Pathogen Profile #10

Hello Robigalia Reader and welcome back to another week of Robigalia, delivering the latest in plant pathology directly to your inboxes.

This week’s roundup is a bit longer than usual, but is all about a fungal pathogen threatening your morning coffee and impacting smallholder farmers. If you’re like me and rely heavily on your morning cup of joe, you’re going to want to read this one.

Coffee leaf rust (CLR), caused by the fungus Hemileia vastatrix, is the most important disease affecting Arabica (Coffea arabica) and Robusta (Coffea canephora) coffee worldwide. The disease can lead to significant economic losses, with previous epidemics destroying coffee production in entire countries.

Like many rust fungi, copious spore production facilitates the spread of H. vastatrix, with spores easily spreading by wind and rain. The spread of H. vastatrix from Africa to South America in the 1970s was believed to have occurred via wind currents carrying spores across the Atlantic Ocean. Spores have even been recovered from spore traps mounted on airplanes at altitudes of around 1000 meters! Wind also facilitates the spread within plantations, along with rain, which causes the spores to splash from infected leaves to healthy ones.

Once a spore lands on the leaf surface, under favourable conditions the spores will germinate and penetrate the leaves through the stomata. Here, the fungus grows within the leaf cells, feeding off the plant’s nutrients before erupting out of the leaf surface to spread once again. This eruption presents as yellow to orange powdery spots/lesions on the undersides of coffee leaves, with corresponding yellow areas on the upper leaf surface. Infection often leads to defoliation, and also affects fruit development causing poor bean quality, or whole plant death. All of which ultimately impact yield.

Colonisation played a significant role in the global spread of CLR globally. CLR was first reported in 1861 near Lake Victoria in East Africa, the native region of coffee plants. The disease quickly spread to Ceylon (now Sri Lanka), which was a British colony at the time, devastating coffee plantations there by 1869. Colonial trade routes facilitated the movement of coffee plants and potentially infected material between colonies and to Europe. Within a few years of reaching Ceylon, coffee rust had spread to other British colonies like India, and Dutch colonies such as Sumatra and Java.

European colonial powers established large-scale coffee plantations in their tropical colonies, creating vast monocultures that were highly susceptible to disease spread. As coffee rust devastated Asian plantations, coffee production shifted to the Americas, which were initially free of the disease. The Americas remained free of coffee rust until 1970 when it was discovered in Brazil. Once introduced, the disease spread rapidly through South and Central America within a decade, facilitated by the widespread planting of susceptible coffee varieties descended from a single plant.

While all of this is bad news for the price of your morning coffee, the real impact is felt by the 25 million smallholder farmers who are estimated to produce 80% of global coffee supply. In Guatemala, smallholder farmer households reported losing an average of 71% of their coffee production during their worst year of CLR impact. This level of loss can severely affect their livelihoods, as coffee is often their primary source of income. The reduction in coffee yields directly translates to decreased income for smallholder farmers. In Central America, the 2012 CLR outbreak led to over $1 billion in damage, significantly reducing incomes and employment opportunities for small coffee growers. This economic strain can push farmers into poverty and force them to seek alternative livelihoods.

The economic impact of CLR extends beyond coffee production. The unpredictability of coffee yields due to CLR contributes to market volatility. Smallholder farmers, who often lack financial buffers, are particularly vulnerable to these fluctuations, making it difficult for them to plan and invest in their farms. Further, in regions where smallholder farmers rely on coffee as their main cash crop, significant yield losses can lead to food insecurity. Farmers may struggle to afford basic necessities, including food, leading to broader social and economic issues. These economic pressures can lead to migration, as farmers seek better opportunities elsewhere. This migration can result in labor shortages, further complicating coffee production and increasing labor costs for those who remain.

Ordinarily, management practices of pathogens such as H. vastatrix would rely heavily on the use of fungicides and planting resistant varieties, these costs can be prohibitive for smallholder farmers who already operate on thin margins. For instance, the need for frequent fungicide applications increases production costs, which many smallholders cannot afford. To support coffee producers, in 2021 The U.S. Department of Agriculture (USDA) announced a $6 million grant over four years to support research addressing the threat of CLR for farmers in Hawaii and Puerto Rico.

Initiatives such as Maximizing Opportunities for Coffee and Cacao in the Americas (MOCCA) and the State Coordinator of Organic Coffee Producers of Oaxaca (CEPCO) are playing crucial roles in assisting smallholder farmers in the coffee sector. MOCCA as an example provides farmer training on good agricultural practices, building buyer-seller relationships, strengthening suppliers of genetic material for planting, and facilitating access to finance. CEPCO has a similar initiative, with a particular focus on investing in training of women and youth.

If you’re interested in diving into the science of coffee leaf rust, I’ve summarised a few articles below. If you’re a subscriber, scroll down to access my online database which includes full summaries of these, and all other Robigalia featured articles.

Coffee leaf rust papers 

The coffee leaf rust pandemic: An ever-present danger to coffee production

• The review highlights the significant impact of coffee leaf rust on global coffee production, tracing its origins from Ethiopia to its global spread due to colonial trade. It discusses the challenges of managing coffee leaf rust, including fungicide resistance, breeding resistant cultivars, and the exacerbating effects of climate change on the disease's spread.

Unravelling the role of key genes involved coffee leaf rust resistance

• This study identifies and validates key genes in the Híbrido de Timor coffee variety that contribute to resistance against Hemileia vastatrix. Using an interactome approach, it reveals differentially expressed proteins involved in crucial plant defense mechanisms, offering valuable insights for breeding programs aimed at developing rust-resistant coffee cultivars.

Essential Oils and Antagonistic Microorganisms as Eco-Friendly Alternatives for Coffee Leaf Rust Control

• The article reviews eco-friendly alternatives to chemical pesticides for controlling coffee leaf rust, focusing on essential oils and antagonistic microorganisms. These methods show promise in reducing disease incidence and severity while being environmentally sustainable and preventing pathogen resistance.

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Until next week,

Alyssa