, which provides about 33% of the world's food. Drought causes a loss of more than 50% of the average yield of crops. Plants adopt several mechanisms to cope with these stresses, including metabolomics, transcriptomics, proteomics, and genomics. The plant metabolome consists of primary metabolites (essential for growth and development) and secondary metabolites (formed near the stationary phase of growth with no direct role in growth, reproduction, and development). This review analyzed more than 200 published works to provide an overview of the role of primary and secondary metabolites against several abiotic and biotic stressors.

**Methods:** The review describes the instrumentation applied in metabolomics studies, including hyphenated mass spectrometric methods such as gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and nuclear magnetic resonance (NMR). GC-MS is described as the most advanced analytical approach for metabolic profiling in plants, capable of recognizing several hundred compounds including sugars, organic acids, amino acids, alcohols, amines, and fatty acids. LC-MS provides a better alternative for non-volatile compounds, especially after the adoption of ultra-performance liquid chromatography technology. NMR spectroscopy offers advantages in structural content information, reproducibility, and non-destructive measurement, though its sensitivity is much lower than MS-based techniques. The workflow of plant metabolomics analysis comprises three key steps: sample preparation, data gaining, and identification of compounds using statistical analysis. The extraction method of metabolites depends on factors such as plant organ type, physical and chemical properties of targeted metabolites, chemical structure, and solvent used.

**Key Results:** The review details the responses of primary metabolites to abiotic stresses. Amino acids, particularly proline, accumulate under stress conditions and act as osmoprotectants. Proline is produced from glutamate via the enzyme pyrroline-5-carboxylate synthetase (P5CS), and overexpression of the P5CS gene in soybean increased proline content and tolerance to salt stress in transgenic plants. Polyamines (triamine spermidine, tetraamine spermine, and diamine putrescine) accumulate under drought, chilling, heat, heavy metal, and salinity stresses, functioning in maintaining membrane protection and regulating antioxidant systems. Carbohydrates such as sucrose, trehalose, raffinose, and fructans function as osmoprotectants and ROS scavengers. Glycine betaine (GB) plays a significant role in stabilizing macromolecules, shielding photosynthesis, and detoxifying reactive oxygen radicals. Transgenic tomatoes with GB synthesis were more resistant to cold stress and produced fruit at a rate 10 to 30% higher than the wild type. Lipids, particularly phospholipases, lipid kinases, and phosphatases, are involved in signaling responses to temperature, drought, heavy metals, salinity, and pathogen attack.

Regarding secondary metabolites, phenolic compounds (lignins, tannins, flavonoids, isoflavonoids, anthocyanins, coumarins) are produced via the phenylpropanoid pathway and play roles in ROS removal, chelation of heavy metals, and cell wall stiffening. Under drought conditions, ferulic acid decreased while p-coumaric acid and caffeic acid increased in maize xylem sap. Low temperature (16 °C) induced increased anthocyanin levels in red-fleshed apple callus culture. Terpenoids function as phytohormones (abscisic acid, gibberellic acid), phytoalexins, and antioxidants. Diterpene phytoalexins (zealexins, kauralexins, oryzalexins) exhibit antimicrobial properties against pathogenic fungal blast diseases such as rice blast caused by Magnaporthe grisea. Nitrogen-containing secondary metabolites (alkaloids, glucosinolates, cyanogenic glycosides, non-protein amino acids) provide defense against herbivores and abiotic stresses. In Arabidopsis thaliana, drought and waterlogging conditions increased aliphatic compounds of glucosinolate and flavonoids.

**Clinical Implications:** This is a plant science review with no direct clinical implications. However, the findings have significant implications for agricultural sustainability and food security. Understanding the roles of primary and secondary metabolites in stress tolerance can accelerate the selection of superior breeding stock and screening of elite crop types. Manipulating and overexpressing genes related to the biosynthetic pathway of secondary metabolites could be a solution for plant tolerance to environmental stress conditions. The development of stress-tolerant crop varieties through cross-breeding or genetic engineering is essential to meet food security needs for a growing global population. The review emphasizes that progress in omics tools and bioinformatics, along with enhanced assimilation of data from varying molecular levels, is needed to expose the full picture of sustaining mechanisms and identify new biomarkers of resistance toward biotic and abiotic stresses.