Fungal communities on alpine cheese rinds in Southern Switzerland

Abstract Background: The fungal biodiversity on cheese rinds has been extensively studied for some soft cheeses such as Brie, Camembert, and Roquefort, but scant information is available on the microbiota colonizing the rinds of cheese produced in the Southern Switzerland Alps. This study aimed at exploring the fungal communities present on rinds of cheese produced and matured in Southern Switzerland. We used classical techniques such as dilution series, culturing and macro- and microscopical morphology, matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) mass spectrometry, and sequencing, as well as metabarcoding targeting the ITS and β-tubulin gene regions, to characterize the fungal communities present of cheese rinds collected in five ripening cellars. Results: Isolation by serial dilution yielded 201 isolates, of which 39 were yeasts and 162 filamentous fungi. Mucor and Penicillium were the dominant genera. Mucor racemosus, M. lanceolatus, P. camemberti, and P. chrysogenum/rubens were the most frequent species. All but two yeast isolates were identified as Debaryomyces hansenii. Overall, metabarcoding detected 80 fungal species, with Mucor spp. and Penicilliumspp. being the dominant taxa, as opposed to only 9 species recovered by serial dilutions. Culture-dependent and independent methods produced similar results in terms of dominant taxa and similarity of the fungal communities in the five cellars, metabarcoding, however, providing more detailed information. Conclusions: Our study has shown that the mycobiota on the rinds of alpine cheese is a complex community defined by different parameters, including temperature, relative humidity, and type of cheese, as well as microenvironmental and possibly geographic factors.