Adaptation of Fungi to cheese – ArTIFICE

The adaptation of Geotrichum candidum to cheese involves genetic and phenotypic differences between strains isolated from the environment and strains isolated from cheese. To do this, population structure, genomic footprints of adaptation and phenotypic traits that distinguish wild populations from cheese populations are investigated using population genomics approaches, laboratory experiments and functional validation.

Our genomic analyses have shown a genetic differentiation between strains isolated from different types of cheese and strains isolated from other environments, and a subdivision of the cheese population into three populations. We were able to identify candidate genes involved in adaptation. Our phenotypic analyses also revealed differences in terms of growth, color, volatile organic compounds between wild and cheese populations. Geotrichum candidum is therefore adapted to cheese.

Other phenotypic tests will be carried out: proteolysis, lipolysis, mycotoxins.
Also, candidate genes identified as involved in the adaptation of G. candidum to cheese will be disrupted by crispr-cas9 system to validate the involvement of these genes in adaptation.
Finally, I will compare the results found in G. candidum with other cheese fungi already studied (Penicillium camemberti, P. roqueforti, S. cerevisiae) to test the repeatability of evolution.

To address the fundamental question of whether evolution is repeatable or contingent, we need to study parallel adaptation, i.e. independent adaptation events to the same ecological niche. Cheese fungi are excellent models for parallel adaptation studies, as many distantly related species have been selected by humans for cheese making. These recent adaptation events, occurring under strong human selection, provide good models for elucidating adaptation processes. Moreover, fungi are tractable model eukaryotes with many advantages for experimentation and genomic analyses. I will study Geotrichum candidum using genomic, historical and experimental approaches to understand its domestication history and the genomic mechanisms of adaptation. By comparing findings with previous studies on three other cheese-making fungi, I will investigate whether multiple adaptation events to cheese were convergent, with the same mechanisms involved and the same traits/genes/genomic regions targeted.