FUNGADAPT, ArTIFICE: studying cheese for a better understanding of evolutionary mechanisms
Is evolution repeatable or simply the result of chance? It's a question that has plagued scientists for centuries. Jeanne Ropars, researcher at the Ecology, Systematics and Evolution Laboratory (ESE - Univ. Paris-Saclay, CNRS, AgroParisTech), is trying to get closer to the answer by studying new models, cheese fungi.
Cheese lovers have surely come across them, but do they know that Penicillium, the type of fungus found in soft and blue-veined cheeses, is also a great study subject?
Jeanne Ropars, a researcher at the ESE laboratory, became interested in these edible moulds during her thesis. She sequenced their first genomes and wondered about their evolution: were these fungi adapted to their environment and did they evolve in parallel? This issue is now central to two research projects launched in 2020, funded by the French National Research Agency (ANR) and led by the researcher.
The first project, FUNGADAPT, aims to trace the history of the domestication and adaptation mechanisms of Penicillium in cheeses (P. camemberti and P. roqueforti) and cured meats (P. nalgiovense and P. salamii). "Domestication is a good model for studying evolution, because it is the result of a strong, recent selection process based on known traits," explains Jeanne Ropars.
The ArTIFICE project, meanwhile, is dedicated́ to studying the adaptation of the fungus Geotrichum candidum to cheese. A better understanding of this species and its evolutionary history is the key to determining whether phylogenetically different lineages have adapted to the same environment (in this case, cheese) in the same way.
Phenotypic and genetic differentiation
As part of these projects, Jeanne Ropars and her team have collected, isolated and sequenced strains from cheese rinds, as well as from other environments. The aim is to compare their genomes and test whether the cheese strains have developed traits that are beneficial for cheese production compared with wild strains. "To say that a population is adapted to a particular environment, there must be both genetic differentiation (which concerns genes) and phenotypic differentiation (i.e. observable on the organism) compared to the related wild population," explains the researcher.
Result: the cheese strains of the different species studied are highly differentiated from wild strains, at both genetic and phenotypic levels. These domesticated lineages, which diverged millions of years ago, show significant phenotypic convergence compared with their wild relatives. Penicillium in cheese, salami and strains of Geotrichum in cheese in particular develop whiter colonies than the wild strains.
Jeanne Ropars and her team have also demonstrated that Penicillium in cheese grow faster on the cheese environment than on other environments, produce more aromas and are better inhibitors of contaminants. The cheese strains also produce fewer mycotoxins - potentially toxic to humans - than their wild relatives. The team also identified horizontal transfers between the Penicillium in the cheese, explaining these convergent adaptations.
While genetic differentiation between wild and domesticated strains seems undeniable for cheese, the situation is more surprising for P. nalgiovense and P. salamii, the fungi found in salami. Indeed, despite significant phenotypic differences observed between the wild strains and those in sausage, no notable differentiation could be detected at the genetic level.
An alarming degeneration of cheese fungi
In addition to the new insights into the evolutionary mechanisms of fungi, the results of the studies by Jeanne Ropars and her colleagues shed new light on agribusiness. Indeed, the main consequence of rapid fungi selection and domestication is a drastic loss of diversity in cheese fungi populations. "For Camembert, for example, only a single strain, P. camemberti, is currently authorised by the specifications of the Protected Designation of Origin (PDO)," laments Jeanne Ropars. "This strain has been continuously cloned and inoculated into milk by all Camembert manufacturers for over a hundred years."
The problem with this asexual reproduction is that the fungi population, subject to random and sometimes deleterious mutations, is unable to recover lost traits without the addition of new genetic material. In other words, this repeated cloning leads to a degeneration that ultimately leads to the extinction of the species. "Today, P. camemberti is already no longer capable of sexual reproduction," worries the researcher. "It's important to preserve the genetic diversity of this fungus to prevent Camembert from disappearing!"
Regaining lost diversity
How can genetic diversity be reintegrated into the fungi used to make Camembert? Among the avenues considered by Jeanne Ropars, using strains of a species close to P. camemberti, also domesticated and adapted to cheese, seems promising. "P. biforme, the species closest to P. camemberti, would be suitable. It is naturally present in raw milk and is therefore already found on many natural-rind cheeses," explains the researcher.
This species shows considerable genetic and phenotypic diversity, with white, downy strains close to the appearance of P. camemberti, but also bluer strains. "Using it would mean getting rid of the white, downy image of our camemberts," adds the researcher. “We have to accept that they can all be different, more or less white, more or less downy."
Geotrichum candidum, a species also naturally present in raw milk, displays great genetic and phenotypic diversity. During the ArTIFICE project, Jeanne Ropars demonstrated that cheese strains are differentiated from wild strains, and that there are at least three distinct cheese-specific populations. Among them, one has a white, downy appearance, much appreciated by manufacturers. "This population in particular is subject to much stronger selection and its diversity is lower than for the other two," warns the researcher. "Our studies show that we're reproducing the same scenario as for P. camemberti!"
Today, Jeanne Ropars is working closely with local cheesemakers. Her aim is to sample local strains and explore the genetic and phenotypic diversity of cheese fungi. Following the Roquefort PDO model, cheesemakers would then be able to use local strains in their milk, rather than a single strain selected and cloned continuously.
The message from the FUNGADAPT and ArTIFICE projects is clear: too much genetic selection and standardisation of agri-food products risks eliminating certain foods from everyday life. "It's the same with cultivated plants or domesticated animals: if we lose all genetic diversity, nothing will be able to evolve and survive. Diversity is the basis of life!" concludes Jeanne Ropars.
- Ropars J, Giraud T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Curr Opin Microbiol. 2022 ; Dec ; 70 : 102236.
- Ropars J, Caron T, Lo YC, Bennetot B, Giraud T. Domestication of cheese fungi. CR Biol. 2020 Oct 9 ; 343 (2) : 155-176.
- Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T. Independent domestication events in the blue-cheese fungus Penicillium roqueforti. Mol Ecol. 2020 ; 29 (14) : 2639-2660.