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Coffee-killing fungus has acquired genes from its relatives

In a new study from Imperial College London, experts have brought a 70-year-old fungus back to life to understand more about coffee wilt disease. The researchers re-animated cryogenically frozen samples of the fungus to investigate how the disease evolved and how to prevent it from spreading.

The fungus associated with coffee wilt disease has been causing devastating outbreaks in sub-Saharan Africa since the 1920s. It currently affects two of Africa’s most popular types of coffee, Arabica and Robusta.

The new study reveals that the fungus enhanced its ability to infect coffee plants by acquiring genes from a related fungus that causes wilt disease in other crops, including Panama disease in bananas.

According to the researchers, this discovery could help farmers reduce the risk of emerging new disease strains. For example, coffee beans could be planted separately from other crops. Farmers could also work to prevent the build-up of plant debris that may harbor the fungus.

In collaboration with the University of Oxford and the agricultural not-for-profit CABI, the experts report that studying historical samples in CABI’s culture collection could provide a wealth of insights into how crop diseases evolve and help to find new, sustainable ways to fight them. 

“Using ever-higher volumes of chemicals and fungicides to fight emerging crop diseases is neither sustainable nor affordable for many growers,” said study first author Lily Peck.

“If we can instead understand how new types of diseases evolve, we can give growers the knowledge they need to reduce the risk of new diseases emerging in the first place.”

The coffee wilt fungus caused two serious outbreaks of the disease in the 1920s-1950s and the 1990s-2000s. The fungus also killed 55,000 Robusta coffee trees in Tanzania in 2011, destroying the equivalent of over 22 million cups of coffee.

Beginning in the 1920s, coffee wilt disease infected a wide range of varieties. After the disease was brought under control in the 1950s, it reemerged in the 1970s. Two separate disease populations have been identified – one specifically infects Arabica coffee in Ethiopia, and the other infects Robusta coffee in east and central Africa. 

For the current study, two fungal strains from the original outbreak were re-awakened in a secure lab at CABI. The team also activated two coffee-specific fungal strains, the most recent of which was frozen in 2003. Genetic testing was used to look for evidence of how the strains evolved to target specific types of coffee.

The experts discovered that the newer fungi have larger genomes than the earlier strains. They also identified genes that helped the fungi overcome plants’ defenses. The genes turned out to be very similar to those known from a different, closely related fungus that impacts over 120 different crops, including bananas in sub-Saharan Africa.

Strains of the banana-infecting fungus are known to be able to swap genes, but the potential transfer of their genes to a different species of fungi has not been seen before. 

The researchers noted that the two fungal species often live in close proximity on the roots of coffee and banana plants, and so it is possible that the coffee fungus gained these advantageous genes from its normally banana-based neighbor.

Coffee and bananas are often grown together, and coffee plants take advantage of the shade provided by the taller banana plants. The researchers said their findings suggest that growing crops with closely related diseases separately could reduce the possibility of new coffee-killing fungal strains evolving.

Currently in the lab, the researchers are using the re-animated strains to examine how the fungus infects coffee plants. The insights could be applied to different crop plants, where other closely related plant pathogens could make similar leaps and create new diseases. 

Going forward, the experts plan to replicate the study with other diseases stored in CABI’s collection, which includes 30,000 specimens collected over the past 100 years.

“The historical approach shows us what happens to a plant pathogen before and after a new outbreak of disease occurs. We can then study the mechanisms of evolution and improve predictions of how similar outbreaks could occur in the future,” said Professor Timothy Barraclough.

“Our aim is to replicate this study for many plant pathogens, eventually drawing up a ‘rule book’ of how pathogenicity evolves, helping us to prevent future outbreaks where possible.”

The study is published in the journal BMC Genomics.

By Chrissy Sexton, Staff Writer

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