Abstract
Paecilomyces is a frequently genus associated with food spoilage worldwide. Among its species, P. variotii produces the most heat-resistant conidia described to date, while P. niveus and P. dactylethromorphus are potential patulin producers. Recently, P. paravariotii was described as a closely related species to P. variotii and the occurrence in food-related environments remains scarcely reported. In this study Paecilomyces species associated with orange juice processing environments and spoiled products were characterized using multilocus phylogenetic analysis, and strain-level variability in stress tolerance was evaluated under thermal and non-thermal conditions. Twelve isolates were identified and following preliminary heat screening at 58 and 59 °C, six representative strains were selected for thermal inactivation kinetics at 60 °C and exposure to direct cold plasma generated by a gliding arc plasma jet (GAPJ). Phylogenetic analysis revealed a predominance of P. paravariotii, along with P. variotii, P. dactylethromorphus, and P. lecythidis. Thermal assays showed wide variability, with P. variotii being the most resistant and P. dactylethromorphus the most sensitive. Responses to GAPJ-induced oxidative stress mirrored the thermal resistance profiles observed among the strains, with the most resistant strains remaining viable after a 20 to 30-minute exposure. Overall, strain-level variability reflects ecological and environmental influences on fungal stress adaptation, emphasizing the importance of strain-level analyses and ecological context in understanding fungal persistence in food systems. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04970-6.