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« Goodness from the 2014 Winter School in Mathematical and Computational Biology | Main | R, the getting of wisdom* »
Tuesday
Jul152014

Fungi to die for

It’s easy to lose sight of the things that matter, especially if they are too small to see.

So heads-up humans! We—and most of the rest of the planet—would be dead without our fungal friends... (even though some can kill us).

Fungi are so important that Australian bioinformaticians and bioscientists are part of an international effort to identify friends and foes from fungal DNA or, more precisely, from the most widely sequenced DNA region in molecular ecology of fungi known as the Internal Transcribed Spacer (ITS).

The ITS region has been recommended as a “barcode” for fungal species, and the recently released “Warcup” dataset from Australian researchers helps translate this DNA information into species names.

Aspergillus... or maybe last week's consomméI know a fungus when I see one but...

...even though a honey mushroom is believed to be the largest living organism on earth, many species are microscopic (which is why we need to use DNA identification), and 90% of plants depend on them.

“It’s a common misconception that a plant uses its roots to gather nutrients—it’s really fungi that do all the work,” says mycologist Dr David Midgley from the Warcup team. “Bacteria are involved in liberating nutrients from soil, but they’re too small to move those nutrients around—that’s where fungi excel.”

“Current estimates suggest there may be over 5 million different species of fungi. So far less than 1 million have been described” says David. “Given that we’d be dead without them, I think it’s pretty wise to get to know fungi better.”

Enter Warcup

John ‘Jack’ Warcup (1921-98) was a New Zealand born mycologist who made a massive contribution to our understanding of fungi and the role they play in life on earth.

“We thought it would be an excellent way to raise awareness of Warcup’s research by naming the new fungal ITS dataset in his honour,” says bioinformatician Paul Greenfield.  The Warcup ITS dataset is now part of the highly regarded and widely used Ribosomal Database Project (RDP) and freely available to the fungal researchers throughout the world.

“We also want to raise awareness that Vinita Deshpande built this dataset as part of her honours thesis project at University of Sydney, with support from CSIRO,” says Paul.

“It’s been great to encourage and support the next generation of bioscientists to expand our understanding, as John Warcup did”.

Vinita was supervised by Paul Greenfield (CSIRO) and Michael Charleston (University of Sydney), in collaboration with CSIRO mycologists Nai Tran-Dinh and David Midgley.

 

Dr Midgley's fridge contentsWith friends like that, who needs enemies?

The vast majority of fungi are friends.

As well as sustaining plant life on earth, they give us antibiotics including penicillin, drugs such as cyclosporin and lovastatin and enzymes used in paper production, food processing and other industrial settings.

However, there are some killers at large. And not just the mushrooms and toadstools we can see and avoid.

Aflatoxin is the most potent natural liver carcinogen we know,” says Dr Nai Tran-Dinh. “It is produced by fungi called Aspergillus and, right now, there are about 5 billion people exposed to it at uncontrolled levels in their diets.”

While there are controls in Western world agricultural systems, the globalisation of food production makes aflatoxin an international issue.

“Aflatoxin affects crops like corn and peanuts, crops which are harvested, processed, and shipped worldwide for use in food products and feedstocks,” says Nai. “It’s to everyone’s benefit if we can understand, detect and manage Aspergillus better.”

Hidden benefits

...and that’s not the only benefit still to be realised.

“Fungi have huge potential in enhancing agricultural productivity, remediating environmental damage, even prospecting for new bioactive compounds,” says David Midgley.

“Building datasets like Warcup takes us closer to unlocking that potential.”