Root-knot nematodes (Meloidogyne incognita) pose a serious threat to global agriculture, necessitating eco-friendly alternatives to synthetic nematicides. This study explores the innovative use of deep eutectic solvents (DES) to extract bioactive compounds from Artemisia rupestris, offering a sustainable approach to nematode management. Six choline chloride (ChCl)-based DES systems were evaluated, revealing extraction efficiency dependent on the hydrogen-bond donor. ChCl–1,4-butanediol (But) yielded the highest thiophene content (143.65 μg/g), which was 2.9 fold greater than that obtained with ethanol. ChCl–urea (U) and ChCl–citric acid (CA) achieved the highest extraction efficiency for phenolics (267.78 mg/g) and flavonoids (175.32 mg/g), respectively. In vitro assays demonstrated that ChCl–But extracts showed the highest nematode mortality at 86.50 %. Thiophene content showed a strong correlation with bioactivity (r = 0.925), identifying it as the principal bioactive driver. Pot trials confirmed a dose-dependent efficacy, with ChCl–But extracts reducing root galling by 79.59 % and nematode populations by 81.65 %. Moreover, the extracts considerably enhanced tomato plant growth, outperforming the commercial nematicide abamectin. Field trials demonstrated that ChCl–But extracts reduced root galling by 68.37 % and second-stage juvenile nematode densities by 66.30 % while increasing tomato shoot biomass by 59.53 %. Five thiophene derivatives were isolated, exhibiting potent nematicidal activity, with xanthopappin A (compound 3) showing 4.8 fold greater efficacy (LD50 = 2.00 mg/L) than abamectin. This study highlights DES as a sustainable platform for valorizing underutilized plant resources, integrating efficient extraction of bioactive thiophenes with the dual benefits of nematode suppression and crop growth promotion. The findings offer scalable solution for sustainable agriculture, addressing environmental and resistance challenges in nematode management.
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