Category Archives: Rust fungi

Anton de Bary – the Father of Plant Pathology

Yesterday was the birthday of Heinrich Anton De Bary (1831-1888) – the founding father of plant pathology (the study of plant diseases). De Bary was a model scientist: an inspiring teacher – gifted with intelligence, thoroughness and vision. His extensive studies of fungi and cyanobacteria were landmarks of biology. He was the first to unambiguously demonstrate that microorganisms were the cause and not the consequence of plant diseases.

A botanist’s heart in a physician’s body

Anton De Bary was born 184 years ago, on January 26th, 1831 in Frankfurt/Main, Germany. His oddly French name originates from his Waloon ancestors, who had left Belgium in the latter part the 17th century for religious reasons. Anton’s father was a well-to do physician with a strong interest in plants. In those days physicians were often botanists, because the depended heavily on herbs to treat diseases. The elder De Bary had leased an island in the river Main where he set up his private botanical garden. Here, he taught his son what he knew about botany and encouraged him to join the excursions of naturalists associated with the Senckenberg Institute, who collected specimens in the nearby countryside. Encouraged by his father, Anton de Bary went to medical school in Berlin and received his medical doctorate Dr. med in March 1853, at the age of 22, although his dissertation title was a botanic subject “De plantarum generatione sexuali”.

Two days before he received his medical doctorate, De Bary published a book on the fungi that cause rust and smut disease in plants. Quickly, his interest for botany overrode the medical one. He liked to tell that diseases only interested him, until the diagnosis was sure, so after just two month – in the interest of the sick as he added jokingly – he gave up the medical profession and became Privatdozent for Botany at the medical faculty of the University of Tubingen in December 1853.

Two years later – not yet 25 years old – he accepted a position at the small university of Freiburg, where he married Antoine Einert, with whom he had four children. After a five-year stopover in Halle, de Bary succeeded the position of Professor Diederich Franz Leonhard von Schlechtendal at the University of Halle in 1867. As editor of the botanical journal Botanische Zeitung, he exercised great influence upon the development of botany. Finally in 1872, he became a professor for botany at the newly founded University of Strasbourg.

What causes plant diseases? De Bary’s work on wheat rust and potato blight.

Drawing of the potato blight pathogen in Die gegenwärtig herrschende Kartoffelkrankheit, ihre Ursache und ihre Verhütung (1861).

Drawing of the potato blight pathogen in Die gegenwärtig herrschende Kartoffelkrankheit, ihre Ursache und ihre Verhütung (1861).

De Bary’s major scientiftic achievement was that “he brought clarity to the study of fungi and fungal diseases in plants,”1. At his time, the origin of plant diseases was not known. A lot of crude theories lingered around: Microbes were considered to arise spontaneously on diseased or dead plant tissue and plant diseases were believed to be caused by either “the little people”, the devil (to mock people), God (to punish people), static electricity in the air or the weather (Since people became sick when the weather became cold and wet, why wouldn’t potato plants become sick?).

De Bary dismantled a lot of this shoddy science. First, he demonstrated that the spores of Puccinia graminis – the causal agent of wheat rust – were formed from fungal mycelium and not by spontaneous generation. Later, he combined thorough experimentation with microscopic observation to unravel the complicated life cycle of the wheat rust fungus. You may recall from the MEMF article on wheat rust that rust fungi produce not only one type of spores, but five different ones. Some of these spores are not able to cause infection of wheat. De Bary took into account the presence of an alternative host – the barberry plant – and carefully tested which spores could infect which plant by inoculating wheat and barberry plants with the uredospores, teliospores, basidiospores, spermatia and aeciospores.

During De Bary’s childhood, the potato blight disease – that caused the Irish potato famine – occurred in Germany too, but not so destructively. Following his work on the rust life cycle, De Bary in 1860 turned his attention to the potato blight pathogen. Again, he connected the dots of valid preexisting ideas by careful experimentation. He was the first to observe the swimming spores of Phytophthora emerge from their sporangia and penetrate leaves. Soon, he succeeded in infecting healthy potato plants with sporangia taken from diseased leaves. 15 years earlier, Reverend Miles Berkeley had published the revolutionary insight that the potato blight disease was “the consequence of the presence of the mould, and not the mould of the decay…”, but while his work was based on observation, De Bary demonstrated experimentally cause and effect.

De Bary laid the foundation for the study of plant diseases worldwide

Anton de Bary surrounded by students in Strassburg (before 1888).

The scope of De Bary’s work is astonishing. His textbook “Morphologie und Physiologie der Pilze”, published in 1866, marked the beginning of the modern study of fungi. Besides his work on fungal life cycles, De Bary asserted that blue-green algae were bacteria (they are known as cyanobacteria today), demonstrated that yeast are fungi, and coined the term “symbiosis” for “the living together of unlike organisms”. As a teacher, he encouraged his students to exact observation and independent, critical thinking – especially of themselves. “You can’t avoid mistakes during the observation, but you have to know them”, he said. Instead of giving his students a formulated topic, he gave them an object and let them find the study question themselves, because “the right question is already half the work”. He attracted and inspired scientist from all over the world and through his former students (Mikhail Woronin from Russia, William Farlow and Marshall Ward from the US and Schimoyama from Japan) established the study of plant diseases in the many countries.

De Bary died of a tumor of the jaw on January 19, 1888 in Strasburg.



James G. Horsfall 7 Stephen Wilhelm, Heinrich Anton de Bary: Nach einhundertfuenfizg Jahren, Ann. Rev. Phytopathol., 1982

Ludwig Jost, Zum hundersten Geburtstag Anton de Barys. Lebenswerk eines Botanikers des 19. Jahrhunderts. Jena. Verlag von Gustav Fischer, 1930

1 Nicholas P. Money. The Triumph of the Fungi. A rotten history. Oxford University Press. 2006


Coffee rust or Why the British drink Tea instead of Coffee.

© Sarah Maria Schmidt

© Sarah Maria Schmidt

There is not a single morning that I do not start with a cup of coffee. Without caffeine, my brain and body refuse to function. To ensure a thorough supply with coffee throughout the day, I have one espresso machine at home, another at work and a filter coffee machine for guests. I am sharing my passion (and dependency) for coffee with the coffee rust fungus Hemileia vastatrix – an iconic pathogen that made the British drink tea instead of coffee.

(Very) Brief history of coffee culture and trade

Let’s go back in time.

In the early days, coffee was mainly used as medicine and food additive by North African tribes. Around the early 1500s, the Turkish and Arabians had got the hang of it and enjoyed their coffee in socially amiable coffeehouses. By the early 17th century, Europeans got hooked on coffee. Coffeehouses had sprung up in all major cities of Europe and had become popular places to meet, enjoy coffee and discuss philosophy, religion, and politics.

Some smart Dutch businessmen saw their opportunity and began to invest in and trade coffee. They grew coffee in their colonies beginning in Ceylon in 1658. In 1796, control of Ceylon was handed over to the British and British colonials began to clear the Ceylon rain forest to establish coffee plantations. By the 1870s, Ceylon’s plantations were exporting nearly 100 million pounds of coffee a year, most of it to England. For a few decades, Ceylon was the world’s top coffee producer.

Coffee Berries and Flower. © Sarah Maria Schmidt

Coffee Berries and Flower. © Sarah Maria Schmidt

The coffee rust fungus – a perfect parasite

In 1869, the coffee rust fungus Hemileia vastatrix (named for the unusual shape of its spores: smooth on one side, roughened on the other) entered the stage in Ceylon. Coffee rust infections occur on the coffee leaves. The first symptoms are small, pale yellow spots on the upper leaf surface. As these spots grow, masses of orange uredospores (~400.000 per spot) appear on the leave undersurface. The spores germinate on the humid leaf surface and the fungus enters the plant tissue through natural openings. Inside the leaf, the rust fungus forms an intimate connection with the coffee plant by growing a feeding structure – called haustorium – within the living plant cell. Via the haustorium, the rust fungus absorbs its food from the coffee plant – without killing its host. When all the nutrients are sucked out, the infected leaves prematurely fall off and eventually the tree dies, often before it can produce coffee berries. The fallen leaves are still full of fungal spores.Rust fungi produce spores in huge amounts. One orange spot contains more than 400.000 uredospores. This means that a single, heavily infected coffee plant can produce millions of infectious spores, which are blown by the wind to other coffee plants.

Coffee Rust. © Sarah Maria Schmidt

Coffee Rust. © Sarah Maria Schmidt

Coffee rust turned Ceylon into a country of tea growers

After Hemileia’s arrival on Ceylon, annual coffee harvests in Ceylon plummeted. Many coffee growers were ruined. Former coffee plantations were left to rot. A few far-sighted growers recognized that the plantations could be turned over to tea-growing. One of them was the Scotsman Thomas Lipton, who purchased five ex-coffee plantations in 1890 to grow tea, which he sold in his grocery chains. He was the first to sell tea in boxed small quantities to make it available for everyone. Ever since the raging of coffee rust, Ceylon is known as the exporter of the world’s finest teas.

Tea that the British like to enjoy in the morning, afternoon and evening. Instead of a delicious cup of coffee! 1


1 Some people claim that it was not coffee rust, but the bad quality of the Ceylon coffee that turned the English into tea drinker.

Sources:; The Triumph of the Fungi. A rotten history. Nicholas P. Money. Oxford University Press. 2007.


Cereal Killer: Stem Rust Threatens World Wheat Supply

Wheat stem rust (Puccinia graminis f. sp. tritici) has caused devastating epidemics of wheat in the history of mankind. It can destroy entire wheat harvests – leaving nothing but black stems and shrivelled grains. Currently, a new variety, Ug99, is spreading from Africa towards Central and South Asia, where 20% of the world’s wheat is produced.

Last MEMF blog’s entry was about Norman Borlaug, who saved millions of lives by developing high-yielding and stem-rust resistant wheat cultivars that spurred the Green Revolution. This blog will focus on the pathogen that he was fighting: stem rust.


Stem rust plagues wheat and threatens our daily bread

Stem rust is such a devastating disease, because it attacks the crop that is most intimately connected with human civilization: wheat. Without the cultivation of cereals by hunter-gatherers in the Fertile Crescent, there would have been no civilization. Today, wheat is cultivated on 25% of the global arable land. After rice, it is the second most important grain crop of the world and accounts for one fifth of humanity’s calorie intake (rice has a similar share, all other foods combined account for the rest). From South Asia through to Central Asia across the Middle East and on to North Africa, wheat is a staple food (meaning the main dietary component). Can you imagine the Italians without pasta, North Africans without couscous, Indians without Chapatis or the Lederhosen-wearing inhabitants of Bavaria without Weissbier?

Next to these traditional wheat-eating (and drinking) regions, some 40 million tons of wheat are imported every year to Sub-Saharan countries. Wheat used to be a minor crop there, but nowadays it is important crop for Sub-Saharan food security.

The over-complicated life cycle of stem rust fungi

The first symptoms of stem rust are beautiful -from my very personal point of view. Bright-orange, “rusty” pustules occur on the wheat leaf surface and stems containing up to 350.000 urediniospores. Urediniospores are asexual spores. Asexual means that the spores are genetically identical clones of one another. If the conditions are favourable (Stem rust likes it hot and humid.), the fungus produces so many urediniospores that they form huge orange clouds above the fields and quickly infect every single plant. The spores are dispersed by the wind and can infect wheat plants that are grown thousands of miles away.

Currently, this asexual life cycle (read: No Sex!) of stem rust is the most important. This is due to large-scale eradication of a horny bush named barberry. Wondering what barberry has to do with a disease of wheat?

This question leads us to the complicated life cycle of rust fungi – one of the most complicated ones on earth. If you think that your (sex) life is complicated, you don’t want to be a rust fungus. Next to the clonal urediniospores, stem rust also mates on wheat and produces black teliospores. Teliospores are sexual spores. In other words, they are new varieties emerged from the recombination of their parents’ genetic material. The stem rust’s children, if you want.

Teliospores cannot infect wheat. They infect barberry – as an alternative host. On the barberry plant, the stem rust fungus celebrates a bacchanal, producing at first small clusters of pycnia that excude pycnidiospores a sticky honeydew. The honeydew attracts insects, which will carry the pycnidiospores to other parts of the barberry plant where they mate again and grow through to the lower leave surface to release dikaryotic aeciospores. Like the teliospores, aecsiopores are not able to infect the plant on which they are produced. Instead they are disseminated by wind and rain to young wheat plants and start the infection cycle as new genetic varieties all over again.


Yes, you counted correctly! Stem rust produces four different kinds of spores on two different plants. It took scientists decades to put together the pieces of this complicated lifecycle (If you got lost, there is a cute animation about the rust lifecycle.). Anton de Bary finally succeeded in 1860. The sexual life cycle of stem rust involving the telio -, pycnio- and aeciospores does not play a big role in stem rust infections in Europe and the US. Farmers early on recognized the vicious connection between barberry and stem rust infections leading to large-scale barberry eradication program in Europe and the US in the early 20th century. However, the new variety from Africa, Ug99, might have evolved on a barberry plant.

Rust never sleeps – Ug99 is on a deadly trail towards Europe and Asia

So, what is Ug99?

Ug99 – Ug for its country of origin, 99 for the year it was confirmed – is a highly aggressive strain from Uganda that overcame most wheat resistance genes. It was Norman Borlaug, the Father of the Green Revolution, who had created most of the stem-rust resistant wheat varieties. His masterpiece was a complicated cross-hybridization of a segment from a rye chromosome into wheat. This chromosome segment not only contained resistance genes to stem rust – among them the durable Sr31 gene -, but also genes that increased grain yields. This made the new cultivars quickly popular in the whole world. They were so effective that stem rust declined to almost insignificant levels everywhere by the mid-1990s.

Until Ug99 entered the stage! Ug99 can overcome more wheat resistance genes, including Sr31, than any other stem rust variety before. The fungus changes rapidly by single step mutations and already consists of seven varieties with different virulence patterns. It spreads quickly through Africa and the Arabian Peninsula. In 2004, it spread from Uganda to Kenya, and then to Ethiopia and southern Sudan causing up to 80% yield loss in Kenya and Uganda. In 2007, Ug99 jumped the Red Sea and is now widespread in Yemen and Iran. So far, Ug99 did not arrive in one the major wheat producing countries: China, India, the US and Russia. If it does, our daily bread is threatened: 80-90% of the global wheat cultivars are susceptible to Ug99.


What do scientists do? Concerted effort – the Borlaug Global Rust Initiative

Norman Borlaug was immediately alarmed when he learned about Ug99. At the age of 91, he took up the fight against stem rust once again. By 2005, he had drummed up an international consortium of scientists from CIMMYT, ICARDA, FAO and the ARS of the US Department of Agriculture – the Borlaug Global Rust Initiative. Coordinated by Cornell University the BGRI concentrated efforts on developing and deploying new effective resistance of wheat stem rust by stacking four or five resistant genes. So far, the researchers produced 60 experimental wheat varieties. The new wheats have only one drawback: lower yield (the opposite of Borlaug’s wheat varieties).

Lower yields make their use unpopular in countries where Ug99 has not yet arrived – including the major wheat producers. Thus, the threat of wheat stem rust prevails! As Borlaug said: “Rust never sleeps.”


Sources: FAOstats;; Schumann, G.L. and K.J. Leonard. 2000. Stem rust of wheat (black rust). The Plant Health Instructor. DOI: 10.1094/PHI-I-2000-0721-01. Updated 2011.