Identification of the metabolites regulated in soybean-Rhizobia symbiosis through solid phase microextraction coupled with LC-MS

•TF-SPME is a non-exhaustive and low-invasive sampling technique.•The free metabolites in the soybean nodules were extracted through SPME.•SPME was carried out without any physical removal of the nodules.•This method holds promise as a tool to determine the nodule metabolic alterations.•The metabolic alterations can fingerprint soil stress and soybean viability.