Carbon nanomaterials such as single-walled carbon nanotubes (SWCNTs) offer a new possibility for phyto-nanotechnology and biotechnology to improve the quality and quantity of secondary metabolites in vitro. The current study aimed to determine the SWCNTs effects on Thyme (Thymus daenensis celak.) seed germination. The seedlings were further assessed in terms of morphological and phytochemical properties. Sterile seeds were cultured in vitro and treated with various concentrations of SWCNTs. Biochemical analyses were designed on seedling sample extracts for measuring antioxidant activities (AA), total flavonoids (TFC) and phenolic contents, and the main enzymes involved in oxidative reactions under experimental treatments. The results indicated that an increase in SWCNTs concentration can enhance the total percentage of seed germination. The improvement was observed in samples that received SWCNTs levels of up to 125 µg ml−1, even though seedling height and biomass accumulation decreased. Seedling growth parameters in the control samples were higher than those of grown in SWCNT-fortified media. This may have happened because of more oxidative damage as well as a rise in POD and PPO activities in tissues. Additionally, secondary metabolites and relevant enzyme activities showed that maximum amounts of TPC, TFC, AA and the highest PAL enzyme activity were detected in samples exposed to 62.5 µg ml−1 SWCNTs. Our findings reveal that SWCNTs in a concentration-dependent manner has different effects on T. daenensis morphological and phytochemical properties. Microscopic images analysis revealed that SWCNTs pierce cell walls, enter the plant cells and agglomerate in the cellular cytoplasm and cell walls. The findings provide insights into the regulatory mechanisms of SWCNTs on T. daenensis growth, germination and secondary metabolites production.

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