Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese

Abstract

Fermented foods provide novel ecological opportunities for natural populations of microbes to evolve through successive recolonization of resource-rich substrates. Comparative genomic data have reconstructed the evolutionary histories of microbes adapted to food environments, but experimental studies directly demonstrating the process of domestication are lacking for most fermented food microbes. Here, we show that during adaptation to cheese, phenotypic and metabolomic traits of wildPenicilliummolds rapidly change to produce domesticated phenotypes with properties similar to those of the industrial cultures used to make Camembert and other bloomy rind cheeses. Over a period of just a few weeks, populations of wildPenicilliumstrains serially passaged on cheese had reduced pigment, spore, and mycotoxin production. Domesticated strains also had a striking change in volatile metabolite production, shifting from production of earthy or musty volatile compounds (e.g., geosmin) to fatty and cheesy volatiles (e.g., 2-nonanone, 2-undecanone). RNA sequencing demonstrated a significant decrease in expression of 356 genes in domesticated strains, with an enrichment of many secondary metabolite production pathways in these downregulated genes. By manipulating the presence of neighboring microbial species and overall resource availability, we demonstrate that the limited competition and high nutrient availability of the cheese environment promote rapid trait evolution ofPenicilliummolds.IMPORTANCEIndustrial cultures of filamentous fungi are used to add unique aesthetics and flavors to cheeses and other microbial foods. How these microbes adapted to live in food environments is generally unknown as most microbial domestication is unintentional. Our work demonstrates that wild molds closely related to the starter culturePenicillium camembertican readily lose traits and quickly shift toward producing desirable aroma compounds. In addition to experimentally demonstrating a putative domestication pathway forP. camemberti, our work suggests that wildPenicilliumisolates could be rapidly domesticated to produce new flavors and aesthetics in fermented foods.

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

“…1 ). The application of systems biology approaches combined with community reconstructions can identify specific microbial interactions that drive community composition 51 , 74 , determine a genetic basis for particular microorganisms to live in a fermented food environment 75 and recreate the domestication processes that generated the industrial cultures used in fermentations 76 , 77 . Ultimately, findings from those studies will help to address product variation and quality issues that occur even when starter cultures are used.…”

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

“…Except for P. roqueforti , all these other mold species are only known from cheese, suggesting they are adapted (“domesticated”) to this particular habitat. In particular, P. camemberti derives from the wild ancestor Penicillium commune in a quick adaptation process that involves reduced reproductive output, reduced mycotoxin production, reduced pigmentation and, significantly, a change in the volatile compound profile from earthy to cheesy [ 114 ]. The genetic basis of this rapid “evolution” has proven to be through gene regulation instead of genome changes [ 114 ].…”

Rapid selection response to ethanol inS. eubayanusemulates the domestication process under brewing conditions

“…This persistent directional selection involved correlated selection of other traits, such as osmotic stress tolerance and efficient nitrogen uptake [70]. In general, domesticated fungi used in fermented foods exhibit genomic rearrangements, fewer spores and produce desirable volatile compounds [9]. These domestication signatures have been reported in other systems, such as Aspergillus and Penicillium, where a transition to environments rich in carbon and nitrogen sources led to extensive metabolism remodeling when used to produce cheese [8,9].…”

“…Domestication is a stereotyped adaptive process (a "domestication syndrome", see [6,7]) within a human-created environment, where several characteristics can be tracked and defined as 'domestication signatures'. These signatures are present in different fungal species, including Aspergillus oryzae in soy sauce [8], Penicillium molds associated with cheese [9] and S. cerevisiae [10,11] together with S. pastorianus [12], responsible for beer fermentation. In this context, spore production and viability, metabolic remodeling, changes in volatile compound production, transcriptional re-wiring and faster growth rates are considered key traits and goals of microbe domestication.…”