Transcriptomic and metabolomic integrated analysis of microalgae-mediated regulatory mechanisms in Perilla frutescens responding to saline-alkali stress

Saline-alkali stress is a critical factor limiting the growth and yield of Perilla frutescens , a medicinal and edible cash crop. Although microalgae have shown potential in alleviating saline-alkali-induced damage to P. frutescens , their synergistic regulatory mechanism remains unclear. This study established four treatment groups: control (S-I-), saline-alkali stress (S+I-), microalgae treatment (S-I+), and combined saline-alkali + microalgae treatment (S+I+). Physiological observations and multi-omics analyses were performed to explore microalgae’s role in enhancing P. frutescens ’ saline-alkali tolerance. Physiologically, S + I + exhibited significantly superior growth parameters to S + I- and comparable to S-I-. It also resulted in recovered thickness of leaf and stem tissues, improved stomatal aperture, enhanced ion homeostasis, strengthened photosynthetic function, and stabilized the antioxidant system. Transcriptomic analysis identified 2628 differential expressed genes (DEGs) between S + I + and S + I-, enriched in phenylpropanoid biosynthesis and flavonoid biosynthesis pathways. Metabolomic analysis detected 947 differential metabolites (DEMs), mainly enriched in flavonoid biosynthesis. Integrated multi-omics analysis revealed significant enrichment of DEGs and DEMs in the phenylpropanoid-flavonoid pathway. After microalgae inoculation, most enzyme-related genes in this pathway were downregulated, while genes like UGT72E were upregulated; most metabolites decreased, but key substances such as ferulic acid accumulated. This study confirms microalgae alleviate saline-alkali stress in P. frutescens via multi-dimensional regulation: repairing morphological and anatomical structures, maintaining ion homeostasis and photosynthetic stability, mitigating oxidative and osmotic damage, with the phenylpropanoid-flavonoid pathway as the core molecular mechanism. It provides theoretical support and practical solutions for microalgal biofertilizer development, saline-alkali land bioremediation, and sustainable cultivation of medicinal and edible crops. • Microalgae restore Perilla growth and anatomy under saline-alkali stress. • Microalgae improve photosynthetic stability and stomatal function. • Oxidative and osmotic damages in Perilla are alleviated by microalgae. • Microalgae maintain ion homeostasis in Perilla under saline-alkali stress. • Phenylpropanoid-flavonoid pathway is the core molecular response mechanism.