Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation

Domestication des champignons du fromage

Biodiversity is more than ever threatened by several global phenomenons such as the continued destruction of natural habitats, intensive agriculture and climate disturbance. It is therefore urgent to better understand how biodiversity is generated and maintained, in order to be able to act against the collapse of biodiversity. Domestication provides an interesting framework for understanding the mechanisms of adaptation and the role of genetic diversity in the generation and maintenance of biodiversity. Darwin used domestication as a model to understand how species arise and to establish the basis of the theory of evolution. Indeed, domestication is a specific case of adaptation, involving strong and recent selection and rapid divergence into separate evolutionary lineages. Although we are not the only species at the root of domestication events, humans have domesticated a large number of both animals and plants. Additionally, some microorganisms, including fungi, have also been domesticated for a variety of tasks such as controlled fermentation, the production of antibiotics, and consumed directly. Fungi are good eukaryotic models for studying evolution, because phylogenetically related species occupy different ecological niches, and they have many experimental and genomics assets (e.g. relatively easy manipulation within a lab setting, short generation times, small and often haploid genomes). One such setting, where fungi domestication has been championed, is in the production of cheese. Penicillium camemberti is the typical white and fluffy mold on the surface of cheeses such as Camembert and Brie. We have shown that P. camemberti is the result of domestication in several steps, leading to different varieties. The first domestication event led to the emergence of the domesticated blue-gray mold named P. biforme, found on fresh goat cheese. A second, more recent domestication event resulted in the clonal lineage P. camemberti. Both domesticated species P. camemberti and P. biforme show advantageous traits for cheese ripening compared to the closest related wild species. Within the P.camemberti species, we identified two varieties (camemberti and caseifulvum) with contrasting phenotypes in terms of growth, color, mycotoxin production and ability of contaminant inhibition. The white and fluffy camemberti variety is inoculated on camembert-type cheeses, while the gray and less fluffy caseifulvum variety is inoculated on other cheeses such as Saint Marcellin. Geotrichum candidum is a dimorphic fungus (yeast and filamentous form) found naturally in milk. Genomic analyses revealed three monophyletic clades, one comprising only wild strains, a mixed-origin clade comprising wild and cheese strains, and a clade containing only cheese strains. The cheese strains have different phenotypes from the wild strains, such as slower growth on all media, including cheese, high production of desirable volatile compounds and lower proteolytic activity. Within the cheese clade, we identified three populations with contrasting phenotypes. In contrast to P. camemberti, the G. candidum cheese populations are genetically diverse and show evidence of recombination; thus, there is not one clonal lineage used as a ferment but several genetically and phenotypically different strains. However, one of the cheese populations shows evidence of a more advanced state of domestication, with less genetic diversity than the other populations, a denser mycelium and an ability to inhibit contaminants more efficiently, similar to that of P. camemberti. Penicillium camemberti is the result of the selection of a single mutant, whereas the species G. candidum still has a great diversity. Thus, with these two species, we have a contrasting view of cheese fungi domestication.Aujourd'hui, la biodiversité est plus que jamais menacée par une destruction massive des environnements naturels, l'agriculture intensive et le dérèglement climatique. Il est donc plus qu'urgent et indispensable de mieux comprendre comment la biodiversité est générée et se maintient, pour être en mesure d'agir contre l'effondrement de la biodiversité. La domestication fournit un cadre intéressant pour comprendre les mécanismes d'adaptation et le rôle de la diversité génétique dans la génération et le maintien de la biodiversité. Darwin se sert d'ailleurs de la domestication comme modèle pour comprendre comment les espèces apparaissent et établir les bases de la théorie de l'évolution. En effet, la domestication est un cas spécifique d'adaptation, impliquant une sélection forte et récente et une divergence rapide en lignées évolutives séparées. L'être humain a domestiqué un grand nombre d'animaux et de plantes. Certains micro-organismes, dont les champignons, ont aussi été domestiqués pour fermenter les aliments, produire des antibiotiques, et pour leur qualité gustative. Les champignons sont de bons modèles eucaryotes pour étudier l'évolution, car des espèces phylogénétiquement proches occupent des niches écologiques différentes, et ils possèdent de nombreux avantages pour les études expérimentales (e.g. faciles à cultiver au laboratoire, temps de génération courts) et génomiques (petits génomes souvent haploïdes). Penicillium camemberti est la moisissure blanche et duveteuse typique en surface des fromages tels que le Camembert et le Brie. Nous avons montré que P. camemberti est le fruit d'une domestication en plusieurs étapes, menant à différentes variétés. Un premier évènement de domestication a conduit à l'émergence de la moisissure domestiquée bleue-grise nommée P. biforme, qu'on retrouve par exemple sur les fromages frais de chèvre. Un deuxième évènement de domestication, plus récent, a donné la lignée clonale P. camemberti. Les deux espèces domestiquées P. camemberti et P. biforme montrent des caractères avantageux pour l'affinage des fromages comparé à l'espèce sauvage proche. Nous avons aussi identifié deux variétés de P. camemberti aux phénotypes contrastés en termes de croissance, de couleur, de production de mycotoxines et de capacité d'inhibition des contaminants. La variété camemberti, blanche et duveteuse, est inoculée sur les fromages type camembert, alors que la variété caseifulvum, grise et moins duveteuse, est inoculée sur d'autres fromages comme le Saint Marcellin. Geotrichum candidum est un champignon retrouvé naturellement dans le lait. Les analyses génomiques ont révélé trois clades monophylétiques, un clade comprenant uniquement des souches sauvages, un clade d'origine mixte comprenant des souches sauvages et du fromage et un clade comprenant uniquement des souches isolées de fromage. Les souches du fromage ont des phénotypes différents des souches sauvages, comme une croissance plus lente sur tous les milieux, même fromage, une production importante de composés volatils souhaitable et une activité protéolytique plus faible. Au sein du clade fromage, nous avons identifié trois populations aux phénotypes contrastés. Les populations du fromage sont génétiquement diversifiées et montrent des traces de recombinaison ; il n'y a donc pas eu sélection d'une lignée clonale utilisée comme ferment mais de plusieurs souches génétiquement et phénotypiquement différentes. Une des populations du fromage montre des traces d'un état plus avancé de domestication, avec une diversité génétique moins importante que les autres populations, un mycélium plus dense et une capacité à inhiber plus efficacement des contaminants, comme P. camemberti. Penicillium camemberti est le résultat de la sélection d'un unique mutant alors que l'espèce G. candidum possède encore une grande diversité. On a donc, avec ces deux espèces, une vision contrastée de la domestication des champignons du fromage

Domestication of cheese fungi

Aujourd'hui, la biodiversité est plus que jamais menacée par une destruction massive des environnements naturels, l'agriculture intensive et le dérèglement climatique. Il est donc plus qu'urgent et indispensable de mieux comprendre comment la biodiversité est générée et se maintient, pour être en mesure d'agir contre l'effondrement de la biodiversité. La domestication fournit un cadre intéressant pour comprendre les mécanismes d'adaptation et le rôle de la diversité génétique dans la génération et le maintien de la biodiversité. Darwin se sert d'ailleurs de la domestication comme modèle pour comprendre comment les espèces apparaissent et établir les bases de la théorie de l'évolution. En effet, la domestication est un cas spécifique d'adaptation, impliquant une sélection forte et récente et une divergence rapide en lignées évolutives séparées. L'être humain a domestiqué un grand nombre d'animaux et de plantes. Certains micro-organismes, dont les champignons, ont aussi été domestiqués pour fermenter les aliments, produire des antibiotiques, et pour leur qualité gustative. Les champignons sont de bons modèles eucaryotes pour étudier l'évolution, car des espèces phylogénétiquement proches occupent des niches écologiques différentes, et ils possèdent de nombreux avantages pour les études expérimentales (e.g. faciles à cultiver au laboratoire, temps de génération courts) et génomiques (petits génomes souvent haploïdes). Penicillium camemberti est la moisissure blanche et duveteuse typique en surface des fromages tels que le Camembert et le Brie. Nous avons montré que P. camemberti est le fruit d'une domestication en plusieurs étapes, menant à différentes variétés. Un premier évènement de domestication a conduit à l'émergence de la moisissure domestiquée bleue-grise nommée P. biforme, qu'on retrouve par exemple sur les fromages frais de chèvre. Un deuxième évènement de domestication, plus récent, a donné la lignée clonale P. camemberti. Les deux espèces domestiquées P. camemberti et P. biforme montrent des caractères avantageux pour l'affinage des fromages comparé à l'espèce sauvage proche. Nous avons aussi identifié deux variétés de P. camemberti aux phénotypes contrastés en termes de croissance, de couleur, de production de mycotoxines et de capacité d'inhibition des contaminants. La variété camemberti, blanche et duveteuse, est inoculée sur les fromages type camembert, alors que la variété caseifulvum, grise et moins duveteuse, est inoculée sur d'autres fromages comme le Saint Marcellin. Geotrichum candidum est un champignon retrouvé naturellement dans le lait. Les analyses génomiques ont révélé trois clades monophylétiques, un clade comprenant uniquement des souches sauvages, un clade d'origine mixte comprenant des souches sauvages et du fromage et un clade comprenant uniquement des souches isolées de fromage. Les souches du fromage ont des phénotypes différents des souches sauvages, comme une croissance plus lente sur tous les milieux, même fromage, une production importante de composés volatils souhaitable et une activité protéolytique plus faible. Au sein du clade fromage, nous avons identifié trois populations aux phénotypes contrastés. Les populations du fromage sont génétiquement diversifiées et montrent des traces de recombinaison ; il n'y a donc pas eu sélection d'une lignée clonale utilisée comme ferment mais de plusieurs souches génétiquement et phénotypiquement différentes. Une des populations du fromage montre des traces d'un état plus avancé de domestication, avec une diversité génétique moins importante que les autres populations, un mycélium plus dense et une capacité à inhiber plus efficacement des contaminants, comme P. camemberti. Penicillium camemberti est le résultat de la sélection d'un unique mutant alors que l'espèce G. candidum possède encore une grande diversité. On a donc, avec ces deux espèces, une vision contrastée de la domestication des champignons du fromage.Biodiversity is more than ever threatened by several global phenomenons such as the continued destruction of natural habitats, intensive agriculture and climate disturbance. It is therefore urgent to better understand how biodiversity is generated and maintained, in order to be able to act against the collapse of biodiversity. Domestication provides an interesting framework for understanding the mechanisms of adaptation and the role of genetic diversity in the generation and maintenance of biodiversity. Darwin used domestication as a model to understand how species arise and to establish the basis of the theory of evolution. Indeed, domestication is a specific case of adaptation, involving strong and recent selection and rapid divergence into separate evolutionary lineages. Although we are not the only species at the root of domestication events, humans have domesticated a large number of both animals and plants. Additionally, some microorganisms, including fungi, have also been domesticated for a variety of tasks such as controlled fermentation, the production of antibiotics, and consumed directly. Fungi are good eukaryotic models for studying evolution, because phylogenetically related species occupy different ecological niches, and they have many experimental and genomics assets (e.g. relatively easy manipulation within a lab setting, short generation times, small and often haploid genomes). One such setting, where fungi domestication has been championed, is in the production of cheese. Penicillium camemberti is the typical white and fluffy mold on the surface of cheeses such as Camembert and Brie. We have shown that P. camemberti is the result of domestication in several steps, leading to different varieties. The first domestication event led to the emergence of the domesticated blue-gray mold named P. biforme, found on fresh goat cheese. A second, more recent domestication event resulted in the clonal lineage P. camemberti. Both domesticated species P. camemberti and P. biforme show advantageous traits for cheese ripening compared to the closest related wild species. Within the P.camemberti species, we identified two varieties (camemberti and caseifulvum) with contrasting phenotypes in terms of growth, color, mycotoxin production and ability of contaminant inhibition. The white and fluffy camemberti variety is inoculated on camembert-type cheeses, while the gray and less fluffy caseifulvum variety is inoculated on other cheeses such as Saint Marcellin. Geotrichum candidum is a dimorphic fungus (yeast and filamentous form) found naturally in milk. Genomic analyses revealed three monophyletic clades, one comprising only wild strains, a mixed-origin clade comprising wild and cheese strains, and a clade containing only cheese strains. The cheese strains have different phenotypes from the wild strains, such as slower growth on all media, including cheese, high production of desirable volatile compounds and lower proteolytic activity. Within the cheese clade, we identified three populations with contrasting phenotypes. In contrast to P. camemberti, the G. candidum cheese populations are genetically diverse and show evidence of recombination; thus, there is not one clonal lineage used as a ferment but several genetically and phenotypically different strains. However, one of the cheese populations shows evidence of a more advanced state of domestication, with less genetic diversity than the other populations, a denser mycelium and an ability to inhibit contaminants more efficiently, similar to that of P. camemberti. Penicillium camemberti is the result of the selection of a single mutant, whereas the species G. candidum still has a great diversity. Thus, with these two species, we have a contrasting view of cheese fungi domestication

Comptes Rendus Biologies

International audiencemodel for studying adaptation since Charles Darwin. Here we review recent studies on thegenomics of adaptation and domestication syndrome in two cheese-making fungal lineages, Penicilliumroquefortiused for maturing blue cheeses, and the Penicilliumcamemberti species complex usedfor making soft cheeses such as Camembert and Brie. Comparative genomics have revealed horizontalgene transfers involved in convergent adaptation to cheese. Population genomics have identified differentiatedpopulations with contrasted traits, several populations having independently been domesticatedfor cheese making in both P. roqueforti and the Penicillium camemberti species complex, and having undergone bottlenecks. The different cheese populations have acquired traits beneficial forcheese making in comparison to non-cheese populations, regarding color, spore production, growthrates on cheese, salt tolerance, lipolysis, proteolysis, volatile compound or toxin production and/orcompetitive ability. The cheese populations also show degeneration for some unused functions suchas decreased ability of sexual reproduction or of growth under harsh conditions. These recent findingshave fundamental importance for our understanding of adaptation and have applied interest forstrain improvement

Domestication of the Emblematic White Cheese- Making Fungus Penicillium camemberti and Its Diversification into Two Varieties

International audienceDomestication involves recent adaptation under strong human selection and rapid diversification and therefore constitutes a good model for studies of these processes. We studied the domestication of the emblematic white mold Penicillium camemberti, used for the maturation of soft cheeses, such as Camembert and Brie, about which surprisingly little was known, despite its economic and cultural importance. Whole-genome-based analyses of genetic relationships and diversity revealed that an ancient domestication event led to the emergence of the gray-green P. biforme mold used in cheese making, by divergence from the blue-green wild P. fuscoglaucum fungus. Another much more recent domestication event led to the generation of the P. camemberti clonal lineage as a sister group to P. biforme. Penicillium biforme displayed signs of phenotypic adaptation to cheese making relative to P. fuscoglaucum, in terms of whiter color, faster growth on cheese medium under cave conditions, lower amounts of toxin production, and greater ability to prevent the growth of other fungi. The P. camemberti lineage displayed even stronger signs of domestication for all these phenotypic features. We also identified two differentiated P. camemberti varieties, apparently associated with different kinds of cheeses and with contrasted phenotypic features in terms of color, growth, toxin production, and competitive ability. We have thus identified footprints of domestication in these fungi, with genetic differentiation between cheese and wild populations, bottlenecks, and specific phenotypic traits beneficial for cheese making. This study has not only fundamental implications for our understanding of domestication but can also have important effects on cheese making