Researchers analyze the performance of a bacterium in the fight against coffee rust

Researchers analyze the performance of a bacterium in the fight against coffee rust

Performance of the bacterium in the fight against coffee rust

image: The research is partly basic science, studying the bacteria’s resilience in a harsh environment – coffee leaves – and partly biotech, to see if the bacteria inhibits the development of a pathogen
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Credit: Jorge Mondego/IAC

A study supported by FAPESP analyzed the potential of a bacterium for the 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 review BMC Microbiology.

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

“This was a fundamental scientific study, in which we sought to understand the behavior of bacteria that inhabit the leaves of coffee trees. First, there are several compounds that are harmful to bacteria and can be used to attack them,” said Jorge Mauricio Costa Mondego, last author of the article. Mondego is a researcher affiliated with the Plant Genetics Center of the Agronomic Institute of Campinas (IAC). He holds a PhD in Genetics and Molecular Biology from the State University of Campinas (UNICAMP) in the State of São Paulo, Brazil.

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

Besides this fundamental scientific front, the study also addressed the challenges of applied sciences. Researchers set out to find out if the bacteria that inhabit coffee leaves can fight the fungus that causes coffee rust. The first step was to identify the expressed sequence tags (ESTs) of Arabica coffee and C. canephora produced by the Brazilian Coffee Genome Project (Projeto Genoma EST-Café) funded by FAPESP and the Brazilian Agricultural Research Corporation (EMBRAPA).

“I was the first author, alongside ramon vidalprofessor at UNICAMP, of an article in which we compiled the sequences expressed by Arabica. It was published in 2011. We weren’t thinking in terms of metagenomics yet, but we did, more or less accidentally,” Mondego said.

Accidental metagenomics

The researchers found sequences they considered contaminating in the middle of the coffee leaf ESTs. “We took these sequences, entered them into the database and concluded that they appeared to be from Pseudomonas spp, a genus of bacteria. said Mondego. “This stimulated the curiosity of our research group, led by Goncalo Pereira, also a professor at UNICAMP. We asked ourselves: What if we had done metagenomics unintentionally? Do these bacteria really live on coffee leaves?

At the time, Mondego was already a researcher at the IAC. A few years later, he was able to work with Leandro Pio de Sousa, the first author of the article published in BMC Microbiology. Sousa was a student who had a science initiation scholarship and now holds a doctorate 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 lives on coffee leaves. If this were the case, the previous conclusions would be confirmed. He accepted immediately,” Mondego said.

They isolated the bacteria from 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 bracket. “We collected the bacteria, extracted their DNA and sequenced one, which we called MN1F,” he said.

They made several interesting discoveries about MN1F, which has a secretion system that reflects its need to survive in a harsh environment filled with fungi and other bacteria. “The secretion system produces antibacterial and antifungal compounds. This suggests it could be used for biological control,” he said. They also detected a number of proteins associated with protection against water stress.

The next step was physiological experiments, in which bacteria were grown in different media to confirm the researchers’ observations about the genome. “Biological experiments proved several inferences to be correct. We showed that the bacterium indeed has a considerable ability to resist high osmotic pressure, which can be considered analogous to the effects of drought on coffee leaves,” explained Mondego. “In addition, MN1F is able to degrade phenolic compounds that can be harmful to it. It breaks down these plant compounds and converts them into material for its own survival.

The researchers then conducted a battery of tests to find out if MN1F could be used for biological control, preventing or inhibiting the development of H. wastatrix, the fungus responsible for coffee rust. The tests took place under greenhouse and laboratory conditions, including an attempt to inhibit in vitro germination of the fungus. In all experiments, the bacterium was found to be able to inhibit the development of spores (reproductive units) and mycelium (the filamentous network containing the genetic material of the fungus).

Besides Mondego and Sousa, the article is signed by Matheus Aparecido Pereira Cipriano (IAC), Mario Jose da Silva (Center for Molecular Biology and Genetic Engineering, UNICAMP), Flavia Rodrigues Alves Patricia (Institute of Biology, São Paulo Agrifood Technology Agency, APTA), Sueli dos Santos Freitas (IAC) and Marcelo Falsarella Carazzolle (Genomics and Expression Laboratory, Institute of Biology, UNICAMP).

About the São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public institution whose mission is to support scientific research in all areas of knowledge by granting scholarships, fellowships and grants to researchers linked to educational institutions University and Research from the State of São Paulo, Brazil. FAPESP is aware that the best research can only be done by working with the best researchers at the international level. Therefore, it has established partnerships with funding agencies, institutions of higher education, private companies and research organizations in other countries known for the quality of their research and has encouraged scientists funded by its grants to further develop their international collaboration. You can find out more about FAPESP at and visit the FAPESP news agency at to keep up to date with the latest scientific advances that FAPESP is helping to achieve through to its many programs, awards and research centers. You can also subscribe to the FAPESP press agency at

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