Salt stress exerts a negative impact on plant growth and productivity ^[1][64]. Plants respond to salt stress by undergoing changes in their metabolic activity to counteract the toxicity induced by excessive salt levels ^[1][64]. Salinity often causes osmotic imbalance and ionic toxicity in plants, leading to membrane disruption and cellular dehydration in the cytoplasm ^[2][65]. These changes in ionic and osmotic components can result in either an increase or decrease in the accumulation of plant secondary metabolites. In vitro studies have revealed a decline in anthocyanin accumulation in salt-sensitive species ^[3][66], while the decrease in phenolic, anthocyanin, and flavonoid content under salt stress conditions was less pronounced in salt-tolerant clones ^[4][67]. Proline, which regulates stress signals and serves as an osmotic buffer, energy sink, and protector of membranes and proteins, shows increased accumulation in the roots of Alfalfa under salt stress ^[5][68]. Various studies have observed the accumulation of polyphenols and flavonoids under salinity stress in plants like Hordeum vulgare and Cakile maritma ^[6][7][69,70]. Transcription factors GmCAM4 and GmERFo57 play crucial roles in providing resistance to salinity stress in Glycine max ^[8][71]. Spinacia oleracea demonstrates resistance against saline soil by enhancing the production of 20-Hydroxyecdysone (20E) ^[9][72]. Furthermore, alkaloids such as vincristine and reserpine in Catharanthus roseus and Rauvolfia tetraphylla, respectively, increase under saline conditions ^[10][73].

Drought severely impacts plants’ biochemical and physiological processes, causing disruptions in the electron transport chain and leading to the production of reactive oxygen species (ROS) like H₂O₂, OH⁻, and O₂⁻. These ROS inflict oxidative damage on lipids, nucleic acids, and proteins, and also disrupt the photosynthetic mechanism of plants. Drought severity varies among plant species and is often accompanied by increased solar radiation and temperature ^[11][74]. The stress disturbs plant metabolism, reduces cell turgidity and signalling, and impairs energy storage, plasma membrane structure, and resource allocation ^[12][75].

To cope with drought stress, plants have developed response mechanisms that involve the accumulation of secondary metabolites such as phenolics, terpenes, and alkaloids. These secondary metabolites help regulate ionic balance and enzyme activity, repair oxidative damage, and maintain the connection between the phenotype and genotype of plants ^[13][14][76,77]. However, increased production of these metabolites can lead to reduced biomass in some plant species ^[15][78]. For instance, under drought stress, plants like Artemisia annua and Catharanthus roseus increase secondary metabolite production by several times ^[16][79]. Drought stress induces elevated expression of PAL genes, responsible for flavonoid synthesis, in roots of Scutellaria baicalensis ^[17][80]. In Chenopodium quinoa, the accumulation of saponin changes under different drought stress conditions ^[18][81]. Drought stress also affects the carotenoid and chlorophyll ratio in plants. Notably, Bellis perennis and Ophiorrhiza mungos show enhanced production of camptothecin, alkaloids, and phenolic compounds, respectively, under drought conditions ^[19][20][82,83].

Drought stress has varying effects on the concentrations of secondary metabolites in the roots and leaves of Bupleurum chinensis plants. For example, saikosaponin concentrations in the roots increase during vegetative and reproductive growth, while leaf rutin concentrations decrease significantly during these stages ^[21][84].

These studies underscore the intricate interplay between abiotic stresses and plant physiological responses, leading to diverse responses of secondary metabolites against drought stress.

Elevated temperatures lead to reduced development and early leaf senescence in plants. The impact of temperature on the production of secondary metabolites varies among different plant species ^[22][23][85,86]. Heat treatments can cause enzyme inactivation, and lipid and protein denaturation negatively affect membrane integrity. Under temperature stress, carotenoid and β-carotene accumulation in Brassicaceae are reduced ^[22][85]. Acidic pH combined with a high temperature in hairy root culture promotes the accumulation of flavonolignans in Silybum marianum ^[24][87]. Some plants, like Melastoma malabathricum, show increased anthocyanin and biomass production at lower temperatures compared to higher temperatures ^[25][88]. Daucus carota responds to heat shock by increasing terpene accumulation, while the production levels of α-terpinolene decrease at the same temperature. Short-term temperature treatment enhances isoprene production synthesized through the nonmevalonate pathway (MEP), which is believed to counteract the negative effects of heat shock ^[26][27][89,90]. Different temperature ranges can significantly affect the level of secondary metabolites in plants, as observed in Amaranthus cruentus ^[28][91]. Salicylic acid and phenolic content in flowering plants ^[29][92] and phenolic compounds in gymnosperms ^[30][93] were found to decrease with increasing temperature. In tea plants, the concentration of catechin levels increases when treated with higher temperatures ^[31][94].

Light plays a critical role in plant metabolism and the production of secondary metabolites. Stable light intensity regulates photosynthesis and dry matter accumulation. However, abnormal irradiation can lead to photodamage and negatively affect photosynthetic reaction centres, causing photoinhibition, which limits plant survival, growth, and development ^[32][95]. The production and accumulation of secondary metabolites from various precursor elements depend on light intensity and the lengths of the photoperiod ^[33][34][96,97]. Different plant species respond differently to the quality, intensity, and length of photoperiod (day length) ^[35][98]. Appropriate light intensity regulates the accumulation and quality of flavonoids, alkaloids, spermine, and hexadecanoic acid ^[34][36][97,99]. For example, Melastoma malabathricum cell cultures exposed to different light intensities and full irradiance or complete darkness showed varying anthocyanin yield and biomass accumulation ^[25][88]. In vitro cultured seedlings of Hyptid marrubiodes exhibited increased production of flavonoids in red light, while rutin accumulation increased in white and blue light ^[37][100]. UV light treatment generally has a positive effect on the synthesis of secondary metabolites; however, at higher irradiation doses of UV-C and UV-B, some plants may react with decreased growth, abnormal metabolic activity, and photosynthesis ^[38][101].

Exposure of Asparagus officinalis to UV-B results in higher activity of peroxidase and phenylalanine ammonia-lyase, which ultimately enhances the accumulation of quercetin-4′-O-monoglucoside ^[39][102]. In Catharanthus roseus, UV-B light exposure significantly influences the production of vinblastine and vincristine, both used in treating leukemia and lymphoma ^[40][103]. Moreover, a combination of UV light (280–320 nm) with red light stimulates anthocyanin production in Malus domestica ^[41][104], while UV irradiation on Fagopyrum esculentum increases the content of quercetin ^[42][105]. Several studies have shown that UV light treatment is associated with increased phenolic compounds and ROS scavenging systems ^[43][106].

Additionally, the duration of light exposure plays a role in affecting secondary metabolite concentration. For example, light intensity and wavelength had a considerable effect on the accumulation of secondary metabolites in the leaves of Flourensia cernua ^[44][107]. Similarly, Ipomea batatus demonstrated differential effects on the concentration of phenolic compounds and flavonoids with enhanced levels observed upon exposure to longer light duration ^[45][108]. In green algae, Dunaliella baradawil, the accumulation of indoleamines like melatonin and serotonin increased under different photoperiod treatments ^[46][109].

Plants respond differently to metal toxicity, resulting in variations in the accumulation and production of secondary metabolites due to the differential mobility of heavy metals that alter plant components, leading to reduced biosynthesis of plant defence compounds ^[47][110]. The adaptation and tolerance of plants against heavy metal stress are associated with the signalling molecules responsible for the synthesis and accumulation of secondary metabolites ^[48][111]. For example, Hypericum perforatum showed decreased accumulation of hypericin and pseudohypericin when exposed to nickel stress ^[49][112]. Nickel can either increase or inhibit the synthesis and accumulation of anthocyanin content in different plant species ^[50][51][113,114]. Brassica juncea treated with Fe, Mn, and Cr showed increased plant oil content ^[52][115]. Toxicity under high copper chloride (CuCl₂) conditions activates the defence mechanism in Viburnum ichangense, leading to the accumulation and biosynthesis of ichangoside and phenolic diglycoside ^[53][116]. Salix purpurea exhibits an increased accumulation of phenolic compounds and salicylic acid under Cu- and Ni-stress conditions ^[54][117].