Boron is an essential microelement for plant growth. Tomato is one of the most cultivated fruits and vegetables in the world, and boron deficiency severely inhibits its yield and quality. However, the mechanism of tomato in response to boron deficiency remains largely unclear. Here, we investigated the physiological and molecular bases of the boron deficiency response in hydroponically grown tomato seedlings. Boron deficiency repressed the expression of genes associated with nitrogen metabolism, while it induced the expression of genes related to the pentose phosphate pathway, thereby altering carbon flow to provide energy for plants to cope with stress. Boron deficiency increased the accumulation of copper, manganese and iron, thereby maintaining chlorophyll content and photosynthetic efficiency at the early stage of stress. In addition, boron deficiency downregulated the expression of genes involved in cell wall organization and reduced the contents of pectin and cellulose in roots, ultimately retarding root growth. Furthermore, boron deficiency markedly altered phytohormone levels and signaling pathways in roots. The contents of jasmonic acid, jasmonoy1-L-isoleucine, trans-zeatin riboside, abscisic acid, salicylic acid, and SA glucoside were decreased; in contrast, the contents of isopentenyladenine riboside and ethylene precursor 1-aminocyclopropane-1-carboxylic acid were increased in the roots of boron-deficient tomato plants. These results collectively indicate that tomato roots reprogram carbon/nitrogen metabolism, alter cell wall components and modulate phytohormone pathways to survive boron deficiency. This study provides a theoretical basis for further elucidating the adaptive mechanism of tomato in response to boron deficiency.

Cadmium (Cd) toxicity not only affects plant growth and development, but also affects human health through the food chain. Several studies have demonstrated that Selenium (Se) alleviates Cd stress in plants; however, whether and how Se-alleviated Cd stress by regulating the structure of soil microbial community remain largely unclear. Here, we investigated the alleviating effects of exogenous applied Se (foliar spraying or root application) on plant growth under Cd stress in perilla (Perilla frutescens L.) by measuring the biomass, photosynthetic fluorescence parameters, root cell wall components and soil microbial community structure and diversity. Under Cd stress, perilla seedlings supplemented with Se increased chlorophyll content. Foliar spraying Se increased the levels of relative chlorophyll content (ΦII), photosynthetic system II (Φ_PSII) and electron transport rate (ETR) in perilla leaves under Cd stress; while, root application of Se increased the levels of photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), water use efficiency (WUE) and stomatal limitation value (Ls) under Cd stress. Compared with Cd toxicity alone, root application of Se increased the contents of hemicellulosic 1 and hemicellulosic 2 in the cell wall of perilla roots. Cd toxicity or root application of Se did not affect soil bacterial community diversity. Root application of Se increased the relative abundance of Proteobacteria, Bacteroidetes, Fibrobacteres, Sphingomonas and Nitrosospira in Cd-contaminated soil, and thereby improving soil microbial community structure, finally promoting the growth of perilla seedlings.

Iron (Fe), as one of the essential micronutrients for plants, plays a pivotal role in regulating growth and development through homeostatic balance. Fe deficiency is a common agricultural stress that causes visible leaf chlorosis and impairs plant growth. In this study, Arabidopsis thaliana seedlings grown under Fe deficiency for 4 days were subjected to 6 h Fe resupply via foliar spray or root supply, followed by measurements of chlorophyll fluorescence and metal ion contents in leaves and roots. Fe deficiency significantly reduced Fe levels and the maximum quantum yield of fluorescence (Fv/Fm), while increasing copper (Cu) accumulation in roots. Zinc (Zn) and manganese (Mn) levels were also altered, depending on tissue type. Fe resupply restored Fv/Fm, increased Mn levels, and rebalanced micronutrient content. MicroRNA (miRNA) mediates adaptation to Fe deficiency via post-transcriptional regulation in plants. However, the involved regulatory networks of miRNAs under stress conditions during Fe resupply following deficiency remain poorly understood. These physiological changes prompted us to explore the underlying regulatory networks using miRNA-seq and mRNA-seq. The bioinformatics analysis identified differentially expressed miRNAs responsive to Fe stress, with the Fe-deficiency-specific cis-element IDE1 characterized in their promoter regions. By integrating miRNA-seq and mRNA-seq datasets, we constructed a regulatory network and identified 13 miRNAs harboring IDE1 motifs alongside their functional target genes. Three critical Fe homeostasis modules were proposed—miR396b-LSU2, miR401-HEMA1, and miR169b-NF-YA2—that link Fe homeostasis to chlorophyll synthesis, sulfur (S) responses, and developmental signaling. This study integrates physiological phenotyping with transcriptomic insights to provide a comprehensive view of Fe deficiency and recovery in Arabidopsis.