Researchers Analyze Performance of Bacterium in Combating Coffee Rust

Dec 21, 2022

By Ricardo Muniz

A new study has analyzed the potential of a bacterium for biological control of the fungus Hemileia vastatrix, which causes coffee rust, a major challenge for Brazilian coffee growers. An article on the study is published in the journal BMC Microbiology.

The symptoms of coffee rust are yellow spots like burn marks on the leaves of the plant. The disease impairs photosynthesis, making foliage wither and preventing bean-producing cherries from growing until the tree resembles a skeleton. It is typically controlled by the use of copper-based pesticides, which can have adverse effects on the environment.

"This was a basic science study, in which we set out to understand the behavior of bacteria that inhabit the leaves of coffee trees. First of all, there are several compounds that are harmful to bacteria and can be used to attack them," said Jorge Maurício Costa Mondego, last author of the article.

"Second, leaves are environments that undergo significant environmental pressures, such as sunlight and rain. We wanted to understand how bacteria that live on coffee leaves can withstand both the compounds produced by the coffee plant and the stresses of rain and sun," he said.

Besides this basic science front, the study also addressed applied science challenges. The researchers decided to find out whether bacteria that inhabit coffee leaves can combat the fungus that causes coffee rust. The first step consisted of identifying the expressed sequence tags (ESTs) of Coffea arabica and C. canephora produced by the Brazilian Coffee Genome Project (Projeto Genoma EST-Café).

"I was the first author, alongside Ramon Vidal, a professor at UNICAMP, of an article in which we compiled the sequences expressed by C. arabica. It was published in 2011. We weren't yet thinking in terms of metagenomics, but that's what we did, more or less accidentally," Mondego said.

Accidental metagenomics

The researchers found sequences they considered contaminating in the midst of the coffee leaf ESTs. "We took these sequences, fed them into the database, and concluded that they appeared to be from Pseudomonas spp, a genus of bacteria.," Mondego said. "This stimulated the curiosity of our research group, which was led by Gonçalo Pereira, also a professor at UNICAMP. We asked ourselves, 'What if we've done metagenomics without meaning to? Do these bacteria really live on coffee leaves?'"

At the time, Mondego was already a researcher at IAC. A few years later, he was able to join forces with Leandro Pio de Sousa, first author of the article published in BMC Microbiology. Sousa was a student who had a scientific initiation scholarship and now holds a Ph.D. in genetics and molecular biology from UNICAMP.

"I invited Leandro to work with me on this study, which was designed to see if Pseudomonas really does live on coffee leaves. If so, the previous findings would be confirmed. He agreed immediately," Mondego said.

They isolated bacteria from the coffee leaves and put them in a culture medium. Under ultraviolet light, it is possible to characterize Pseudomonas, which looks purple and can easily be selected in the medium. "We collected the bacteria, extracted their DNA and sequenced one, which we called MN1F," he said.

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Video: Why Your Food Future Could be Trapped in a Seed Morgue

In a world of PowerPoint overload, Rex Bernardo stands out. No bullet points. No charts. No jargon. Just stories and photographs. At this year’s National Association for Plant Breeding conference on the Big Island of Hawaii, he stood before a room of peers — all experts in the science of seeds — and did something radical: he showed them images. He told them stories. And he asked them to remember not what they saw, but how they felt.

Bernardo, recipient of the 2025 Lifetime Achievement Award, has spent his career searching for the genetic treasures tucked inside what plant breeders call exotic germplasm — ancient, often wild genetic lines that hold secrets to resilience, taste, and traits we've forgotten to value.

But Bernardo didn’t always think this way.

“I worked in private industry for nearly a decade,” he recalls. “I remember one breeder saying, ‘We’re making new hybrids, but they’re basically the same genetics.’ That stuck with me. Where is the new diversity going to come from?”

For Bernardo, part of the answer lies in the world’s gene banks — vast vaults of seed samples collected from every corner of the globe. Yet, he says, many of these vaults have quietly become “seed morgues.” “Something goes in, but it never comes out,” he explains. “We need to start treating these collections like living investments, not museums of dead potential.”

That potential — and the barriers to unlocking it — are deeply personal for Bernardo. He’s wrestled with international policies that prevent access to valuable lines (like North Korean corn) and with the slow, painstaking science of transferring useful traits from wild relatives into elite lines that farmers can actually grow. Sometimes it works. Sometimes it doesn’t. But he’s convinced that success starts not in the lab, but in the way we communicate.

“The fact sheet model isn’t cutting it anymore,” he says. “We hand out a paper about a new variety and think that’s enough. But stories? Plants you can see and touch? That’s what stays with people.”

Bernardo practices what he preaches. At the University of Minnesota, he helped launch a student-led breeding program that’s working to adapt leafy African vegetables for the Twin Cities’ African diaspora. The goal? Culturally relevant crops that mature in Minnesota’s shorter growing season — and can be regrown year after year.

“That’s real impact,” he says. “Helping people grow food that’s meaningful to them, not just what's commercially viable.”

He’s also brewed plant breeding into something more relatable — literally. Coffee and beer have become unexpected tools in his mission to make science accessible. His undergraduate course on coffee, for instance, connects the dots between genetics, geography, and culture. “Everyone drinks coffee,” he says. “It’s a conversation starter. It’s a gateway into plant science.”