Anchusa officinalis (L.) interacts with various microorganisms including arbuscular mycorrhizal fungi (AMF). Recently, the AMF Rhizophagus irregularis MUCL 41833 has been shown to modulate the metabolome of A. officinalis. However, little information is available on the impact that different AMF species may have on primary and secondary plant metabolites. In this study, four AMF species belonging to the genus Rhizophagus (R. irregularis MUCL 41833, R. intraradices MUCL 49410, R. clarus MUCL 46238, R. aggregatus MUCL 49408), were evaluated for their potential to modulate A. officinalis metabolome under controlled semi-hydroponic cultivation conditions. An untargeted metabolomic analysis was performed using UHPLC-HRMS followed by a multivariate data analysis. Forty-two compounds were reported to be highly modulated in relation to the different AMF associations. Among them, six new secondary metabolites were tentatively identified including two acetyl- and four malonyl- phenylpropanoid and saponin derivatives, all presenting a common substitution at position C-6 of the glycosidic moiety. In addition, an enhanced accumulation of primary and secondary metabolites was observed for R. irregularis and R. intraradices, showing a stronger effect on A. officinalis metabolome compared to R. clarus and R. aggregatus. Therefore, our data suggest that different AMF species may specifically modulate A. officinalis metabolite production.

Alkanna tinctoria (L.) Tausch is a valuable medicinal plant known for its root-derived hydroxynaphthoquinone enantiomers, alkannin/shikonin (A/S), which exhibit significant pharmaceutical and cosmeceutical potential. However, its limited natural distribution and overharvesting pose conservation challenges, necessitating sustainable cultivation and extraction strategies. The application of Natural Deep Eutectic Solvents (NaDESs) has garnered significant attention as sustainable alternatives to conventional solvents. However, their toxicity in living plant systems remains largely unexplored. This study presents the successful establishment of an ex situ hydroponic cultivation system using the nutrient film technique (NFT) to grow A. tinctoria under greenhouse conditions. The system promoted plant acclimatization, vigorous root development, and initial production of A/S derivatives. In parallel, the toxicity evaluation of a bio-based NaDES, LeG_5_20 (levulinic acid–glucose, 5:1, with 20% water), applied as a circulating medium, was assessed. Physiological stress responses of the plants to NaDES circulation were assessed through non-destructive measurements, including stomatal resistance, photosynthetic and transpiration rates, and sub-stomatal CO₂ concentration. Short-term (24 min) exposure to NaDES showed no significant adverse effects, while longer exposures (4–8 h) induced marked stress symptoms and loss of leaf area. These findings demonstrate the feasibility of integrating green hydroponic systems with eco-friendly extraction solvents and provide a framework for further optimization of plant age, solvent exposure time, and system design to enable sustainable metabolite recovery without plant destruction.