Australia
September 7, 2012
Source: GRDCs
Molecular tests routinely provide rapid and sensitive ways to quantify changes in populations of microorganisms in soil. Yet it is only 15 years since a team at the South Australian Research and Development Institute (SARDI), led by Dr Alan McKay and Dr Kathy Ophel-Keller, released the first DNA-based soil tests.
This group continues to lead the world in the development of molecular diagnostic tools for agriculture.
Initially these were promoted to grain growers, but it is as research tools that they have revolutionised practices and trial possibilities.
Prior to the launch of the ‘Root Disease Testing Service’ in 1997, there was no test to quantify the common root pathogen Rhizoctonia. A bioassay existed for take-all but required a skilled operator to score disease severity on plant roots.
“The bioassay took up to eight weeks to produce a result, each soil sample had to be tested separately and could only be used for one disease,” says Alan McKay.
The initial research in partnership with CSIRO identified DNA sequences unique to Rhizoctonia and to take-all. This provided the equivalent of a fingerprint for both pathogens, enabling them to be distinguished from the millions of other organisms in the soil.
The main breakthrough was the development of the high throughput system to extract DNA from large (500 gram) soil samples, with funding help from the SA Grains Industry Trust. With support from colleague Dr Herdina, a specialist in developing molecular tests, this system took three years to perfect.
In 1997, the Rhizoctonia and take-all tests were launched and made available to growers through fertiliser companies as an add-on to the existing soil nutrient testing services. In the first year 1100 soil samples were processed: “It nearly killed us,” recalls Dr McKay. Three years later, a commercial partner, C-Qentec, relaunched the service as PreDicta B.
“Originally, it took a week to run the assay. Today the equivalent part of the test takes two hours and 250 samples can be tested in a day and each for multiple diseases,” says Dr McKay.
The laboratory, based in Adelaide, now processes about 25,000 samples each year, the majority of which are for researchers.
Present and future
The number of tests developed has also increased, from the two in 1997 to more than 100. These are for a range of nematode and fungal pathogens as well as beneficial organisms.
Developing tests for beneficial soil organisms presents greater challenges than for pathogens, because they often work in complexes: “We are making progress, especially with mycorrhizal fungi and the disease suppressive organism Trichoderma,” Dr McKay says.
Another development is the use of DNA tests to identify air-borne pathogens present in a district from spores caught in a spore trap. From this research, funded by the National Plant Biosecurity CRC, it is expected that early warning systems for foliar disease could be developed. Without the DNA tests such a process would not be logistically or economically possible.
Nearly 60 research projects, mainly in the grains industry and across all cropping regions, are making use of these molecular tests delivered by SARDI. Many also use the tests to checkbackground pathogen levels in trial plots to ensure they are sufficiently ‘clean’ and that pathogens will not be influencing treatment outcomes.
Several trials supported by the GRDC demonstrate how the DNA-based soil tests enable researchers to quantify changes in soil pathogens in relation to treatments.
In the southern region, SARDI and DPI Victoria researchers are using the assays to assess the effects of different varieties on populations of cereal cyst nematode, Pratylenchus neglectus and P. thornei. In the northern region, NSW DPI and the Northern Grower Alliance are using the service to monitor variety effects on levels of P. thornei.
The scale of field trials being assessed would not be possible using the previous techniques that are based on extracting and counting the nematodes. The capacity of the DNA assays means the influence of season and soil type can also be brought into the analysis.
The southern region trials use paired plots of low and high nematode populations to assess how much yield each variety can potentially lose to each nematode species. These results will be used to classify the variety tolerance rating for each of the three nematodes and to determine how tolerance might vary between regions and seasons. It is hoped these trials will provide more useful information to growers on resistance and tolerance to these nematodes.
Demand for PreDicta B by growers has been limited. The main reason for this has been lack of confidence in interpreting the results in all regions. Dr Grant Poole (SARDI) has recently been employed on a GRDC project to develop disease risk categories for PreDicta B in the northern and western regions.
In the northern grains region the DNA assay for P. thornei has been calibrated in collaboration with Dr Stephen Neate and Dr Jason Sheedy, and a broader range of tests has been used to assess 248 focus paddocks in collaboration with Dr Steven Simpfendorfer at NSW DPI.
To calibrate the DNA tests in the western region, Dr Poole is working with Dr Martin Harries and the Plant Pathology group led by Bill McLeod (DAFWA) to establish relationships between pathogen DNA levels pre-sowing and root disease severity in more than 150 focus paddocks across WA over three seasons. The ultimate aim is to understand the relationship between pathogen level in the soil, environment and yield loss.
The paddocks represent a vast range of seasons, soil types and crop sequences. Soil samples are taken pre-sowing and plants are sampled at anthesis, a point where the relationship between root damage and crop loss has been found to be most highly correlated.
So far Dr Poole has shown that around 60 per cent of variation in root health at anthesis can be explained by a combination of historic temperature and rainfall data (which defines different districts), soil type and pre-sowing pathogen levels. The team is now working on the best way to incorporate annual seasonal data into the model. It is hoped this information can form the basis for a web-based regional decision support tool to help growers better understand the soil-borne disease risk in low, medium and high rainfall seasons in specific paddocks. This should minimise the risk of unexpected losses.
“This ability to predict yield loss from the test results has been the missing link. This new research will hopefully make the PreDicta B a much more useful decision support tool for growers and for researchers help provide more objective data on the drivers of root health,” Dr Poole says.
Species
