Many scientific discoveries are serendipitous—the result of chance. Seeing evolution in action in a cheese cave turned out to be exactly that for Benjamin Wolfe , associate professor of biology, and his colleagues.
Back in 2016, Wolfe convinced his former post-doc advisor to drive with him to Jasper Hill Farm in Vermont to get samples of a special cheese called Bayley Hazen Blue, a ruse for her boyfriend to propose marriage at the spot where they first met. Wolfe ended up keeping that cheese in the freezer in his lab. "I'm notorious for not throwing samples away just in case we might need them," he says.
But when graduate student Nicolas Louw picked up recent samples of Bayley Hazen Blue from the Jasper Hill caves—large, damp rooms built into the side of steep hills—he discovered the cheese, previously coated with a leafy green layer of fungus, was now chalk white on the outside.
"This was really exciting because we thought it could be an example of evolution happening right before our eyes," said Wolfe. "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." Wolfe and his colleagues reported the finding in Current Biology .
Understanding how fungi adapt to different environments can help us in areas of food security and health, too, says Louw. "Somewhere around 20% of staple crops are lost pre-harvest due to fungal rot, and an additional 20% are lost to fungi post-harvest," he said. "That includes the moldy bread in your pantry and rotting fruit on market shelves. The biggest threat to global food security is just rot from mold." Understanding how to control this problem while preventing fungal adaptation is an agricultural priority.
A Small but Key Mutation
When wheels of cheese are placed to ripen in natural or artificial cave environments, they form microbial rinds on their surface made up of communities of bacteria, yeast, and filamentous fungi (molds). These wild microbes are picked up from soil, plant, and marine environments and end up colonizing and adapting to the environments of the cheese caves.
What caused the Penicillium solitum fungi on the Jasper Hill cheeses to change color? A student in one of Wolfe's advanced microbiology laboratory courses on microbiomes found the answer. Jackson Larlee, A24, discovered that the change was prompted by the disruption of a gene called alb1.
"Alb1 is involved in producing melanin," Louw explained. "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."
It's a process called "relaxed selection," when an environmental stressor is removed, and that happens to many organisms when they adapt to dark conditions, from Mexican cave fish to salamanders to some insects. It's almost always a loss of pigments and melanin. Some creatures become blind, then increase their ability to sense food in other ways.
The fungi gave the Wolfe lab an opportunity to identify the genetic mechanisms that led to a small evolutionary change. "We found that the change was not just one mutation that swept through the whole colony, but the color shift came about through many types of mutations independently," said Louw.
Some of the fungi had point mutations—single DNA base pair changes—at different locations in the genome. Others had a large insertion of DNA caused by something called a transposable element. Transposable elements, once called "jumping genes," pop out of one location and insert themselves into another in the genome.
In this case, transposable elements were inserting themselves ahead of the alb1 gene, which disrupted its expression, effectively knocking it out. Transposable elements can cause a lot of damage, but this time, it was an advantage for the fungi to forego production of melanin—allowing it more energy to grow. Thus, the white wheels of cheese in the Jasper Hill cave.
Aspergillus fungi are in the same family as Penicillium. They are found in the soil, on decaying plants, in household dust and ventilation systems and in massive quantities in the air. Most of the time they are harmless, but some strains can cause severe lung infections. Understanding how they become locally adapted and lodged in the lung environment could help researchers understand and prevent these infections.
For now, the Wolfe lab, in collaboration with Jasper Hill Farm, is exploring another benefit of evolving and domesticating fungi—creating new types of cheese with improved aesthetics, taste, and texture. They inoculated fresh brie cheese with the novel white mold and let it grow and ripen the cheese for two months.
The result: "It's slightly nuttier and less funky," said Louw. "I think it's delicious." Based on a taste testing panel, the new cheese has promising attributes that will be further fine-tuned in future batches of cheese at Jasper Hill Farm.
"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.
