A group of researchers in Brazil are on the brink of a promising sustainable solution to one of the coffee industry’s biggest threats, yet funding issues could see their research cease if no one steps in to progress the project.
The coffee industry has overcome many challenges during its long history, from promoting regenerative farming practices to prevent soil degradation to introducing new approaches to reduce deforestation. Yet, one of its biggest threats remains at large. It’s estimated that coffee leaf rust, also known as Hemileia vastatrix or CLR, a fungal disease that infects the leaves of coffee plants and hinders their ability to produce cherries, causes billions of dollars of economic damage to the industry each year.
For farmers whose crops are impacted by the disease, this results in lost revenue and compromised quality and supply. In some cases, growers abandon the coffee trees and seek income from alternative crops or even attempt to migrate to other regions or countries.
The disease was first identified in Africa in the mid-19th century and has since spread to all coffee-producing countries. It’s largely dispersed through wind currents and rain splashes. Animals and humans can also transport the fungus to new leaves and play a role in spreading the disease from tree to tree and farm to farm.
Symptoms of coffee leaf rust include yellow spots on the upper side of the leaf that darken to brown as they become necrotic and the plant tissues collapse. More evident is the orange, rust-coloured sporulation on the underside, which inspired the name for the disease.
The coffee production of an infected tree can be reduced by up to 50 per cent, and some may eventually die due to the loss of leaves and inability to photosynthesise. While the issue has plighted the industry for centuries, in the past few decades there have been several major outbreaks, including in Hawaii in 2020 which marked the first incident in what was thought to be one of the last coffee-producing regions to be free of the disease.
Other notable outbreaks include in Colombia between 2008 and 2011, which saw the country’s coffee production reduced by almost a third, and the ‘Big Rust’ outbreak in Latin America, which started in 2012 and is said to be the most serious epidemic since the one Sri Lanka endured in the 1880s. Among the scientific community, it is widely acknowledged that climate change could be contributing to these recent outbreaks.
Changing rainfall patterns and rising temperatures are thought to favour the worsening severity of the disease. For decades, one of the solutions to coffee leaf rust has been growing Arabica coffee at higher elevations as the fungus requires warm environments, yet rising temperatures means even these greater altitudes are now warm enough to sustain it.
Over the years, many solutions have been put forward to control coffee leaf rust. Traditional practices include maintaining healthy plants, removing weeds that may compete with the plant for nutrients, removing weak or diseased trees, and pruning to reduce humidity around the leaves. However, the most common treatment involves spraying crops with fungicides, a method that mycologist Professor Robert Barreto of the Federal University of Viçosa (UFV) in Brazil says may result in unwanted residues in the harvested product and negative environmental impacts.
“A lot of farmers are relying on fungicides and pesticides in general, but we know this results in residues, both on the cherries and in the soil. The industry doesn’t want to hear about residues anymore and in some major consuming regions we’re seeing increasing restrictions, such as in Europe,” says Prof Barreto.
A more natural solution that has been relied upon is planting resistant varieties of coffee. First identified in the 1980s, several varieties have been championed for their resistance to coffee leaf rust, including the so-called Timor hybrids and Timor hybrid derived cultivars, such as Lempira.
However, according to Prof Barreto, reliance on one or few resistant varieties has proven to be a risky method of crop management.
“There was a major coffee leaf rust outbreak in Honduras in 2017. About 45 per cent of coffee grown in the country was Lempira, which was favoured for its high productivity and resistance to CLR. But this resistance broke down and as a result the losses in the country were huge – it was a nightmare,” he says.
“Breeding has provided good benefits in the fight against the disease and the esearch in finding resistant varieties continues. However, relying on resistance alone is a problem, as is continuing to move plantations up to higher altitudes – eventually coffee farmers will run out of mountain.”
“Relying on resistance alone is a problem, as is continuing to move plantations up to higher altitudes.”
A nature-based solution
Over the past decade, Prof Barreto and his team at UFV have been working on a different solution that uses the power of nature to control CLR. Using his background in fungi and fungal taxonomy, his team has explored the use of fungi as biological control agents to reduce the impact of the disease.
The research team are based in the university’s Department of Plant Pathology in Minas Gerais, Brazil’s largest coffee-producing region, which was established as one of Brazil’s responses to the CLR crisis after it was found in the country during the 1970s.
“Up until around 10 years ago, my work focused on the use of fungi as tools for the biological control of weeds,” he says.
“Following the outbreaks of CLR in Central America in 2006, the United States (US) was very concerned about the collapse of the coffee industry and the possibility of massive migration of farmer families across Mexico into the US. At the time, colleagues based in the Centre for Agriculture and Bioscience International (CABI) suggested the rust crisis might offer the opportunity for an entirely novel approach to tackle CLR.
“An emergency CLR summit was place at their headquarters in Guatemala City, where I presented the suggestion of using classical biological control against CLR. That’s where this research project really began.”
Every organism has natural enemies that help promote balance in nature. The use of these natural enemies to control undesirable and often invasive species is called biological control. The modern biopesticide approach provides products to control pests in agriculture, but the earlier approach, called classic biological control (CBC), has been in use for more than 100 years.
CBC is applied biology at play and is far from an exact science. One of the most notorious examples of the method’s failure was the introduction of cane toads to control the cane beetle in Australia in the 1930s, which saw the toad quickly adapt to the environment and become an invasive pest.
Because of incidents such as this strict protocols now surround CBC, but Prof Barreto believes a mistrust of the method remains.
His team have hypothesised a natural enemy of CLR may have been “left behind” in Africa as the CLR fungus spread to the rest of the world, and CBC could have a role to play in managing the disease.
“CLR is an exotic pathogen, and the classical biological rule is to find a coevolved natural enemy from the centre of origin and then collect it, study it, clarify whether it’s reliable and safe to use, and introduce it to the diseased populations to reestablish the equilibrium,” says Prof Barreto.
With initial research funding from World Coffee Research (WCR), in 2015 Prof Barreto and a team of Brazil-based researchers started their search for natural enemies of CLR alongside African research partners. The team journeyed to the wild coffee forests of Ethiopia, Kenya, and Cameroon on the hunt for CLR-fighting fungi.
“It was a fascinating experience. We visited forests where coffee still grows spontaneously – some of the old trees towered above our heads,” says Prof Barreto.
“It was in these forests we found a diversity of things we’d never seen before. The Trichoderma genus of fungi is considered one of the stars in the field of biological control agents, and in Africa we identified and collected 16 different Trichoderma species either growing directly on CLR lesions or naturally growing as symbionts inside healthy coffee plants.
“Our conjecture was that these might behave as bodyguards for the coffee plants, protecting them from CLR as well as other aggressors”
The team also visited parts of South America, particularly areas where coffee occurs spontaneously inside forest fragments and abandoned plantations nature has reclaimed. They were surprised to find these searches resulted in complete absence of Trichoderma, the total opposite to the observations in Africa.
“The discovery of the novel Trichoderma in Africa may explain why Africa has not experienced as aggressive CLR epidemics as other regions,” says Prof Barreto.
From this collection phase of the project, the team assembled a list of about 1500 isolates. An elimination process brought that number down to 600 of the most interesting pathogens and fungi, which were then tested under controlled conditions in the laboratory, and then in greenhouses, to see if they had an impact on CLR. Now, after ten years of hard work, that list has been whittled down to 10 promising fungal isolates.
“There are some very exciting isolates in the final group. For example, we found that a species of Cordyceps belonging to a group that includes many insect pathogens, is effective against CLR and greatly reduced the disease in infected plants,” says Prof Barreto.
In controlled tests, several other fungal isolates, including Aspergillus, Calonectria, Clonostachys, Fusarium, and Trichoderma, reduced CLR severity by up to 90 per cent.
The field trial hurdle
The decade-long body of research has now reached the small field-trial stage, in the hopes the best lab and greenhouse results can be repeated in real-world situations. From here, the research has the potential to be turned into a series of viable products that can be deployed on farms across Brazil and beyond. However, the project has hit a roadblock: it’s run out of funding.
“It is becoming increasingly difficult to obtain funding for research such as this. Traditionally, grants would be acquired from the public sector, but unfortunately the tide has changed,” says Prof Barreto.
“We have found several very promising isolates that we believe can help manage CLR. It is now the time for the industry to step in and fund this research as this is hugely important to the whole coffee-production chain and a significant market for the biocontrol industry as well.”
Hanna Neuschwander, Senior Advisor at WCR, which was involved in the initial stages of the project, believes continuation of the work stands to benefit the entire industry.
“This is a vital turning point for the coffee sector. Across major origins – from Central and South America to Africa – producers face rising pressure to reduce chemical inputs due to environmental concerns and increasingly strict residue regulations,” she says.
“A cost-effective, naturally derived solution to CLR fits perfectly into a broader push for sustainability, especially when combined with existing breeding programs and integrated pest management approaches. These fungal ‘bodyguards’ could significantly reduce reliance on synthetic fungicides, stabilise yields, and preserve the ecological balance on coffee farms.
“These products could be a key resource for the industry but bringing them to market requires continued screening of additional isolates, establishing rigorous safety protocols, and making these biocontrol products broadly available to farmers.”
Although he retired last year, Prof Barreto is still very much involved in keeping the project alive.
“It is time for the whole project to be taken over by someone else. The potential of what we’ve found to date is so great that the industry should be interested and inspired to get involved,” he says.
“This is an urgent issue and decision-makers need to think outside the box. The concern of the coffee industry with the path towards a sustainable future for coffee needs to be directly linked with action towards the innovation in the natural management of weeds, pests and diseases.
“Without their support, academia can only advance slowly. These projects take time and won’t provide an instant solution, but what we have found is very exciting and should be continued to be explored. The potential is very clear.”
This article was first published in the July/August 2025 edition of Global Coffee Report. Read more HERE.
