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The objective of this study was to evaluate fungal and patulin contamination, together with its correlation with the volatile compounds (VCs), in ‘Fuji Mishima’ apples (up to 25% decayed) under controlled atmosphere (CA) and dynamic controlled atmosphere with respiratory quotient (DCA-RQ) of 1.3 combined with different partial pressures of carbon dioxide (0.8, 1.2, 1.6 and 2.0 pCO 2 ). Fruits were stored under the above conditions for 8 months at 0.5 °C plus 7 days shelf life at 20 °C. Toxigenic fungi and patulin accumulation were found in apples from all treatments.  Penicillium expansum  was the most prevalent species. For all storage conditions, patulin concentrations were above the maximum level allowed in Brazil (50  μg  kg −1 ) with an exception of DCA-RQ1.3 + 0.8 kPa CO 2 . This condition, with lower pCO 2 , showed the lowest patulin accumulation, below the legal limit. The CA provided the highest patulin concentration (166 μg  kg −1 ). It was observed that fungal growth could also contribute to changes in the volatile composition. Styrene and 3-methyl-1-butanol are considered  P. expansum  markers in some apple cultivars and were detected in the samples. However, it was not possible to identify volatile organic compounds (VOCs) that are biomarkers from  P. expansum , because there were other fungi species present in all samples. In this study, styrene, n-decanoic acid, toluene, phenol and alpha-farnesene were the compounds that showed the most positive correlation with patulin accumulation. On the other hand, a negative correlation of patulin with acids has been shown, indicating that in treatments with a higher patulin concentration there were less acidic compounds.

Fungal growth, patulin accumulation and volatile profile in ‘Fuji Mishima’ apples under controlled atmosphere and dynamic controlled atmosphere