Soil borne diseases in Australian wheat and the use of PreDicta B, a testing service for soil samples


An interview with Dr. McKay of the South Australian Research and Development Institute (SARDI), Australia.

Basel, Switzerland
November, 2012


Dr. McKay

Dr. Alan McKay leads the soil biology and molecular diagnostics section of the South Australian Research and Development Institute (SARDI) and is involved in many projects related to the management of soil borne diseases. We spoke with Dr. McKay about his experience with soil borne diseases in Australia and PreDicta B, a DNA-based soil testing service that was developed by his team with the support of growers through the South Australian Grains Industry Trust and the Grains Research and Development Corporation.


Dr. McKay what would you say are the major soilborne pathogens in wheat that farmers are struggling with in Australia?

The two major pathogens that we struggled with in Australia – previously – are cereal cyst nematode and Take-all. Today, these pathogens rarely cause serious losses because of the adoption of good management strategies, which include use of non-host-crops (canola or pulse crops) and resistant varieties.


Now Rhizoctonia solani AG 8 is probably the main soil borne pathogen in our winter rainfall cereal zone. It is a big problem in the lower rainfall regions and seasons, especially in minimum-till systems. Growers tend to know which fields are affected; so, they are not inclined to test for it. However, the impact of Rhizoctonia has changed over the years as crops are sown earlier. Many growers are not necessarily recognizing some of the changed impact as being caused by Rhizoctonia. Other soil borne pathogens of concern include the root lesion nematodes Pratylenchus thornei and P neglectus.


Does crop rotation have an impact?

It was generally thought that rotation did not affect Rhizoctonia levels, however recent research involving CSIRO and SARDI, has shown that canola is useful to reduce Rhizoctonia. However, the effect only benefits the next crop – usually wheat, after which Rhizoctonia levels are again high.


Are there other anastomosis groups (AGs) relevant in Australia?

The most relevant AG in cereals is AG 8 (which is also a big problem in onions). AG 2-1 occasionally causes serious losses in canola and in some pulse crops.


What parameters impact the disease severity at a given level of Rhizoctonia in the soil at seeding?

Pathogen level alone is not the sole determinate of disease. Environment (soil type, rainfall, temperature, etc.) and soil microbial activity play a very important role as well.


The most serious damage caused by Rhizoctonia happens to seedlings when root development is slow due to cold soil or constrained by lack of moisture or compaction layers. Under these conditions, the typical bare patches will be visible in the field.


Many growers do not realise that the fungus can also attack crops during mid-to-late tillering, which causes uneven growth during winter. Crops that are sown early, while the soil is warm, often show no symptoms until mid-winter when soil temperatures drop below 10°C. Under these circumstances, it is mainly the crown roots which are attacked, which reduces tiller number and height (and causes the characteristic root spear tips). Many growers do not recognize the disease when this type of symptom is caused by Rhizoctonia because shallow soil and other conditions can cause similar symptoms. Still, Rhizoctonia damage at these stages can result in a yield loss of 10-20%.


Generally, Rhizoctonia AG 8 is well adapted to low rainfall conditions and soils with low biological activity, but it can occur in high rainfall regions as well. Recent research has shown that summer rainfall can reduce the Rhizoctonia AG8 inoculum when summer weeds are controlled. Frequent summer rainfall can reduce Rhizoctonia AG 8 to low levels until seeding. However, it can still cause problems in districts with long cold winters which slow root development.


What should a farmer consider to do in areas that are at higher risk levels for Rhizoctonia?

These management practices used in Australia:

  • sow early
  • cultivate below the seed to facilitate rapid root growth away from the Rhizoctonia
  • control summer weeds (they dry the soil which favours Rhizoctonia, plus grassy weeds can host Rhizoctonia)
  • plant canola in your rotation to reduce Rhizoctonia levels for the following wheat crop

New seed treatments under development for Australia should provide additional management tools. Work is also underway to evaluate banding these products at seeding, an approach that is also showing promise.


What is PreDicta B?

PreDicta B is a commercial service provided to farmers by SARDI that identifies the major soil borne pathogens which pose a significant risk to broadacre crops in Australia prior to seeding (B in PreDicta B=broadacre). The key strength of this DNA-based technology is that it can quantify a range of different organisms in a single sample. It is currently available for the soil borne pathogens Take All (Gaeumannomyces graminis var tritici (Ggt) and var avenae (Gga), Rhizoctonia bare patch (Rhizoctonia solani AG8), Crown rot (Fusarium pseudograminearum and Fusarium culmorum), Blackspot of peas (Mycosphaerella pinodes, Phoma medicaginis var pinodella and Phoma koolunga) and for Nematodes: cereal cyst nematode (CCN), root lesion nematode (Pratylenchus neglectus and thornei) and stem nematode (Ditylenchus dipsaci).


For the analysis 500 grams (g) of soil consisting of 45 soil cores (3 from 15 different spots per field to address spatial variability) are required to provide a good sensitivity and reliable results. The assays are very sensitive. For example, the test for CCN can detect one cyst in a 500 g soil sample. The service is delivered by agronomists who have been through a PreDicta B training course. These agronomists then use local knowledge to customize advice to their clients.


During the last ten years, we have trained more than 1400 agronomists throughout southern Australia. Our course covers the latest approaches to disease risk management, interpreting the DNA test results and sampling. It is upgraded regularly to assist agronomists in providing the latest advice to farmers who use the service.


How can this tool help growers manage soil borne diseases in their crops?

PreDicta B can help growers measure the soilborne pathogen levels in fields (or different production zones within fields) before sowing the crop. Soilborne pathogens levels are an important component of disease risk and this information is useful when making management decisions for the field.


PreDicta B was introduced in 1997. The range of tests has expanded over the years. It is respected by growers and consultants, but the number of soil samples submitted for testing has not grown much over the years (i.e. about 600 samples submitted a year from 300-400 farmers). The reason is probably that once the agronomists and farmers have tested a number of fields with different rotations, they often see patterns which they use to plan future rotations. However, this does not take into account the pathogen shifts which can occur with changes in management and growing seasons over time.


What has grown strongly over the years is the use of the technology in field trial research.


In what type of field trial research is PreDicta B mostly used?

The technology is being used in a wide range of field trials to evaluate how different management strategies and crop varieties can control a range of soil borne pathogens and plant parasitic nematodes. We are also using it to generate data to model soil borne disease risk across different cropping regions. In that case, we monitor the pathogens through different phases of the crop rotation (wheat, canola, barley etc.), as well as capture the soil type and weather data. The resulting data will be used to develop a model in which PreDicta B data may provide better disease risk assessments for a given field and location.


Another application is to assess the impact of new varieties on the different plant parasitic nematodes in the field. Most nematode resistance screening is done using controlled conditions in glasshouses or growth rooms. We are now starting to use the field trials established to assess the tolerance of a variety to the different nematodes, as well as to assess resistance (i.e. the effect on the nematode population). The different environments, seasons and regions in which these trails are conducted should enable us to give better variety recommendations for the different regions and nematode risk categories.


What challenges do you still face with this tool?

At this time, PreDicta B is probably most useful for growers where a single major pathogen is constraining yields, as it is hard to interpret the results of pathogen complexes. However, single major constraints to yield are becoming less common. Over the past 20 years, our cropping systems and varieties have improved. The ability to assess pathogen complexes is one of the aspects we are working on to improve our models.

Do you think that PreDicta B would work in other regions?

There are two things that need to be considered when using PreDicta B in new regions: First the specificity of the DNA tests was checked in our region but they may detect non-target species in other regions. Second, risk categories may also differ due to differences in environment and crop varieties etc. and need to be investigated before delivery to growers, which will take a few years.


For more information:

Rhizoctonia Fact Sheet (updated 2016) by the Grains Research and Development Corporation (GRDC) of the Australian Government Agricultural Department of Agriculture, Fisheries and Forestry that has been put together by Dr. Vadakattu Gupta with support of various Australian researchers including Alan McKay.



Dr. Alan McKay was interviewed by Dr. Melanie Goll, Technical Innovation Manager, Syngenta. Melanie holds a Ph.D. in plant pathology and focuses on seed treatment development, especially fungicides and nematicides.