Proteomic analysis reveals metabolic adaptations of Mucor plumbeus during antagonistic interactions with Pichia jadinii

• Proteomics identified molecular responses of M. plumbeus to yeast antagonism. • Carbohydrate-rich medium preserved anabolic and growth function. • Protein-rich medium induced oxidative stress and structural defences in M. plumbeus. • Differentially abundant proteins identified markers of fungal vulnerability. • Results provide molecular bases to direct the design upcoming pilot‑scale validation. The genus Mucor is a major contributor to fungal contamination and the subsequent loss of stored products. Elucidating the molecular mechanisms underlying fungal responses to biocontrol agents is essential for developing sustainable, fungicide-free management strategies. This study employed a proteomic approach to investigate the metabolic adaptations of Mucor plumbeus during antagonistic interaction with the yeast Pichia jadinii PJ433 across diverse substrates. Antagonistic assays were conducted using inhibition halo and dual culture methods across five media. Based on the screening results, yeast malt culture (YMC) and skim milk (SM) media were chosen for comparative proteomic analysis. M. plumbeus was cultured under indirect antagonism from P. jadinii , and protein changes were quantified by mass spectrometry. Functional enrichment was assessed with Gene Ontology tools. P. jadinii exhibited antifungal activity against M. plumbeus , with dominance indices of 8 in YMC and SM media. A total of 990 proteins were identified by proteomic analyses, of which 206 (20.8%) were detected in both media, 439 (44.3%) were unique to YMC, and 138 (13.9%) to SM. The metabolic response of M. plumbeus to antagonistic yeast was dictated by the medium composition: YMC promoted carbohydrate metabolism and biosynthetic pathways, whereas SM intensified proteolysis, lipid metabolism, and oxidative stress-related responses. Core metabolic functions remained conserved across media, indicating fundamental survival mechanisms. M. plumbeus demonstrated remarkable metabolic plasticity, adapting its proteome according to nutrient availability and antagonistic pressure. The differential protein abundance patterns reveal distinct survival strategies: rapid anabolic growth in carbohydrate-rich environments (YMC) versus stress adaptation and defensive responses in protein- and lipid-rich environments (SM). These findings offer molecular insights that could serve as a foundation to guide future pilot-scale and storage-validation studies required to evaluate efficacy under industrial conditions.