Pursuing the mystery of disease-suppressive soils

Disease-suppressive soils have been identified in all grain production regions of Australia. The GRDC is funding a suite of projects to identify and harness the biological traits associated with suppressive soils

Growers fortunate enough to have soils that can withstand crop damage in the presence of disease know just how useful this soil characteristic is. But the mechanisms of disease suppression are still largely a mystery.

Managing soils to enhance disease suppressiveness would be a major step forward in agronomy, so the GRDC is funding several projects to further the industry’s understanding of this valuable natural phenomenon.

One of the main aims of the research is to find ‘signatures’ of disease-suppressive communities among soil microorganisms and develop biomarkers. The project involves collaboration among CSIRO, the Victorian Department of Environment and Primary Industries (DEPI) and the Queensland Department of Agriculture, Fisheries and Forestry (DAFF).

Photo of Helen Hayden

Victorian DEPI research scientist Helen Hayden
at work in a non-suppressive site at Avon,
South Australia.

PHOTO: Claire Allen, Victorian DEPI

By investigating the genetic composition of these communities, researchers hope to assess the impact of various farming system management practices and to develop an integrated approach to disease control.

Project 1

Biological suppression of root lesion nematodes

Queensland DAFF senior microbiologist Nikki Seymour is examining the biological suppression and control of root lesion nematodes (Pratylenchus thornei and P. neglectus). Root lesion nematodes cost Australian growers more than $250 million a year and are a particular problem in the northern grains region.

Existing control relies on an integrated management program that includes the use of tolerant or resistant varieties, crop rotation and good farm hygiene. Even then, cost impact on production can be high. 

However, studies have consistently shown that suppressiveness to root lesion nematodes does exist in a variety of soils. 

Suppressiveness has also been examined at different depths in the soil profile. Nematode populations tend to be highest at depths of 30 to 60 centimetres.

Soil from 0 to 15cm is much more suppressive than soil from 30 to 45cm.

More than 100 northern region soils have been surveyed for the presence of natural enemies of root lesion nematodes (Pasteuria bacteria, nematode-trapping fungi and predatory nematodes). 

This project is looking to identify the key organisms involved in the suppression of root lesion nematodes and which soils might best support these organisms.

Project 2

Microbial fingerprinting using ‘-omics’ technology

All soils can suppress soil-borne root diseases to some extent through the activity of soil microbes. However, this ability may occur on a scale from highly suppressive to poorly suppressive, making it difficult to identify the traits responsible.

This project aims to apply measures based upon ‘-omics’ technologies to examine disease-suppressive soils for the fungal pathogen Rhizoctonia solani.

Photo of a wheat crop

A characteristic bare patch in a wheat crop caused by Rhizoctonia solani in a non-sprressive soil in Avon, South Australia.

PHOTO: Helen Hayden

Soils samples were collected from sites at Avon in South Australia and around Salmon Gums in Western Australia.

Mechanisms of disease suppression are identified using RNA sequencing technology to examine the genes that are switched on in suppressive and non-suppressive soils prior to sowing and six to eight weeks after sowing, when young plants can be infected by R. solani.

Photo of wheat plant samples taken at seven weeks old with Rhizoctonia solani-infected roots.

Wheat plant samples taken at seven weeks old with Rhizoctonia solani-infected roots. The root systems are stunted and have brown spear tips that are characteristic of the disease.

The team uses proteomics* and metabolomics** to look at which genes give rise to proteins and the metabolites they produce within cells and are released into the soil.

Victorian DEPI research scientist Helen Hayden says: “We are interested in finding things that are only in suppressive soils that may have a role in blocking Rhizoctonia from infecting wheat and barley plants.”

Project 3

Molecular approach to microbial communities

An array of microbial communities can be involved in disease suppression in the field.

This project aims to:

  • characterise disease-suppressive communities in detail using high-throughput DNA sequencing techniques; and
  • identify the ecosystem features that can support disease suppression in cereal-growing regions of southern and eastern Australia.

Results from DNA sequencing indicated a diverse fungal community (917 distinguishable species) and measurable differences between suppressive and non-suppressive communities.

Most of the differences associated with suppressive soils were narrowed to fewer than 40 species.

This research is the first step in developing ‘microbial signature profiles’ for disease-suppressive communities to identify and monitor their dynamics in field soils.

Vadakattu Gupta, principal research scientist at CSIRO Adelaide, says: “The molecular component of the research is undertaken at sites in SA, where researchers have detailed information on disease suppression in different seasons.

“Disease-suppressive soils are mainly found under management systems that supply higher levels of biologically available organic carbon, which supports the activities of disease-suppressive communities.”

More information:

Pauline Mele, Victorian DEPI,
03 9032 7083,

* A proteome is the entire complement of proteins that can be expressed by a cell, tissue or organism. Proteomics is the study of proteomes and their functions.
** A metabolite is a substance formed in or necessary for metabolism. Metabolomics is the study of the set of metabolites within an organism, cell or tissue.


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GRDC Project Code CSP00135, DAQ00164, DAV00105, DAW00201

Region North, South, West