Soil health, soil biology, soilborne diseases and sustainable agriculture

Author: Graham Stirling | Date: 23 Feb 2016

Take home message

  • Healthy soils contain a myriad of beneficial organisms that suppress soilborne pathogens through competition for habitat and food; production of antibiotics and toxins; or via predation or parasitism.
  • Organic carbon is the single most important soil health indicator. Increases in soil organic carbon (particularly biologically-available forms) are intimately linked to the size, composition and activity of the soil microbial community; enhanced retention and cycling of nutrients; improved aggregate stability; and increased water-holding capacity.
  • Key management practices to promote healthy soils are continuous inputs of organic matter; permanent plant residue cover; a diverse rotation sequence; minimum tillage; and avoidance of compaction through traffic control.
  • Once good farming systems are in place, incremental improvements can be made through cover crops and legumes in the rotation; integration of crop and livestock production; organic amendments and mulches; improved nutrient-use efficiency; optimised water management; site-specific management of inputs and integrated pest management.
  • Pastures can play an important role in improving soil health, reducing losses from soilborne diseases, and managing risk in Australia’s broadacre cropping systems. There are many benefits to be gained by integrating crop and animal production, but the extent of the gains will be determined by the level of management inputs and the skill and passion of the land manager.
  • While livestock may be detrimental to soil health, negative impacts can largely be overcome with best-practice management:  grazing must be carefully monitored to maintain soil cover (at least 50-70%); rotational grazing can assist to more evenly distribute nutrient returns across a paddock and minimise soil compaction from grazing; and another option is to convert the herbage from pastures into hay or silage and use it to feed animals off-site.


Our capacity to feed the world’s ever-increasing human population is dependent on the thin layer of soil covering the earth’s surface. It not only provides a physical support for plants but also filters water, detoxifies pollutants and provides a home for a huge range of beneficial organisms that decompose organic matter, supply nutrients to plants and compete with the fungal, bacterial and nematode pathogens that cause disease. However, this non-renewable resource is continually subject to water and wind erosion, is further degraded by compaction and tillage, is rendered unproductive by salinisation and desertification, and is easily ruined by mismanagement.

This paper explains the inextricable link between soil health and sustainable agriculture - agriculture can only survive in the long-term if soils are farmed in ways that not only repair historical damage but also improve their physical, chemical and biological properties. It argues that a soil cannot be considered healthy unless it contains an active and diverse soil biological community and then goes on to provide a list of the management practices that can be used to improve a soil’s biological status. These and many other topics are covered in much greater detail in a new publication, ‘Soil health, soil biology, soilborne diseases and sustainable agriculture. A guide’, details for which can be found at the end of the paper.

Organisms in the soil food web and their function

A teaspoon of a fertile agricultural soil will contain tens of millions of bacterial cells, more than 10 km of fungal hyphae, thousands of protozoa, hundreds of nematodes and numerous insects, mites and small animals. Some of these organisms will damage the roots of plants but the main role of the soil biological community is to provide the following ecosystem services:

  • improve the soil’s structural characteristics
  • fix nitrogen from the atmosphere
  • help plant roots take up water and nutrients
  • minimise losses of nutrients to the environment
  • mineralise nutrients from organic matter
  • degrade pollutants, pesticides and other contaminants
  • produce compounds that promote plant growth
  • protect plants from attack by pests and pathogens

Unfortunately, some of the organisms that provide these services have disappeared from our agricultural soils.  Thus, many soils now retain water and nutrients less efficiently and are affected by structural problems such as hard setting and surface sealing. Also, pests and pathogens rather than beneficial organisms tend to dominate the soil biological community, and this means that crops often fail to reach their yield potential.

The key role of carbon in maintaining soil health and sustaining the soil biological community

One of the main reasons growers face root disease and soil health problems is that the amount of organic matter in their soil has declined to unacceptable levels.  Since the carbon in soil organic matter stabilises soil structure, promotes aggregation of mineral particles, increases water infiltration rates, improves water holding capacity, stores and releases nutrients and contributes to cation exchange, it has a huge impact on soil properties. It is also important from a biological perspective, as it nourishes the organisms that cycle nutrients and compete with pests and pathogens.

In agriculture, organic carbon is obtained from four sources:

1) crop residues that accumulate on the soil surface

2) root exudates and the decomposing remains of old roots

3) manure from grazing animals

4) amendments such as compost that are imported from elsewhere. 

Although organic inputs to soil should ideally come from a range of sources, the above sources all play a vital role, individually and collectively, in sustaining the soil food web. Bacteria and fungi multiply rapidly when a new food source becomes available and they commence the decomposition process. A myriad of litter transformers and ecosystem engineers (arthropods, earthworms and enchytraeids) then break up this material and incorporate it into soil, increasing the rate of decomposition. Provided carbon inputs are regular and the decomposition process is allowed to proceed unhindered, the end result is higher soil carbon levels and an active and diverse biological community capable of providing a huge range of benefits (see the figure below).

Figure 1. Impacts of soil organic matter on soil properties

Figure 1. Impacts of soil organic matter on soil properties

Impact of natural enemies on soilborne pathogens

The fungi, bacteria and nematodes that cause soilborne diseases do not exist in isolation. They live in a complex and dynamic environment and are associated with an enormous number of other organisms that interact with them in many different ways.

  • Competition.  This is a universal phenomenon within the soil food web, as a huge range of microbes and small animals are continually competing for habitable space, or for food sources. When a competing soil organism accesses a resource before it can be acquired by a pathogen (e.g. it utilises root exudates that may be required to stimulate spore germination or enhance the infection process), it diminishes the capacity of the pathogen to cause disease.
  • Antibiosis. Many soil bacteria and fungi produce soluble or volatile antibiotics that kill, inhibit or repel other organisms. These antibiotics may act against plant pathogens, with one of the best-studied examples being suppression of the take-all pathogen of cereals by a group of antibiotic-producing bacteria known as the fluorescent pseudomonads.
  • Toxin production and lysis. Some soil organisms produce toxins that immobilise or kill neighbouring organisms, while others produce enzymes that digest the cell wall or cuticle of their prey.  Both these mechanisms are thought to contribute to the biological control of soilborne fungal pathogens.
  • Predation. This occurs when one organism (the prey) is killed by another, often larger, organism (the predator). Protozoans, nematodes and microarthropods all have the capacity to consume other soil organisms. Some predators feed indiscriminately on a wide range of organisms while others have quite specific food preferences.
  • Parasitism.  Parasites are highly adapted species that live in or on another organism (the host) and obtain all or part of their nutritional resources from that host.  Bacteria and viruses are known to parasitize protozoans and nematodes, but fungi are probably the most important parasitic organisms in soil. Numerous fungal parasites of arthropods and nematodes are known, and mycoparasitism (parasitism of one fungus by another) is also relatively common.

In a healthy soil, all the above mechanisms will be operating, and this means that the soil has some capacity to suppress the pathogens that cause disease.  The most common form of disease suppression (usually referred to as 'general’, ‘non-specific’ or ‘organic matter-mediated’ suppression) is most likely to be observed in soils with high levels of organic matter. Numerous organisms are involved, and they act collectively through the mechanisms listed above.

A second form of disease suppression (usually known as ‘specific’ suppression) results from the activities of a limited number of relatively specific antagonists, and typically develops in situations where pest populations have remained high for some time. Parasites that are adapted to using the pest as a food source take advantage of the situation and multiply rapidly, causing high levels of mortality.

Enhancing suppression of soilborne diseases in grain crops

Rhizoctonia is an important pathogen of Australian cereal crops, but on-farm observations in South Australia over the last 30 years have shown that when the soil is managed appropriately, naturally-occurring antagonists will keep it under control. Although the organisms responsible for suppressing the disease have not been identified, recent studies using DNA-based techniques have shown that the bacterial and fungal communities in disease- suppressive and non-suppressive soils are quite different. A range of bacterial taxa and several groups of fungi known to exhibit antifungal activity are found in higher frequencies in suppressive soils.  What is clear from this work is that disease suppression is not due to a single microbial group. It almost certainly involves many different biocontrol microbes and it is likely that they interact synergistically to suppress the pathogen.

Field and glasshouse trials have shown that soils become suppressive to Rhizoctonia root rot when practices such as cultivation and stubble burning are removed from the farming system and replaced with full stubble retention, limited grazing, more frequent cropping, limited or no cultivation and nutrient inputs that are sufficient to meet crop demand. Thus, a combination of practices that increase inputs of biologically available carbon are required to enhance levels of disease suppression.

Another example of general disease suppression occurs in the northern grain-growing region, this time against root lesion nematode (Pratylenchus thornei), a widely distributed pest.  Nematode population densities are particularly high at depths below about 25 cm but are usually much lower in surface soils, partly because organic carbon levels in this zone are high enough to support a diverse range of natural enemies, including nematode trapping fungi and predatory nematodes.  The challenge of the future is to increase soil carbon levels down the soil profile, thereby enhancing predatory activity at depth.

The best known Australian example of specific disease suppression is the natural control of root-knot nematode (Meloidogyne spp.) on grapevines by a bacterial parasite (Pasteuria penetrans). A closely related species of this bacterium has been found on root-lesion nematodes in the northern grain-growing region. Although levels of parasitism are relatively low at present, the proportion of parasitised nematodes is expected to increase with time, provided the host-parasite relationship is not disturbed by tillage. However, continuing research is required to determine whether Pasteuria will eventually provide some control of this important pest.

Improving soil health in grain farming systems

If an agricultural soil is to provide a full range of ecosystem services, the following crop and soil management practices must be integrated into the farming system. Benefits will be limited if only some of these practices are adopted.

  • Continuous inputs of organic matter
  • Permanent plant residue cover
  • A diverse rotation sequence
  • Minimum tillage
  • Avoidance of compaction through traffic control.

Once the above practices are integrated into a farming system, incremental improvements can then be made by focusing on the following:

  • Biomass-producing cover crops
  • Inclusion of legumes in the rotation
  • Integration of crop and livestock production
  • Organic amendments and mulches
  • Improved nutrient-use efficiency
  • Optimised water management
  • Site-specific management of inputs
  • Integrated pest management.

Although the practices listed above provide farmers with a range of management options, the actual practices that can be integrated into a farming system will be influenced by climatic factors, production goals and the economic realities of farming. Thus, it is impossible to be prescriptive about best-practice farming systems to improve soil health. Many potentially useful technologies and practices are available, and it is up to the land manager to adapt them to local conditions and constraints.

Pastures as a tool to improve soil health in grain cropping systems

One of the most effective ways of increasing levels of soil organic matter and improving the health of soils used for cropping is to integrate a pasture phase into the farming system. Carbon inputs into the soil will increase under pasture, as perennial plants have a higher root to shoot biomass ratio than annual crops, and grow for a longer proportion of the year. Because pasture soils are not regularly disturbed by tillage implements, this carbon tends to remain in the soil rather than being lost to the atmosphere as CO2.

Although research has shown that pastures increase soil microbial biomass and enhance biodiversity, it is important to recognise that the livestock which graze them may impact negatively on soil health. Their most important effects are listed below.

  • Soil structural degradation. Trampling by sheep and cattle can impact negatively on soil structure. However, compaction effects are mainly limited to the upper 15 cm of soil and tend to be concentrated in animal traffic areas such as gateways, camps, and around troughs. Recent research indicates that crops which follow a well-managed pasture are usually not markedly affected by the shallow surface compaction caused by livestock.
  • Ground cover and soil erosion. Livestock contribute to soil erosion by removing ground cover and loosening the soil surface, so stocking rates need to be carefully managed.
  • Drying of the soil profile. In rain-limited environments, pasture will utilise stored soil water that could otherwise be used by the following crop.
  • Spatial relocation of nutrients. Grazing animals excrete most of the nutrients ingested from pasture, but in the absence of appropriate management, they tend to be concentrated in stock camps and/or lost from urine patches.
  • Redistribution of weed seeds. Livestock spread weed seeds when they graze, and bury them by trampling.

The conclusion that can be drawn from the points made above is that livestock may be detrimental to soil health, but their negative impacts can largely be overcome with best-practice management.  Grazing must be carefully monitored so that a minimum level of soil cover (at least 50-70%) is always maintained, while practices such as rotational grazing can be used to more evenly distribute nutrient returns across a paddock, and to minimise the soil compaction effects of grazing animals. Another option is to convert the herbage from pastures into hay or silage and use it to feed animals off-site.

The take-home message is that pastures can play an important role in improving soil health, reducing losses from soilborne diseases, and managing risk in Australia’s broadacre cropping systems. There are many benefits to be gained by integrating crop and animal production, but the extent of the gains will be determined by the level of management inputs and the skill and passion of the land manager.

Further reading and information

A new book targeted to growers and advisers explains how to build an active and diverse soil biological community capable of improving soil structure, enhancing plant nutrient uptake and reducing losses from soilborne diseases. Written by soil biologists with experience in a wide range of farming systems, the book cited below provides an overview of the management practices that can be used to restore the health of agricultural soils, enhance plant resilience to stress and improve profitability and sustainability.

Stirling GR, Hayden, HL, Pattison AB, Stirling AM (2016) Soil health, soil biology, soilborne diseases and sustainable agriculture. A guide. CSIRO Publishing, Melbourne. 280 pp. ISBN 9781486303045

Contact details

Dr Graham Stirling
Biological Crop Protection Pty. Ltd.
3601 Moggill Road, Moggill, QLD, 4070
Ph: 07 3202 7419
Mb: 0412 083 489