Soil Biology and Molecular Diagnostics

The South Australian Research and Development Institute (SARDI) Soil Biology and Molecular Diagnostics science program has unique, world-leading expertise and infrastructure to develop and deliver DNA-based tests for quantification of fungal and nematode pathogens, weed seeds, beneficial soil microflora and plant roots in soil.

The technology developed by the group has been commercialised for grain growers in Australia as the PreDicta B Root Disease Test, which measures levels of a broad range of soil-borne pathogens of cereal and pulse crops.

The core technology has also been modified (PreDicta Pt) for use in horticulture to measure key soil-borne pathogens that impact on the potato and wine grape industries.

Dr Alan McKay leads this program, which has two subprograms:

  • Molecular Diagnostics
  • Soil Microbiology.

Subprograms and research focus

Molecular Diagnostics

We develop and deliver quantitative DNA tests for soil-borne organisms.

Current research includes the development of DNA tests for analysis of

  • free-living nematode communities
  • soil-borne pathogens of potatoes
  • stubble-borne pathogens.

Our work also focuses on:

  • the development of appropriate sampling strategies for soil-borne organisms and plant roots
  • robust and cost-effective sampling strategies are developed and validated for cereal root distribution and stubble-borne pathogens
  • investing significant effort to validate sampling strategies for cost-effective DNA quantification of phylloxera in vineyard soils to quantify place of production freedom
  • developing new fungicide technologies, including strategic placement, for the management of rhizoctonia and fusarium crown rot for the Australian grains industry.

The SARDI diagnostic laboratory has the capacity to extract DNA from samples (up to 500 g) of soil, sediments, plant root systems and other environmental samples. Comprehensive DNA extraction from environmental samples ensures accurate DNA amplification by quantitative PCR assays.

The laboratory is accredited to receive international samples, with appropriate permits, and can process up to 200 samples per day.

The laboratory is equipped with robotic pipetting stations and high-throughput real-time PCR capability.

Current and recently completed research projects include:

  • Molecular Diagnostic Centre for delivery of training and diagnostics for soil-borne disease management (Grains Research & Development Corporation)
  • DNA tests for nematode community analysis (Grains Research & Development Corporation)
  • DNA assays for stubble-borne pathogens of cereals (SA Grain Industry Trust Fund)
  • Diagnostic tests for soil-borne pathogens – international collaboration, part of the Australian Potato Research Program (Horticulture Innovation Australia)
  • Reducing the impact of the parasitic root lesion nematode on cereal crops (led by Lincoln University, New Zealand).
  • Sampling strategies for accurate, cost effective detection of phylloxera for quantifying area freedom status (led by Phylloxera and Grape Industry Board of SA, with Plant Biosecurity Cooperative Research Centre (CRC) and Australian Grape and Wine Authority).

Subprogram contact

Dr Alan Mckay
Phone: (08) 8429 2216

Soil Microbiology

Rhizobium symbiosis

SARDI scientists have extensive experience in the applied aspects of legume symbioses. In particular, the selection of inoculant strains and plant genotypes for improved nitrogen fixation in the field.

Current work in the program focuses on understanding the symbiotic limitations to the symbiotic performance of field pea in southern cropping systems.

Pasture soil-borne pathogens

We have completed several projects to:

  • understand disease constraints to pasture legumes
  • develop tolerant legume genotypes.
  • Medic lines developed with powdery mildew tolerance have demonstrated outstanding field performance and will likely lead to the release of a commercial cultivar.


Several projects are underway which evaluate bio-inoculants for control of soil-borne pathogens such as rhizoctonia and root lesion nematode in cereals. Work includes developing our understanding of the microbiology of disease suppressive soils in broadacre cropping systems.

Practical outcomes for industry

Our research has produced practical outcomes to industry including commercial inoculant strains for the pasture legumes serradella, lucerne and sulla, with further releases planned.

We have developed a range of laboratory, greenhouse and field methods, which are used with a high level of precision to understand symbiotic interactions between different legume species and the rhizobia present in most soils.

Our research team also curates a collection of more than 1,500 strains of root nodule bacteria. This collection is made available to legume agronomists across Australia.

Subprogram contact

Ross Ballard
Phone: (08) 8303 9388

Program Leader

Dr Alan McKay
Science Leader, Soil Biology and Diagnostics
SARDI Sustainable Systems
GPO Box 397 Adelaide SA 5001
Phone: (08) 8429 2216

Page Last Reviewed: 04 Mar 2015
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