A new cheese population in Penicillium roqueforti and 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. The Termignon population indeed 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. 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 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.

Different metabolite profiles acrossPenicillium roquefortipopulations associated with ecological niche specialisation and domestication

“…The non-cheese populations produced, on average, higher concentrations of PR toxin, especially the Lumber/spoiled food population, while the non-Roquefort and Roquefort domesticated populations did not produce any detectable quantities. The Termignon population had an intermediate profile, as previously reported for various growth parameters and carbon source usage (Crequer et al 2023). Such intermediate metabolite production levels are consistent with the hypothesis that the Termignon population represents descendants of an ancestral domesticated population, displaying traits resulting from domestication before the strong selection imposed in recent years by process industrialisation, thus corresponding to a protracted domestication process (i.e.…”

“…Penicillium roqueforti is a highly interesting filamentous fungus from an ecological point of view, as it colonises a multitude of niches thus highlighting its ability to adapt to different environments. This species is especially well known worldwide for its beneficial role in blue cheese production (Gillot et al 2015(Gillot et al , 2017bDumas et al 2020), but has also been isolated from lumber and found as a common contaminant in silage or food products like dairy, fruits and bakery (Pitt and Hocking 2009;Crequer et al 2023). Penicillium roqueforti produces many chemically diverse metabolites, including many so called secondary metabolites, now rather referred to as specialised metabolites, with known bioactive properties.…”

“…More recently, a third cheese population was identified, in Termignon blue cheeses that are not inoculated with P. roqueforti spores, that instead spontaneously colonise these specific cheeses in the French Alps from the environment. These Termignon strains exhibit intermediary phenotypic traits between the cheese and non-cheese populations and likely correspond to descendants of an ancient domesticated population with mild domestication syndrome (Crequer et al 2023). Two genetically different non-cheese populations have been identified, one mostly associated with silage, as well as to a lesser extent spoiled food, and the other with spoiled food and lumber (Dumas et al 2020).…”

“…Five populations have indeed been identified in P. roqueforti , corresponding to three cheese populations and two non-cheese populations (Dumas et al 2020; Crequer et al 2023). A first cheese population, called non-Roquefort, corresponds to a clonal lineage (Dumas et al 2020), and is used worldwide for the production of most kinds of blue cheeses ( e.g.…”

“…Gorgonzola, Cabrales, Stilton and Danablue). This population presents numerous beneficial traits for large-scale cheese making, such as higher salt and lactic acid tolerance, faster growth on cheese and faster lipolysis (Dumas et al 2020; Caron et al 2021; Crequer et al 2023). A second cheese population is mainly associated with the Roquefort protected designation of origin (PDO) (Gillot et al 2015; Dumas et al 2020).…”