A chance discovery in a Vermont cheese cave has given scientists a rare glimpse of evolution unfolding in real time – and the unexpected findings have broad implications for protecting human health, enhancing food security and even delivering new flavors to turophiles.
Tufts University researchers uncovered an evolutionary shift in the mold that coats Bayley Hazen Blue, a well-known Vermont cheese. When the team compared fresh samples from Jasper Hill Farm to ones stored in the lab since 2016, they found that Penicillium solitum had changed color – instead of its usual leafy green surface, which gives the cheese that tint when matured, the fungus was now producing a chalk-white rind.
“This was really exciting because we thought it could be an example of evolution happening right before our eyes,” said Benjamin Wolfe, an associate professor biology at Tufts University. “Microbes evolve. We know that from antibiotic resistance evolution, we know that from pathogen evolution, but we don’t usually see it happening at a specific place over time in a natural setting.”
How this discovery came to be is another fine example of accidental science: In 2016, Wolfe put a chunk of Bayley Hazen Blue in the freezer in his lab (“I’m notorious for not throwing samples away just in case we might need them,” he said). Years later, a graduate student had collected samples of the cheese from its aging caves – damp, dark rooms cut into the hillside – and brought them back to the lab, where Wolfe noticed the change in appearance. This, naturally, began a new research project.
The culprit was a common cheese-cave mold, Penicillium solitum. Genetic analysis showed that its switch from green to white came from disruptions to a gene called alb1, which drives melanin synthesis. Melanin pigments act like a sunscreen – they absorb damaging UV radiation and dissipate it harmlessly, protecting delicate fungal cells. But in the completely dark, humid environment of a cheese cave, that protection is unnecessary. Producing pigment is metabolically costly, so when the selective pressure of sunlight disappears, fungi that disable the pathway save energy and gain a growth advantage. The team found that this “relaxed selection” had occurred multiple times, through different mutations knocking out alb1 – which was an incredible example of parallel evolution unfolding in real time.
Relaxed selection, when an environmental stressor is removed, has occurred in many organisms that adapt to dark conditions. It was the key driver in the Mexican cavefish (Astyanax mexicanus) losing its eyesight, which allowed for more energy to be invested in more "useful" senses to find food. If relaxed selection is the process, then regressive evolution is the result.
“Alb1 is involved in producing melanin,” said Nicolas Louw, the graduate student who retrieved the white-rind cheese samples. “You can think of melanin as an armor that organisms make to protect themselves from UV damage. For the fungi, it creates the green color that absorbs UV light. If you are growing in a dark cave and can get by without melanin, it makes sense to get rid of it, so you don’t have to expend precious energy to make it. By breaking that pathway and going from green to white, the fungi are essentially saving energy to invest in other things for survival and growth.”
While microbial evolution is well documented in antibiotic resistance and emerging pathogens, catching it in a single place, over less than a decade, is extremely rare. In this case, some fungi colonies carried point mutations, while others had acquired insertions from mobile pieces of DNA called transposable elements – also described as “jumping genes,” which hop around the genome and may disrupt regular expression. Each genetic tweak, while different, ultimately silenced alb1, cutting off melanin production and leaving the mold white.
And rather than harming the fungus, the genetically driven loss of pigment was an advantage, letting the mold grow faster and dominate the cave environment.
The researchers then inoculated brie with the new white-strain fungus to see if it didn't just alter the look of cheese but also the taste. The result was a rind that had a slightly nuttier, less funky flavor. This in itself opens up the potential for food scientists to develop new or more desirable cheese flavors.
“Seeing wild molds evolve right before our eyes over a period of a few years helps us think that that we can develop a robust domestication process, to create new genetic diversity and tap into that for cheesemaking,” said Wolfe.
However, the discovery goes beyond cheese. Penicillium fungi is in the same family (Aspergillaceae) as Aspergillus. While Penicillium species are mostly harmless and often useful – cheesemaking, penicillin – some Aspergillus strains are harmful to human health. In particular, inhaling Aspergillus fumigatus can cause serious lung problems, including invasive pulmonary aspergillosis, aspergilloma, allergic asthma, pneumonitis and allergic bronchopulmonary aspergillosis.
By studying how Penicillium adapts in cheese caves, scientists can gain insights into how Aspergillus adapts inside the lung environment, potentially finding new ways to treat these varied health conditions.
What's more, fungi destroy around 40% of global crops, before and after harvest, making them one of the biggest threats to food security. Knowing how quickly molds adapt to new environments – and which genes drive those changes – could help researchers design better ways to stop rot in storage and transport.
The findings again highlight how many scientific breakthroughs, particularly those sourced from nature, have come through chance. Nearly 100 years ago, in 1928, Scottish physician Alexander Fleming famously noticed that, in a moldy Petri dish, Penicillium notatum had destroyed the bacteria around it (even if penicillin would still be more than a decade away from development). Meanwhile, a soil sample collected from Rapa Nui (Easter Island) in 1964 would eventually lead to the discovery and development of bacteria-killing rapamycin – now a leading target in geroscience.
The study was published in the journal Current Biology.
Source: Tufts University
