A new cheese population inPenicillium roquefortiand adaptation of the five populations to their ecological niche

Abstract

Domestication is an excellent case study for understanding adaptation and multiple fungal lineages have been domesticated for fermenting food products. Studying domestication in fungi has thus both fundamental and applied interest. Genomic studies have revealed the existence of four populations within the blue-cheese-making fungus Penicillium roqueforti. The two cheese populations show footprints of domestication, but the adaptation of the two non-cheese populations to their ecological niches (i.e. silage/spoiled food and lumber/spoiled food) has not been investigated yet. Here, we reveal the existence of a new P. roqueforti population, specific to French Termignon cheeses, produced using small-scale traditional practices, with spontaneous blue mould colonisation. This Termignon population is genetically differentiated from the four previously identified populations, providing a novel source of genetic diversity for cheese making. Phenotypically, the non-Roquefort cheese population was the most differentiated, with specific traits beneficial for cheese making, in particular higher tolerance to salt, to acidic pH and to lactic acid. Our results support the view that this clonal population, used for many cheese types in multiple countries, is a domesticated lineage on which humans exerted strong selection. The Termignon population displayed substantial genetic diversity, both mating types, horizontally transferred regions previously detected in the non-Roquefort population, and intermediate phenotypes between cheese and non-cheese populations. The lumber/spoiled food and silage/spoiled food populations were not more tolerant to crop fungicides but showed faster growth in various carbon sources (e.g. dextrose, pectin, sucrose, xylose and/or lactose), which can be beneficial in their ecological niches. Such contrasted phenotypes between P. roqueforti populations, with beneficial traits for cheese-making in the cheese populations and enhanced ability to metabolise sugars in the lumber/spoiled food population, support the inference of domestication in cheese fungi and more generally of adaptation to anthropized environments.

Generation of diversity in the blue cheese moldPenicillium roquefortiand identification of pleiotropic QTL for key cheese-making phenotypes

“…For three extrolites (MPA, PR toxin and roquefortine C), we identified QTLs with intervals included in their biosynthesis cluster, with non-Roquefort alleles associated with lower production levels. The lower MPA production level associated with the non-Roquefort allele is likely due to the deletion in the mpaC gene that was identified in the non-Roquefort population (Gillot et al 2017;Crequer et al 2024). We also found a QTL in a region including the PR toxin biosynthesis gene cluster, with lower production level of the PR toxin but accumulation of its production intermediates, eremofortins A and B, associated with the non-Roquefort allele at the PR toxin biosynthesis cluster.…”

“…The plates were incubated at 25°C in the dark for seven days and then stored at -20°C until extrolite analysis. For extrolite extractions, we used an optimized "high-throughput" extraction method (Lo et al 2023;Crequer et al 2024). Briefly, 2g-aliquots (the entire YES culture obtained from a well) were homogenized after thawing samples with a sterile flat spatula then 12.5 mL of acetonitrile (ACN) supplemented with 0.1% formic acid (v/v) was added, samples were vortexed for 30 sec followed by 15 min sonication.…”

“…These horizontally transferred regions include in particular two very large regions called Wallaby and CheesyTer, which encompass genes with functions in lactose metabolism or competition against other microorganisms. The non-Roquefort lineage further displays footprints of positive selection in genes involved in volatile compound production (Dumas et al 2020) and has lost the ability to secrete the mycophenolic acid (MPA) mycotoxin, an immunosuppressant used for preventing transplant organ rejection (Matas et al 2013), because of a deletion in a key gene (mpaC) of its biosynthesis pathway (Gillot et al 2017;Crequer et al 2024). Penicillium roqueforti can secrete other metabolites, i.e.…”

Domestication of different varieties in the cheese-making fungusGeotrichum candidum

“…We did not detect higher salt tolerance or higher lipolysis ability in cheese populations. Higher salt tolerance and lipolysis rates have been reported in the non-Roquefort P. roqueforti population compared to non-cheese populations, but not in the Roquefort P. roqueforti population 35, 79 . The dry-cured meat Penicillium fungi even had lower lipolysis rates 77 .…”

Domestication in dry‐cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision

“…For example, P. roqueforti is used for blue‐veined cheeses and P. camemberti is used for soft cheeses, such as Brie and Camembert. Both fungi have recently emerged as useful models for adaptation and domestication studies (Ropars et al, 2015, 2020; Dumas et al, 2020; Cheeseman et al, 2014; Ekseth et al, 2014; Williams et al, 1986; Bodinaku et al, 2019; Crequer et al, 2023). The Saccharomyces cerevisiae, P. camemberti and P. roqueforti populations used in the food industry have specific traits that are beneficial for food production and enable them to thrive in their human‐made environments to a much greater extent than other populations (Dumas et al, 2020; Marsit & Dequin, 2015; Ropars et al, 2020), providing evidence of genuine domestication.…”