The fastest and smuttiest CRC PhD project…

VANMEURSA — Mon, 20 Dec 2010 01:00:56 +0000

Alistair McTaggart, of Queensland’s Department of Employment, Economic Development and Innovation, has just completed his CRC PhD project through Queensland University of Technology. In landmark work, he has completely revised the taxonomy of three large genera of smut fungi, Ustilago, Sporisorium and Macalpinomyces. This project has important biosecurity implications as this group of fungi includes many economically important pathogens such as Ustilago maydis (boil smut of maize) and Sporisorium scitamineum (sugarcane smut).

While working on a PhD is complex and certainly not a race, at this stage, Alistair will have submitted his thesis in record time. He started his PhD on 1 January 2008 (hats off to him for starting on a public holiday), had his final seminar on 2 December 2010 and says he will be submitting his thesis for examination on 24 December 2010 (just in time to relax and enjoy Christmas). This makes his whole PhD project a total of two years, 11 months and 24 days to complete.

Alistair says he attributes this to having a well designed project with a lot of support from his supervisors and also from the CRC in terms of professional development and the opportunity to travel and enhance his research outcomes.

In an effort to continue to expand his knowledge in this area, he has already secured a post-doctoral position at Louisiana State University to work on the systematics of rust fungi and to construct a rust database. With his US visa sorted out, he’s looking to head over in early 2011, where Alistair says he is “looking forward to learning something new, buying a few guitars, listening to blues music, meeting some Southern women, eating some gumbo and rockin' plant pathology.”

Alistair also says he is a little sad to finish because “he’ll never get to work on something like that again”, which could leave readers with the question of what was his project about?

Once called the ‘insidious black harvest’, smut fungi infect commercially important plants such as wheat, and grasses more generally, to produce vast amounts of fine black spores. In addition to food security threats, the mere presence of spores in a shipment of grain can – and has – posed threats to Australia’s export trade.

While smut fungi are very host-specific – infecting a narrow range of grasses – the spores from different species tend to look the same under the microscope. That makes diagnostics difficult to all but the most accomplished mycologists.

Alistair says smuts form a huge taxonomic group containing more than 500 species. The morphological features used to classify smuts can create confusion, he says, and the current classification does not accommodate the vast diversity of smut species discovered over the years.

“It is my job to try and resolve this taxonomic muddle by finding natural groups for these smut fungi,” he says. “To detect the natural groupings we have been studying morphology and using DNA sequence data to trace relationships based on similarities and divergences that occurred during evolution.”

Of particular interest is a region of the smut genome that encodes ribosomal RNA – molecules required by the cell to make proteins. In this region is the so-called ITS (the internal transcribed spacer), a stretch of DNA that has been proposed as the ‘barcode’ for all fungal organisms.
Parts of the ITS are known to change rapidly during evolution since they do not encode anything vital for fungal survival. These regions eventually become idiosyncratic among fungi. But the ITS also contains sequences that are conserved among closely related smuts. This is useful for identifying groups or genera in phylogenetics studies.

Since the ITS can distinguish both groups and species, Alistair has sequenced the ITS region of all 80 smuts in his collections. “In my groupings, you can see smuts co-evolving with grasses at the tribe and sub-tribe taxonomic levels,” he says. “So smuts of cereals like wheat, oats, and barley that are closely related also have similar morphological characters. Smuts that occur on outback Spinifex grasses similarly form a closely related group.”

The CRC wish Alistair the best of luck during the thesis examination process and look forward to him returning to Australia with valuable training in how to identify exotic rusts, and to help keep Australia safe from the nasties!

Photo caption: Alistair McTaggart accepts his award for Best Student Poster at the 2009 Science Exchange.

Photo acknowledgement: Di Harris Photographic

Collection of smut fungi from northern Western Australia

VANMEURSA — Wed, 22 Jul 2009 01:51:19 +0000

More than 50 specimens of smut fungi were collected during a field trip to the Mitchell Plateau, Western Australia. These specimens will be incorporated into a phylogenetic study using morphological and molecular methods. Three taxa of smut fungi new to science were identified amongst the collection and these will be described in separate publications.

A 10 day fungal survey of the Mitchell Plateau and Kimberley region in northern Western Australia discovered a rich diversity of smut fungi and allowed many fresh specimens to be collected for DNA extraction and morphological analysis. The survey yielded 60 collections of diseased plant material, including 32 different smut taxa in ten genera. Several collections of rusts (Basidiomycota, Pucciniales), downy mildews (Oomycota, Sclerosporales) and ergots (Ascomycota, Hypocreales) were also made and lodged in the Queensland Primary Industries and Fisheries, Plant Pathology Herbarium (BRIP). DNA will be extracted from this material and stored in the Biosecurity Bank.

The smut specimens will be amplified at over five molecular loci from different regions of protein coding, mitochondrial and ribosomal DNA. This data will be combined with morphological data for an intensive phylogenetic analysis, attempting to resolve the taxonomy of the Ustilago/Sporisorium/Macalpinomyces complex of smut fungi, which includes several important plant pathogens such as Sugarcane smut (Ustilago scitaminea) and loose smut of Sorghum (Sporisorium cruentum). Molecular data will be used to help resolve the complicated taxonomy of these fungi as well as to design molecular probes for applications in diagnostic nanotechnology.

The collecting trip has substantially increased knowledge about the distribution of smut fungi in Australia, including the discovery of new endemic taxa. Understanding the biodiversity of all organisms in Australia is extremely important for quarantine and conservation.

CRC for Plant Biosecurity - McTaggart

The fastest and smuttiest CRC PhD project…

Collection of smut fungi from northern Western Australia