Ciprofloxacin and glyphosate co-exposure alters soybean development and reprograms metabolic pathways

The increasing occurrence of pharmaceutical residues and herbicides in agricultural soils raises concerns about their impacts on crop development. Here, we first screened the effects of 22 emerging contaminants on soybean (Glycine max L.) germination and subsequently assessed the individual and combined effects of ciprofloxacin (CIP) and glyphosate (G) during early development. A multidisciplinary strategy was applied, integrating morphophysiological measurements, stress-related biomarkers, and ^{^1}H NMR-based metabolomic profiling from germination to the R1 stage. Soybean seedlings exposed to CIP (0.10 and 1.00 mg L^-1), alone or with G, showed dose-dependent phytotoxicity, with CIP 1.00 mg L^-1 significantly reducing shoot length, leaf number, and biomass. Remarkably, co-exposure with glyphosate modulated CIP-induced effects in a parameter-dependent manner, with both attenuation and enhancement depending on the measured trait. At R1, proline and GABA showed slight, non-significant increases, while metabolomics revealed reduced glucose and elevated alanine and squalene, suggesting alterations in energy, amino acid, and lipid metabolism. These metabolic disruptions were attenuated under co-exposure. Overall, CIP significantly alters soybean physiology and metabolism, while G modulates CIP-induced effects in a parameter-dependent manner, showing both attenuation and enhancement depending on the evaluated trait. The findings highlight the ecological relevance of pharmaceutical-herbicide mixtures and demonstrate the value of metabolomics for detecting early biochemical responses in crops.