Fungal communities on alpine cheese rinds in Southern Switzerland

Abstract

Background: The biodiversity of the mycobiota of soft cheese rinds such as Brie or Camembert has been extensively studied, but scant information is available on the fungi colonizing the rinds of cheese produced in the Southern Switzerland Alps. This study aimed at exploring the fungal communities present on rinds of cheese matured in five cellars in Southern Switzerland and to evaluate their composition with regards to temperature, relative humidity, type of cheese, as well as microenvironmental and geographic factors. We used macro- and microscopical morphology, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, and sequencing to characterize the fungal communities of the cheeses, and compared them with metabarcoding targeting the ITS region.

Results: Isolation by serial dilution yielded 201 isolates (39 yeasts and 162 filamentous fungi) belonging to 9 fungal species. Mucor and Penicillium were dominant, with Mucor racemosus, M. lanceolatus, P. biforme, and P. chrysogenum/rubens being the most frequent species. All but two yeast isolates were identified as Debaryomyces hansenii. Metabarcoding detected 80 fungal species. Culture work and metabarcoding produced comparable results in terms of similarity of the fungal cheese rind communities in the five cellars.

Conclusions: Our study has shown that the mycobiota on the rinds of the cheeses studied is a comparatively species-poor community influenced by temperature, relative humidity, type of cheese, and manufacturing steps, as well as microenvironmental and possibly geographic factors.

Keywords: High-throughput sequencing; ITS; MALDI-TOF MS; Metabarcoding; MinION; Mycobiome.

Fig. 1

A Example of a typical ripening cellar (Cellar D, Formazzora). B Interior of Cellar D (Formazzora), showing the cheese storage on larch boards. C Close-up of a typical Ticino alpine cheese form. D A typical Ticino alpine cheese form at the end of the ripening phase (Cellar C, Campo la Torba)

Fig. 2

Analysis of the ecological data collected by cultural methods and metabarcoding. In A and B, green circles indicate cellar A (Bolla and Carassina), orange ticks cellar B (Bresciana), blue diamonds cellar C (Campo La Torba), magenta triangles cellar D (Formazzora), and grey squares cellar E (Pontino). In C and D, A–E indicate the cellars as described in Table 1. A, B Whittaker plots. The number of individuals of each OTU are sorted in descending order; the proportion of the total number of individuals for each species is plotted on the log scale against the OTU rank, presenting the richness of each species ranked from the most (rank 1) to the least frequent rank. The steep plots indicate communities with high dominance. A Samples studied by metabarcoding using OTUs with frequencies >1%. B Samples studied by cultural methods. C, D Plot of the evenness vs. richness data for each cellar. C Metabarcoding data, using OTUs with frequencies >1%. D Culture data

Fig. 3

A Results of the MDS of the data collected by metabarcoding, computed using only OTUs with frequencies of reads > 1%. B Results of the MDS of the data collected by serial dilution. A-E indicate the cellars as described in Table 1. Samples that are geometrically close to each other in the graph are colonised by similar fungal communities