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Editor’s Note: This article first appeared in Roast Magazine‘s July/August 2019 issue, and is reprinted here with permission. You can view the original piece in a free online preview here and download a pdf of the article, courtesy Roast Magazine.

Coffee Leaf Rust: Past, Present and Future in the Fight Against Fungus

Part I

By Chris Kornman

“LUCKY” is not likely to be the first descriptor you’d hear from coffee farmers when discussing their careers. Successful coffee production isn’t the result of chance. The job takes skill, dedication, intuition and resilience. Yet coffee is fickle, and prone to innumerable afflictions; even the most fastidious farmer’s trees fall victim to disease. One of the vilest afflictions known to coffee is a fungus known as rust.

Among the coffee producers I’ve been privileged to meet is a subset of proactive conservationists and forward-thinkers. Their fields were not immune to recent epidemics of coffee leaf rust (CLR, or roya in Latin America) sweeping through the coffeelands. They were unlucky, like the rest, but they were quick to learn and adapt.

One such producer is Alejandro Solis, who manages his family’s farms, Finca Injertal and Finca Huixoc, near the cities of San Pedro Necta and La Democracia in Huehuetenango, Guatemala. A third-generation farmer, Solis has the privilege of running large and successful operations blessed with abundant spring water. Even so, he has also observed climatic changes over the years. He is a conscientious coffee caretaker, and it became apparent to him that investment in climate technology throughout his farms would provide his family, his farm and his employees with security to continue growing coffee into the future.

His gathered climate data has been used to help predict temperature and rainfall, and contributed toward an impressive scientific report led by Dr. Peter Baker at Climate Edge, a U.K.-based firm that aims to empower farmers with predictive weather and temperature models.

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Alejandro Solis, manager of his family’s farms, Finca Injertal and Finca Huixoc, in Huehuetenango, Guatemala. Photo courtesy of Royal Coffee

Not long ago, Solis confided in me that roasters “need to know what coffee farmers are facing these days. With unpredictable and unstable weather, the risks of producing coffee have increased. Flowering, planting, fertilizing, harvesting and all other labors are greatly influenced by weather—as is, of course, quality. So, I think this topic is always important for everybody to learn.”

On Huixoc, at 130 hectares, farm management is no small undertaking. The farm crosses a wide range of elevations, from 1,150 meters to nearly 1,700 meters, and in recent years it has experienced rather dramatic average high temperature increases. “During our rainy season, which lasts between five and six months,” Solis explains, “there are ample conditions for outbreaks, especially when temperatures rise and there is enough humidity.” On Huixoc, rains begin as early as February, usually peak in April, May and June, and can extend through August. These wet summertime conditions—warm and damp weather—are ripe for roya.

Solis’s approach to containment must be clinical to be successful on a farm at his scale.

“We have implemented an integrated management system to manage [rust] and keep it below levels which would not affect our productivity too much,” he says. “We do careful monitoring every month. We regulate our shade trees in very moist areas. We try to provide the best nutrition possible, and we have replanted some specific areas where rust is more prevalent with rust-resistant varieties. We have also opened our row spacing in some areas. We also use fungicides to keep inoculum at low levels. If you let the rust level get too high, there is nothing you can do to stop it.”

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Coffee leaf rust in Guatemala. Photo by Lily Kubota

He elaborates, “After the rust outbreak in 2012–2013, we have seen how the rust fungus adapts to higher altitude and moist climates, where we have most of our coffee planted. We know we are never going to eradicate it.”

That word “never” hangs in the air, thick like smoke. Coffee’s most recent rust crisis was an alarm bell for a fire that’s been smoldering for more than a century. Without a deep knowledge of rust’s history and behavior, and the preventive measures in which roasters can participate, I fear we’re just fanning the flames. Let’s take a deep look at the interaction between rust, coffee and ourselves as we prepare for the next steps into an uncertain future.

 

GROUND ZERO

On November 6, 1869, a three-paragraph report with three footnotes and an illustration ran in The Gardeners’ Chronicle and Agricultural Gazette. Written by Reverend M.J. Berkeley and his assistant C.E. Broome, the notice identified a newly described species on the island of Sri Lanka (called Ceylon at the time). It was not a coffee species, or even a plant, but a fungus.

“We have recently received from our excellent friend Mr. Thwaites a specimen of a minute fungus which has caused some consternation amongst the coffee planters in Ceylon, in consequence of the rapid progress it seems to be making amongst the coffee plants,” reads the first sentence (biodiversitylibrary.org/page/33107926).

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Image courtesy of Missouri Botanical Garden, Peter H. Raven Library

Berkeley and Broome proposed Hemileia vastatrix as its scientific name and classified it under the order of rust fungi. Somewhat coy in their description of “consternation,” the pair buried the lede in the translation of the species name. The Latin word vastitas means “devastation.”

Coffee leaf rust fungus had also been noticed a few years earlier in western Kenya, near Lake Victoria, sometime in 1861 per Talhinhas, et al., in their article “The Coffee Leaf Rust Pathogen Hemileia vastatrix: One and a half centuries around the tropics,” published in Molecular Plant Pathology in 2016. Many Ethiopian farmers have been aware of its existence for years, without much noting significant problems it may have caused—likely the fortuitous result of having abundant genetic diversity in their country’s montane forests.

The monoculture coffee plantations across the Arabian Sea, however, would not be so lucky. On Sri Lanka, where farmers had little knowledge of the disease or its treatment, the infection rapidly spiraled out of control. The British, having wrested colonial domain from the Dutch at the turn of the century, were populating plantations at a fever pitch, establishing their first coffee farm in 1825.

The boom and bust of Sri Lanka coffee plantations is shocking both in its magnitude and brevity. By 1840, just 15 years after the first plantings, coffee was the island’s leading export commodity. In 1873, exports peaked at over 111 million pounds (more than 840,000 bags), enough to place it third in global production volume at the time, trailing only the stalwart Dutch colonial coffee mainstay of Java and 19th-century breakout super-producer Brazil (Kushalappa, Ajjamada, C. & Albertus B. Eskes. Coffee Rust: Epidemiology, Resistance, and Management. CRC Press, Inc. (1989) 178). Yet, by the late 1890s, there would hardly be a tree left on the teardrop of India, all dead—or uprooted and replaced—because of rust (Ukers, William Harrison. All About Coffee. Tea and Coffee Trade Journal Company (1922) 236-237).

Coffee leaf rust was impossible to contain in Sri Lanka. The fungus jumped from island to mainland and back, on the trade winds and on travelers, and utterly decimated coffee production throughout the Eastern Hemisphere. Coffee leaf rust spread throughout the Indian and Pacific oceans, India and Indonesia, the Philippine Islands (once fourth in global arabica production behind Ceylon), and the Hawaiian Islands; even Bourbon trees on Réunion Island were not spared. Sri Lanka’s coffee leaf rust outbreak would pull the linchpin in an unprecedented shift of arabica production to the Western Hemisphere in the span of less than 30 years.

 

KNOW YOUR ENEMY

Coffee leaf rust is a member of a vast order of problematic fungi. While most fungal species contribute to the complex circle of life by feeding on decomposing matter found on the dead, rust fungi are not so easily satiated. The 8,000 identified rust species are “obligate biotrophs,” which means they require a living host to survive. They are parasites.

Rust fungi are ancient, likely evolving around the same time as the first flowering plants on Earth. Other than CLR, one of the most familiar species, Puccinia graminis, known as “stem” or “black” rust, affects wheat.

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Image courtesy of Evan Gilman

In ancient Mesopotamia, a sweeping epidemic decimated wheat crops around 1300 B.C. Without the knowledge of microorganisms, farmers called the disease “red barley sickness” and had little option for respite other than prayers to the gods of harvest. Most scholars denote this as the first recorded rust outbreak in human history.

In fifth-century southern Europe, another wheat rust epidemic left vulnerable a once venerable empire. The fungus caused a wheat shortage likely bearing partial responsibility for the fall of the Roman Empire (aimelab.wixsite.com/aimelab/the-rust-fungi). Prior to the civilization’s fall, ancient Romans even had a god for rust: Robigus. Sacrificial red animals—frequently puppies—were offered to the rust deity during the spring festival of Robigalia, as frightened farmers hoped to avoid the scourge on their crops.

To this day, rust fungi are among the most complex organisms known to science. They engage in up to five highly specified life stages and are heteroecious, meaning that to complete their five-stage life cycle they require two separate host species. (See illustration on page 30.)

For wheat rust, the heteroecious host is the ornamental barberry plant, with which the United States engaged in a war after a devastating epidemic around 1916. Since the 1950s, resistant wheat strains have been bred and widely used around the world to so much success that farmers largely turned a blind eye to the relationship between barberry, wheat and rust. Breeding resistance and ignoring barberry worked pretty well, at least until 1999, when a new strain of wheat rust emerged in Uganda, spread rapidly, and wreaked havoc throughout Africa, the Middle East and Asia.

The most obvious symptom of any rust infection is the presence of colorful yellowish or reddish spores that cluster together; on a coffee leaf the circular splotches are immediately recognizable, like the curse of a fungal evil eye. The affliction eventually causes the leaves to drop off the plant, incapacitating the coffee tree. Those trees lucky enough to survive typically lose the fruit from both the infection season and that of the following year.

The burnt orange blemishes, called urediniospores, represent just one of rust’s natural life stages. These spores are clones, rapidly reproducing and infecting nearby trees, floating across large distances on the wind. This epidemic stage of rust can easily devastate coffee populations if uninterrupted. However, its weaknesses are its genetic monoculture and its sensitivity to low temperatures and dry weather.

Yet rust has built-in biological protection from cool, arid climates. Under these conditions, the fungus enters dormancy with a specified alternate teliospore, which begins the process of creating genetic variance. Teliospores are hardier than urediniospores and may live for long periods on dead plant matter, until they fuse a pair of nuclei, then split into four basidiospores—airborne agents that seek a secondary host plant. When they find one, the basidiospores germinate and colonize on top of a leaf, creating a lesion that acts similar to a sexual organ.

These basidiospore colonies, called spermagonia, launch reproductive pycniospores into adjacent colonies, fertilizing receptive cells called hyphae. The fertilized hyphae grow rootlike tendrils that plunge through the underside of the infected leaf and eject an aeciospore, the birth of a microscopic colony; liberated by a light breeze or the coat of a passing traveler, these return genetically unique rust to the primary host.

This twisted two-host relationship is well documented on wheat and barberry, and likely evolved to help rust fungus survive cold winters. Coffee, however, grows in the hot and humid tropics, and arabica will barely tolerate frost, much less freezing temperatures. As a result, Hemileia vastatrix may not even need a second host. While roya has been observed to produce basidiospores, it is speculated this could simply be an evolutionary remnant or a fail safe for hard times. The fact remains, coffee leaf rust can survive easily as epidemic urediniospores, and science is currently unaware of the fungus’s alternate host to the coffee tree.

Think about that for a second. Coffee leaf rust is so versatile and virulent that it doesn’t even need to complete its circuitous life cycle to obliterate a coffee farm. This hints at an immense problem engraved into its nature: Rust will adapt, continuing to prey on coffee well into the future.

 

Continued in Part II