Coffee pests and diseases

Leaf rust: the disease that follows arabica everywhere

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Coffee leaf rust is caused by a fungus, Hemileia vastatrix, that can live only on living coffee leaves. The first sign is pale spots; then masses of orange spores appear on the underside of the leaf, and the leaf falls early. A tree stripped of leaves cannot fill its fruit, and a review of the disease says the damage carries over into following years. The same review cites yield losses of up to 35 per cent and calls rust the most important disease of arabica.

It was first recorded on wild coffee near Lake Victoria in 1861 and described in 1869. Soon afterwards it ended coffee growing in Ceylon, now Sri Lanka. The review traces its spread: around the Indian Ocean and Pacific between 1870 and 1920, to Africa's Atlantic countries in the 1950s and 1960s, and across the Atlantic to Brazil, where it was first reported in 1970, then through South and Central America in the 1970s and 1980s.

The spores that matter are the asexual ones, which re-infect leaves whenever conditions allow. The fungus has more than fifty known races, and the review says the appearance of new ones is associated with resistance in a variety breaking down.

From one spore to a pustule: a model of the rust cycle

CoffeeHQ explanation

A diagram drawn by CoffeeHQ from the life-cycle and epidemiology sections of the review cited above. The stages are the review's; the hours and weeks attached to them come from leaves inoculated in a laboratory and are not field figures.

What turned rust into a crisis in 2008 to 2013

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Rust had been present in Latin America for decades when it caused severe epidemics in Colombia from 2008 to 2011 and in Central America in 2012 and 2013. A study of those years reports that production in Colombia fell by 31 per cent on average over 2008 to 2011 compared with 2007, and in Central America by 16 per cent in the 2012–13 harvest compared with the one before, with a further 10 per cent the year after. The authors note that such figures cannot be cleanly separated from the normal variation between years.

They describe the main drivers as economic and meteorological. Every intense epidemic in the region over 37 years coincided with a period of low profitability, from falling prices or rising costs, in which farms were managed less intensively and the trees became more vulnerable. The weather factor common to both recent epidemics was a narrower daily temperature range, with warmer nights and cooler days, which the authors say probably shortened the time the fungus needs to produce new spores. They call these causes plausible, not proven.

At the time, according to coffee institutes the study cites, about 80 per cent of the coffee in Central America was of susceptible varieties, although resistant ones had been available since the 1990s. Replanting costs money and means at least two years with little or no crop.

Coffee berry disease: so far only in Africa

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Coffee berry disease is caused by another fungus, Colletotrichum kahawae. It infects several parts of the plant, but the losses come from green berries: dark, sunken lesions appear on the fruit while it is expanding. A paper on resistance to it cites crop losses of up to 50 to 80 per cent in years of severe epidemics where no control measures are applied.

It was first reported in Kenya in 1922 and is still restricted to Africa. The same paper records concern about it reaching Latin America and Asia. That is why researchers outside Africa study resistance to a disease their own farmers have never seen.

The berry borer: an insect that lives in the seed

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The coffee berry borer, Hypothenemus hampei, is a small beetle. A review of the pest describes it as the only one of hundreds of insects feeding on coffee that can complete its life cycle inside the coffee seed. The female bores into the fruit, usually near the tip, and lays eggs in tunnels in the bean; the larvae feed on it. Brothers and sisters mate inside the berry, the males die there, and the fertilised females leave to find new fruit.

The review cites damage of more than 500 million US dollars a year and calls the borer the most serious insect pest of coffee worldwide. How many generations it completes in a year depends on temperature: estimates in the studies it cites run from two to thirteen. That dependence on warmth is why the insect features in studies of climate change.

Wilt and nematodes: the two that work out of sight

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Coffee wilt disease is caused by a fungus, Fusarium xylarioides, that enters through roots or wounds and colonises the vessels that carry water; the tree wilts because its water supply is blocked. Two papers by the same research group summarise its history from earlier work: discovered in 1927, it devastated crops in west and central Africa by the 1950s, at first on robusta and excelsa, was countered by sanitation and by planting resistant robusta, re-emerged on robusta in central Africa by the 1970s and was a major problem in east and central Africa by the mid-1990s, in the Democratic Republic of the Congo, Uganda and northern Tanzania. The later paper notes that production in some countries did not recover. Separate strains attack arabica and robusta. The two papers date the arabica strain's appearance in Ethiopia differently, one to the 1950s and one to about the time of the robusta re-emergence; both describe it as widespread there later. An open review of the fungi recorded on coffee, read for its section on this disease, agrees on the essentials: first detected in 1927 in what is now the Central African Republic, found on arabica, robusta and excelsa, a disease of the vessels that the review says can kill a mature tree within about six months of the first visible symptoms, and one after which, it reports, the soil may stay infectious for several years once the trees are removed.

Plant-parasitic nematodes are microscopic worms that feed on roots. The most important on coffee are the root-knot nematodes, of the genus Meloidogyne, which settle inside a root and cause it to swell into knots. A Kenyan field study names more than a dozen species recorded on coffee and makes a practical point of it: the species in a field has to be identified before deciding how to manage it, and in particular which source of resistance to use. The paper that published the genome of one of them, Meloidogyne exigua, calls it the most widely distributed nematode in the coffee areas of Central and South America and cites losses estimated at up to 45 per cent in the state of Rio de Janeiro and 15 to 20 per cent across Central America.

Those are other authors' estimates, and the Kenyan study is frank about how thin the record is elsewhere. Yield loss from nematodes in coffee, it says, is known mostly from Latin America, where figures of 10 to 35 per cent are documented depending on species, while for Africa the data on damage are effectively non-existent. The same study found every one of its seven arabica fields heavily infested with a species never before reported on coffee in Kenya. Above ground the symptoms look like those of poor soil or drought, which is why, its authors say, nematodes are rarely recognised as the cause. They are most aggressive on newly transplanted seedlings, and once established in a plantation they are extremely hard to remove; the advised approach is to plant clean and resistant seedlings in the first place.

Nematodes also open the way for other organisms. A Mexican study describes a disease complex in which root-knot nematodes infect first, fungi and bacteria follow into the damaged tissue, and the root's outer layers thicken, crack and take on the look of cork before the root system dies back. In coffee the advanced stage is known as corky-root disease.

Why wilt attacks arabica in one place and robusta in another

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The two strains of the wilt fungus do not overlap much in the field: one attacks arabica, which grows high and cool, and the other robusta, which grows low and warm. A study published in 2023 asked whether temperature is part of the reason. It reports two kinds of evidence. The first is a curve fitted to a survey of 2002 that recorded the share of trees infected on farms at 51 places in Ethiopia and 60 in Uganda and Tanzania. On robusta the fitted severity peaked at about 38 per cent of trees where the mean annual temperature was about 23 degrees Celsius; on arabica it stayed low across a wide range, peaking at about 4 per cent near 16 degrees. The second is a laboratory assay of four isolates, two of each strain, grown on agar at seven temperatures. There the authors' expectation was only partly met. Both strains grew fastest at about 22 degrees and the arabica isolates did not grow significantly faster in the cold; the robusta isolates grew faster at 20 and 25 degrees. What the arabica isolates did do was produce more spores at 15 degrees and below, and their spores germinated better there.

The authors then run their curves forward to the temperatures one climate model gives for 2060 to 2080 under a middle scenario, and predict that severity could fall by nearly half on average and rise in some regions, among them eastern Congo, Tanzania and Uganda for the robusta strain. For the arabica strain all three of their temperature curves gave that fall; for the robusta strain two did, and the third gave a slight rise. That last step is a projection built on a curve built on one year's survey, and it assumes that only temperature changes. The growth assays are the only part done under controlled conditions, and they were done on agar and not in coffee trees.

A paper of 2024 from the same group, read here for its summary and introduction, proposes how the strains arose: by the transfer of stretches of DNA between the wilt fungus and a related soil fungus, Fusarium oxysporum, with which it has been found in the roots and wood of diseased trees. If that is right, new forms of the disease do not have to wait for slow mutation.

From an infected root to a dying tree: a model

CoffeeHQ explanation

A diagram drawn by CoffeeHQ from the Kenyan and Mexican nematode studies and the papers on wilt. Root-knot nematodes and the wilt fungus are different organisms with different life cycles; what they share is that the damage is done underground, long before anything shows.

How they are managed, in principle

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The approaches the reviews name. None of this is a recommendation for any farm.

Resistant varieties

For rust and berry disease, both reviews call resistant varieties the most effective and durable or sustainable approach. Resistance to rust came largely from the Timor Hybrid, a natural cross between arabica and robusta found on Timor in 1927.

Clean planting material

For nematodes, the measure the Kenyan study reports as advised is starting with clean, healthy, resistant seedlings, because the worms are extremely difficult to remove from an established planting.

Sanitation and the harvest

For the berry borer, clearing dried fruit from the tree and the ground appears in the management programmes the review describes for individual countries, with the note that smallholders often cannot afford the labour it takes.

Natural enemies

The same country accounts list birds and ants, parasitic wasps released for the purpose, and a fungus that infects the beetle, alongside trapping to monitor numbers.

Chemical control

The rust review calls fungicides one of the preferred immediate measures against that disease, and the borer review counts chemical control among the five components of managing the beetle. This page gives no detail of them: what is permitted and appropriate differs by country and crop, and is a matter for local advice.

Keeping trees fed and tended

The study of the rust epidemics found that under-managed farms were the vulnerable ones. Its lesson is economic: a disease can be controlled on paper and still break out when growers cannot afford to tend their trees.

The varieties these diseases produced

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• Timor Hybrid — The plant whose rust resistance was bred into arabica from the 1960s onward, and the ancestor of the two groups below.
• Catimor and Sarchimor groups — Crosses of the Timor Hybrid with Caturra and with Villa Sarchi, made to carry its rust resistance into arabica varieties.
• Ruiru 11 and Batian — Kenyan varieties bred against coffee berry disease as well as rust; a 2026 paper describes their resistance as durable.
• F1 hybrids — A newer route to combining resistance with vigour, with its own constraint: the plants cannot be raised from saved seed.

No product, dose or schedule is named

CoffeeHQ explanation

It names no pesticide, fungicide or nematicide and gives no rate, timing or schedule for anything. It does not cover leaf miners, stem borers, the American leaf spot or other regional problems, because no source on them was read. The loss figures above are each a review's citation of another author, for the conditions that author studied; none is a forecast for any farm.

What to do next

• Timor Hybrid — How one chance cross on an island became the basis of rust-resistant arabica.
• Colombia in the atlas — Fifty years of breeding against one fungus, and why a wet year is a bad year.
• Kenya in the atlas — Where coffee berry disease was first recorded and the varieties bred against it.
• Coffee and climate change — How warming is projected to change where the berry borer can live.