John Gibbons Receives NSF CAREER Grant for Fungi Research

John Gibbons
John Gibbons

You can’t herd them, you can’t put two in a corral and hope they will breed to produce offspring with desirable traits, but the humans of 10,000 to 13,000 years ago figured out how to domesticate molds and other fungi to preserve food, make it tastier and to make wine.

How this happened is “the big question,” says John Gibbons, food science, who this month begins the search for Fungal Domestication Syndrome, supported by a five-year, $729,900 National Science Foundation faculty early development (CAREER) grant. “Almost everything we know about domestication stems from plant and animal models,” Gibbons says. “But fungi have very different underlying population biology and ecology.” His studies will advance knowledge of the effects of fungi domestication and related genomic and evolutionary processes.

Much domestication likely involved“happy accidents,” he points out, so even though microbially preserved food might taste very different than fresh, the guiding principle was “if it didn’t kill you and it was preserved, that was helpful,” he adds. “As long as you can get your food to last longer that’s the key.”

His new grant emphasizes both research and education, so Gibbons plans a “citizen science” component that will invite the public to send samples of homemade or commercial fermented foods to his lab – a kind of “Meet Your Microbe” drive, he says. Students in his genomics lab will isolate and identify microorganisms from these to gain practical experience in microbiology, molecular biology, genomics and bioinformatics.

The genetic detective work will focus on a mold called Aspergillus oryzae, used to make soy sauce, sake, miso and other traditional Asian fermented foods and drinks. Domestication refers to the genetic modification of a plant or animal, usually through breeding, to select for traits that are beneficial to humans, he explains.

Gibbons adds, “It is evolution on steroids; it involves really strong selection and it crams changes into 10,000 years instead of the hundreds of thousands or millions it might normally take.”

With the coming of agriculture, he points out, more people enjoyed a surplus of food for the first time, and they found that the best way to preserve things for long periods is through microbial preservation. Cheese, made by treating milk with bacteria, is a prime example and dates back 10,000 years, he notes. “Right around that same time there is archaeological chemistry evidence that people, probably using the organism that I’ll be studying, made rice wine in China.”

Aspergillus oryzaeis one of the official “national microbes of Japan,” Gibbons notes. “It’s really deep in their culture, and people have shown reverence and respect for it for centuries.”

The project will involve sequencing the genomes of hundreds of the wild progenitor fungi (A. flavus) and hundreds of the tame (A. oryzae) samples in a multilayered approachto identify the genomic regions targeted by artificial selection – “to pinpoint regions that show the footprints of domestication.”

Other experiments will follow to study different traits including toxicity and secondary metabolite production. The researchers will measure growth rate, inhibitory effects on community food microbes, volatile compound profiles and gene expression profiles of A. oryzae and A. flavus strains under diverse conditions.