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The Plant Health Instructor

Volume: 23 |
Year: 2023
Article Type: Case Studies

​​​​​La Roya: Confronting a Coffee Disease Crisis in Costa Rica​​

Kaitlin Diggins1; José González-Acuña2; Mark L. G​leason2

1Cornell University - Plant Pathology and Plant-Microbe Biology, Caldwell Hall, 215 Garden Ave, Ithaca, New York 14850, USA

2Department of Plant Pathology, Entomology, and Microbiology, 2213 Pammel Drive, Iowa State University, Ames, Iowa 50011-1101, USA

Date Accepted: 09 Jun 2023
 Date Published: 13 Jul 2023

Keywords: Coffee, Hemileia vastatrix, rust, fungal pathogens, basidiomycota, organic production

​In this case study, a commercial grower of coffee in Costa Rica is confronted by a devastating disease called coffee rust, which is caused by the fungus Hemileia vastatrix. The grower, María Rojas, has noticed that steadily warming air temperatures and increasing rainfall variability caused by global warming have increased crop damage caused by the rust and cut into her profits. Maria recently converted her family's farm to using organic production practices in order to obtain premium prices in coffee export markets, but organically approved fungicides are less effective against rust than the conventional fungicides she used formerly. To remain profitable despite the increasing risk of rust damage, she needs to consider all her options and develop an effective integrated pest management strategy.



This case study will help students to

  • Strengthen their understanding of the disease triangle concept (host, pathogen, environment) and its implications for designing effective plant disease management strategies.
  • Recognize coffee rust signs and symptoms on coffee plants.
  • Learn why coffee rust poses a significant threat to the livelihood of coffee farmers worldwide.
  • Understand how differences in fungicide options between organic and conventional farming can impact coffee rust management.
  • Assess advantages and disadvantages of management options for combating the most economically threatening coffee disease in the world.​


Diego Alonso Vargas: Field manager who oversees a family-owned organic coffee production at a small-scale plantation in Tarrazú, Costa Rica.

María Rojas: Fourth-generation farmer in Tarrazú, Costa Rica, who exports her organic coffee beans to online sellers in the United States and Europe.

Julián Rodríguez: Project manager in a Costa Rican online coffee-marketing business, which exports the beans worldwide.​


Figure 1. A map of Central America showing the location of Costa Rica. María's coffee plantation is located in the highlands of Tarrazú. (Figure credit: Andrés Arguedas-Chaverri)​​
For generations, María Rojas and her family have been growing Coffea arabica—the coffee species that yields the highest-quality beans in the world—in the highlands of Tarrazú, Costa Rica (Figs. 1 and 2). The Rojas family has owned a 3 ha (7.4 acres) coffee estate since the 1950s, and their production of export-quality coffee beans has been the family's primary income for more than 50 years.

Most of the coffee plantations in Costa Rica are small-scale family farms whose owners take great pride in the quality and taste of their beans (Fig. 3). María sells 100% of the farm's beans to a trusted online retailer, Julián, who is responsible for exporting them to high-end retailers in the United States and Europe.

When María inherited her family's small conventional coffee plantation in Tarrazú (Fig. 2), she decided to embrace organic farming. Her objective was to increase the farm's profitability, since organic coffee beans command a 20–30% higher price than conventionally grown beans. Environmentally conscious consumers may be willing to spend more money on organic beans to support sustainable ways to grow coffee and respect the land, especially when they know the beans come from a small-scale farm that partakes in ethical and socially responsible practices. Another incentive to move to organic production was to lessen reliance on synthetic chemical pesticides and fertilizers to protect the health of her family, her workers, her customers, and the environment. María hired Diego Vargas as a full-time field manager to assist her in making the required 3-year transition from conventional to certified-organic production (see Background and Glossary). The coffee farm is planted entirely with the variety 'Catuaí', which is a cross of 'Mundo Novo' (a natural cross with high yield but susceptible to coffee rust) and 'Caturra' (susceptible to coffee rust, but can produce high-quality beans in María's region).

Figure 2. Harvesting coffee​ in the highlands of Tarrazú, Costa Rica (left), and coffee plantation intercropped with shade trees (right). (Photo credits: [left]; [right])

Figure 3. Hand-picked ripe coffee "cherries" (the fruit that contain the coffee beans) (left) and roasted coffee beans (right). (Photo credits: [left]; The Tico Times [] [right])

María and Diego have maintained good yields in organic production by careful management of plant health. Their practices include spraying organically approved fungicides (most of which contain copper) to protect the coffee plants from their most serious disease threat: coffee rust caused by Hemileia vastatrix, a devastating fungus that infects the leaves. The key period for applying fungicides against rust is the rainy season, which runs from mid-April to mid-November in the Tarrazú region; the risk of rust infection is high during this period because frequent rainfall and warm conditions favor rust outbreaks by encouraging sporulation and rain splash transmission from plant to plant. María and Diego have noticed that the current season has been particularly warm and rainy, with rainfall often persisting for several days in a row and heavy dews each morning.

Figure 4. Underside of a coffee leaf with a late-stage Hemileia vastatrix infection. The spots are composed of thousands of tiny, oran​​ge-colored rust spores. (Photo credit: Plant Pathology Department, ICAFE)

Unfortunately, the rust protection provided by María and Diego's usual organic fungicide-spray program seems to be weakening. When she inspected her crop in September, María noticed some small, bright-green spots (early symptoms of the disease) on the underside of lower leaves. Then, closer to harvest in November, she noticed abundant yellow-orange spots on the undersides of the leaves—the result of massive numbers of spores produced by the coffee rust fungus (Fig. 4). The rust symptoms were severe even though several fungicide sprays had been applied throughout the season. María had seen rust many times before, but the infections had never been so severe. The situation was bad enough that many of the infected leaves were dropping off the plants, leaving bare branches and exposing the cherries to the harsh Costa Rican sun.

María is really worried now. In the past, the cool temperatures at her high-altitude (1,300 m or 4,265 ft above sea level) farm provided some protection from the warmth-loving rust fungus. But year by year, average daily temperatures have been climbing. The warming climate and a particularly rainy season have left her plantation increasingly vulnerable to the disease, as rust spores can be dispersed readily by rain splash from plant to plant. Diego and María estimated that they lost 30% of the value of their harvest in the past year due to damage caused by rust. There were fewer coffee beans to harvest, and the quality of the beans was slipping as well. Alarmingly, the exporters who buy María's beans have started to ask questions about the decline in bean quality.

Figure 5. The disease triangle considers three variables—host, pathogen, and environment—to estimate the level of risk of a crop disease outbreak. In Costa Rica, climate change is expected to provide an increasingly conducive environment for rust epidemics.

María fears that she will be unable to keep up with this rust epidemic. It may force her to declare bankruptcy, sell her family's farm, and look for employment elsewhere. If she switches back to conventional farming, much of her revenue will be lost because the prices for conventional beans are significantly lower than for organic beans. The cost of fungicides can mount up quickly for all coffee farmers, conventional and organic. Conventional coffee farmers have more fungicide choices, and more effective ones, than organic growers. Organic farmers, in contrast, cannot rely on synthetic fungicides to stop the spread of disease, so they must use a variety of integrated pest management (IPM) techniques to minimize yield loss.

María and Diego know that they need to do something different to protect the farm's production and reputation against the steadily worsening threat of rust. They began scouring the Internet for answers. They quickly realized that many small-scale producers in Costa Rica, Guatemala, Colombia, and El Salvador are facing similar challenges from rust.

They also discovered that plant pathologists (disease specialists) in the region's public universities and coffee research centers recommend several options that organic coffee growers could use against rust. They learned that ICAFE (Costa Rican Institute of Coffee) regularly updates their website to warn of regional rust risk ratings, which can be used as a guide to time fungicide sprays efficiently in each part of the country.

These experts also advised María and Diego to improve management of the farm's soil fertility and quality (pH, nutrient content, organic matter content). The reason for this recommendation is that vigorous plants can produce higher yields than weakened plants, even when coffee rust appears. Costa Rica's mostly acidic soils can make coffee growing difficult. If soil amendments like calcium carbonate are not added every few years, the roots of sensitive coffee plants can burn, resulting in stunted growth or a reduction in yield and bean quality.

Another recommendation was to prune the coffee plants and their interplanted shade trees (Fig. 2) more thoroughly to encourage better air movement and rapid drying of the coffee leaves after rainfall, because drier conditions suppress rust outbreaks. They were advised to maintain good sanitation practices, such as prompt removal of pruned branches from the field, to prevent further spread of rust and any other pathogens. Both pruning and improving soil quality can help to reduce the host- and environment-related risks of rust outbreaks (see the "disease triangle" concept in the Background section​).

Increasing the frequency of fungicide sprays during the rainy season is another option. However, fungicides have become increasingly expensive, cutting into the farm's profits. Converting to conventional production, which would allow use of more effective and longer-lasting fungicides, is another option. However, this would sacrifice the substantial price premium María receives for her organic-certified beans and undermine her plan to use more environmentally friendly farming techniques.

In addition, the experts suggested that growers consider changing coffee varieties. Several varieties of C. arabica, as well as hybrids with genes from a more rust-resistant coffee species (like C. canephora, also known as Robusta), offer a higher level of protection against outbreaks. However, the quality of the beans they produce is usually regarded as lower than for the rust-susceptible variety that María grows. Furthermore, coffee is a long-lived crop—up to 20 years—so changing varieties would be costly and have long-lasting impacts.

The coffee disease experts cautioned that none of these management options offers a "silver bullet" against rust, so a combination of several strategies probably will be needed.

While there are many management options to fight back against coffee rust, what would you do if you were María Rojas and the future of your family's organic coffee farm was at stake?​

Discussion Questions

  1. What are the main environmental factors that increase the risk of infection by coffee rust?
  2. What part of the growing season poses the highest risk to coffee production? Why?
  3. Why is only one species of coffee—Coffea arabica—grown in Costa Rica? What are the advantages and disadvantages of this practice?
  4. What might be the disadvantages of spraying fungicides more frequently?
  5. Use the information available and your own knowledge to devise an IPM-based management plan for María that could solve or reduce her problems with coffee rust. For each strategy you propose, consider the advantages and disadvantages for a small-scale farmer.


Coffee is a major export in many Latin American countries. Mountain slopes in Costa Rica—a country located in Central America (Fig. 3)—have a mild climate that is well suited for producing high-quality coffee (Coffea arabica) beans. Tarrazú, a mountainous region in Costa Rica known for its high-quality coffee bean industry, has two well-defined seasons: the dry season (mid-November to mid-April) and the rainy season (May to mid-November).

Costa Rica provides roughly 1% of the world's coffee and exports 90% of its production at relatively high prices due to the high quality of the crop. In 2020, the coffee industry in Costa Rica generated about $332.5 million.3 By Costa Rican law, only C. arabica plants can be cultivated in the country in order to maintain its reputation as a producer of high-quality beans. C. arabica generates higher revenue due to its smoother taste, but it is more challenging to grow than the more vigorous C. canephora (Robusta), which has higher yields per acre but lower bean quality.

A combination of risk factors, including increased rainfall, higher temperatures, the extent of shade, and the presence of rust in nearby plantations, can trigger a coffee rust outbreak. During the rainy season in Costa Rica, as the coffee fruit are growing and maturing, environmental conditions are often highly favorable for infection and spread of the disease. Environmental conditions during this period can tip the balance toward or away from rust outbreaks (Fig. 5). Rust infections can reduce coffee production up to 50% when conditions favor the disease. For small-scale coffee farmers like María, even a small loss in yield or an increase in production costs has a disproportionately large impact on their bottom line.

Management of the Basidiomycete rust fungus Hemileia vastatrix is complex, continuous, and costly. In Costa Rica, most C. arabica cultivars are highly susceptible to rust—particularly at lower altitude, and therefore warmer, regions—resulting in severe defoliation and yield loss. With global warming, however, higher temperatures and more variable rainfall patterns are increasing rust outbreaks and, therefore, worsening crop damage, even at higher elevations. Moreover, plants that are defoliated (lose their leaves prematurely in a previous season) will be weaker the next season, making them more susceptible to rust outbreaks and other diseases.

An IPM approach for coffee rust includes cultural, chemical, and biological practices. Under organic-farming certification programs, where only certified-organic pesticides can be applied, the available fungicide options are few in comparison to conventional farming. Moreover, organic fungicides tend to be less effective and less persistent on plants than conventional fungicides, especially during the rainy season—the high-risk period for rust outbreaks.

Figure 6. Ripening coffee cherries on a coffee tree branch in Tarrazú, Costa Rica. (Photo credit: José González-Acuña)

A key cultural practice in coffee plantations is the management of shade—shade from the coffee plants and from the shade trees that are commonly interplanted in Costa Rican coffee farms (Fig. 2). Coffee and shade trees have to be pruned frequently to maintain a proper balance of shade and sunlight. One of the most common shade trees used to intercrop with coffee in Costa Rica is the 'poró' tree (Erythrina sp.), a rapid-growing, nitrogen-fixing tree. Other intercropped plants, such as avocado, bananas, and citrus, provide a second crop in addition to coffee.

Another challenge is that new rust races (emerging subspecies of the same fungus) have caused outbreaks on previously resistant varieties of C. arabica. This erosion of resistance has prompted coffee breeders worldwide to seek new sources of resistance and bring those resistance genes into varieties with good agronomic traits. Resistance breakdown is a key factor to consider when planning for a long-term enterprise like a coffee plantation, in which the coffee trees can be expected to last for up to 20 years.

If the rust infection is severe enough, most of the leaves can drop off, along with the coffee fruit, called "cherries," that contain the beans (Figs. 3 and 6). While the coffee plant is a woody perennial, it exhibits a "biennial effect," where yields fluctuate from high to low naturally every other year. However, once branches are removed or killed, it takes more than one growing season to generate cherry-producing tissue, so the current year's losses can be compounded by few or no fruit the following year.

The rust fungus relies on the prolonged presence of water on the leaf surface for its spores to germinate, spread, and infect. María has observed an increase in the variability of rainfall, as well as an increase in the total monthly amount. As temperatures creep up, so does the risk of rust outbreaks.

Thus, María is puzzled about how to manage her organic coffee plantation in a changing environment. No single option appears likely to offer a way out of this crisis. The health of her land is also on her mind, and she is hesitant to abandon the organic practices that she has put into practice.​


Agronomic traits: Physiological characteristics that are associated with specific varieties of coffee.

Climate change: Long-term shifts in weather patterns and temperature due to an increase in carbon dioxide emissions and the combustion of fossil fuels.

Conventional: Agricultural production that allows the use of synthetic fertilizers and pesticides.

Epidemic: An infectious disease that has become widespread in a population of a geographic region.

Integrated Pest Management (IPM): The long-term prevention and suppression of pests and diseases through a combination of methods that reduce the use of pesticide applications while prioritizing the health of the environment.

Organic: A type of agricultural production that substitutes naturally derived fertilizers and pesticides for synthetic forms of these products.

Sign: Visible evidence of the pathogen on the plant.

Subspecies: Populations that typically occur in isolated geographic regions and possess different traits but can interbreed.

Symptom: A plant response to biotic or abiotic factors.​


The goal of this case study is to challenge students to develop solutions for an economically devastating and hard-to-manage crop disease called coffee rust (called "la roya" in Spanish). Students are asked to devise a disease management plan after gaining a basic understanding of the ecology of the disease and the available options for combating rust. The case takes place in a plantation in Costa Rica, an important coffee-producing country in Central America.

The case study is designed for class periods ranging from 50 to 90 min in length. The target audience is undergraduate students in classes in plant pathology, horticulture, agronomy, sustainable agriculture, integrated pest management, food systems, tropical crop management, and related disciplines. Based on our experience in teaching this case study, we suggest that students read the provided background information before the class so they can participate meaningfully in discussion.

We tested the case study in a 50-min class period in an introductory course in plant pathology at Iowa State University. We divided the period into three parts. The first was a 5- to 10-min presentation by the instructor that summarized the facts of the case. Next, groups of two to five students explored the discussion questions and brainstormed potential solutions for 15–20 min. During the final 20–30 min, a representative from each group wrote the group's proposed management strategies on the board, followed by a whole-group discussion of the advantages and disadvantages of each strategy.

Based on written replies to a postclass survey, reading the case prior to the discussion strengthened student understanding of the challenges facing the grower in managing coffee rust using organic methods. Students also indicated that both small-group and whole-group discussions stimulated critical thinking by enabling them to weigh the tradeoffs of each management option. These discussions prompted the students to envision combinations of options in an IPM approach.


Avelino, J., Cristancho, M., Georgiou, S., et al. 2015. The coffee rust crises in Colombia and Central America (2008–2013): Impacts, plausible causes, and proposed solutions. Food Security 7:303-321. DOI:

de Resende, M. L. V., Pozza, E. A., Reichel, T., et al. 2021. Strategies for coffee leaf rust management in organic crop systems. Agronomy 11:1865. DOI:

Foreman, W. 2021. "Coffee Killer: Tracking 'La Roya'—The Fungus Threatening Coffee's Future." Sustainable Food Systems Initiative, University of Michigan. April 29 , 2021. 

Gonzalez, V. 2021. Global Agricultural Information Network, San Jose, Costa Rica, 2020. Coffee Annual, vol. 2020-2021.