Assessing the impact and effective testing of root disease
Assessing the impact and effective testing of root disease
Take home messages
- Three key wheat soilborne diseases cost Australian growers an average of $38/ha, with these effects unevenly distributed between or within paddocks.
- Despite the substantial cost, soilborne diseases are often undiagnosed or misdiagnosed, and not often actively managed.
- Although difficult to manage, there are partially effective management options for all soilborne diseases which can be combined into an effective integrated disease management package that complements other aims, such as good weed control.
- Use Predicta® B to quantify disease inoculum level prior to sowing, or periodically to assess management strategy efficacy, and focus management on reducing inoculum levels.
Background
Key soilborne diseases, including crown rot, Rhizoctonia root rot and root lesion nematode, are estimated to cause Australian grain growers more than $500 million per annum in direct yield losses – an average loss of ~$38/ha over every paddock, every year. Of course, other cereals, as well as pulses and canola, also experience losses from root diseases. A new GRDC investment ‘Impact of root diseases on pulse crops in Northern and Southern regions’ is quantifying the losses in lentil, chickpea, faba bean and lupin.
Like all pest and management issues, soilborne disease losses are not distributed evenly between paddocks – some paddocks will experience much greater losses, while others may have very few issues at all. Seasonal conditions, as well as management decisions, also play a big role in determining the extent of losses year to year.
The potential for yield loss is strongly underpinned by the amount of inoculum present in the soil at sowing. This is because, unlike foliar diseases or insect pests, soilborne diseases move relatively little between paddocks or farms in any given season – the pathogen inoculum present in a paddock (or section of paddock) prior to sowing will likely determine risk of root disease.
Assessing inoculum presence and root disease risk is difficult. Root disease inoculum is often long lived in soil, which means it may survive a run of break crops or non-conducive seasons before returning in the host crop, or it may simply go unnoticed in the host crop even when present – root disease often goes unnoticed or is misdiagnosed as nutritional or other soil constraint issues (pH, salinity, waterlogging, etc.). However, having a basic understanding of the diseases that are common in a growing region or season, together with a simple crop inspection strategy and diagnostic support material, can ensure root diseases are identified in-season. Diagnostic support is available through SARDI.
For quantifying root disease risk out of season, SARDI’s Predicta B DNA-based soil testing service provides an invaluable window into what’s in the soil prior to sowing the next crop, and can be used to make management decisions, including the use of seed and soil applied fungicides, tillage, break crop or variety selection. Predicta B also offers growers an opportunity to track inoculum levels over several seasons, to evaluate management strategies over time.
The impact of soilborne diseases
Our best estimates of the yield impacts of soilborne diseases come from previous GRDC investments in crown rot and root lesion nematodes. Current projects are continuing to quantify yield losses from Rhizoctonia in cereals, as well as a range of soilborne diseases of pulses including lentil, faba bean, lupin and chickpea.
Cereals
Crown rot has grown in importance as a yield constraint, both nationally and within South Australia. In 2009, crown rot was estimated to cost Australian wheat growers $79 million per annum. The most recent update, based on an average annual yield loss of 6%, suggests this figure is now as high as $404 million per annum. In southern Australia, yield losses average 2–3% but can be as high as 20%. However, the yield losses associated with crown rot very much depend on season, and crop tolerance – hot, dry finishes tend to exacerbate yield loss. Crown rot is common across all soil types since inoculum is mostly associated with crown stubble rather than soil.
Rhizoctonia root rot has long been considered a major soilborne constraint in South Australia. It is particularly well-adapted to sandy soils and is rarely a problem on clay or clay loam soils. Drier environments also favour Rhizoctonia root rot, since pathogen inoculum is conserved better in drier conditions over summer, and the pathogen spreads easier in cool, dry winters where biological suppression is reduced. Yield loss studies conducted by SARDI over 20 years show a high degree of variability between seasons, ranging from 0–30% in wheat and barley.
New research is being conducted by SARDI to evaluate potential fungicide and biological controls for Rhizoctonia in wheat and barley. In 2023, field experiments at Minnipa and Pinery showed between 0–10% yield loss from Rhizoctonia (where the pathogen was deliberately added). Three fungicide seed treatments (not currently registered) were found to increase yield by ~0.4t/ha, or around 10%, but only in the higher yielding (~3.5t/ha) Pinery site. At Minnipa, where average yield was ~0.72t/ha, there was no effect of additional Rhizoctonia inoculum or of any seed treatment.
Pulses
New research into root diseases of pulses is showing that Rhizoctonia root rot can also affect lentil, with yield losses up to 50% measured at Loxton in 2023 and Pinery in 2024. At a low-yielding site at Loxton in 2023, yield was reduced by 50% under high pathogen inoculum levels. Fungicide treatments applied under high inoculum loads were not effective at improving yield, however they did improve establishment, which may have been beneficial under different seasonal conditions (Figure 1).
Figure 1. Yield (t/ha) of lentil either untreated and without Rhizoctonia (Control), with a high level of Rhizoctonia (High), medium Rhizoctonia (Med), liquid fungicide banded in furrow (Liquid fungicide), seed treated with P Pickel-T® fungicide (P_pickel) and seed treated with an off-label fungicide (Seed trt). While P Pickel-T® is registered for use in lentil for seedling root rot, it is not registered specifically for Rhizoctonia management. All fungicide treatments were applied to plots with a high level of inoculum. Standard error bars are shown and bars with different letters indicate significance differences (P<0.05).
While lentil is regarded as a break crop for Rhizoctonia and consistently shows a benefit to following cereal crops in reducing Rhizoctonia inoculum, growers should be aware that Rhizoctonia has the ability to affect all crops, and if lentil is sown into high inoculum loads after multiple cereal phases, they may suffer yield loss, even while providing break crop benefits.
Fusarium avenaceum (the causal agent of Fusarium root rot) also appears to be important in both lentil and faba bean. Field experiments conducted at Roseworthy in 2023 and Pinery in 2024 have demonstrated 60–79% yield loss in lentil, and 40–60% yield loss in faba bean, when grown under high inoculum conditions. The good news is that the experiments in 2024 (Figure 2, Figure 3) also highlighted that yield loss was reduced at lower inoculum levels, and a seed treatment (off label) was highly effective in reducing disease. SARDI’s Molecular Diagnostic Centre has developed a qPCR assay which can be used to test soil for the presence of this pathogen.
Figure 2. Lentil yield for two times of sowing: TOS1 (standard) and TOS2 (late), without Fusarium avenaceum – CC (uninoculated control), or with different pathogen levels and application methods – LR (low rate: 1g/m), MR (mid rate: 3g/m), HR (high rate: 5g/m), MS (mid rate + spore solution on seed), and MT (mid rate + seed treatment), at the Pinery 2024. Standard error bars are shown and bars with different letters indicate significance differences (P<0.05). Yield is the ‘Predicted Yield’ following an ASREML statistical analysis.
Figure 3. Faba bean yield for two times of sowing: TOS1 (standard) and TOS2 (late), without Fusarium avenaceum – CC (uninoculated control), or with different pathogen levels and application methods – LR (low rate: 1g/m), MR (mid rate: 3g/m), HR (high rate: 5g/m), MS (mid rate + spore solution on seed), and MT (mid rate + seed treatment), at the Pinery 2024. Standard error bars are shown and bars with different letters indicate significance differences (P<0.05). Yield is the ‘Predicted Yield’ following an ASREML statistical analysis.
Soilborne disease management for 2025
Across South Australia, 2024 was one of the driest seasons on record. Autumn had a uniformly low rainfall, followed by a well-below average winter rainfall, perhaps apart from parts of the upper south-east and Eyre Peninsula. Spring conditions were also poor. We are all happy to say goodbye to 2024, however these conditions influence root disease risk heading into 2025 (Table 1).
Table 1: Summary of what to expect and why in 2025.
Disease | 2024 effect - inoculum build up | Summer effect | 2025 opening rain effect |
---|---|---|---|
Crown rot | Likely minimal new infection due to dry winter – regions like the SE an exception. Where infection occurred, spring favoured build-up of inoculum. But most inoculum remains in stubble from 2022–23. | No stubble breakdown = no inoculum breakdown | Early rain will start the breakdown of stubble inoculum, but not enough to reduce risk for 2025. Avoid excessive N application to early sown crops with high crown rot risk. |
Rhizoctonia | Likely large increases in inoculum, especially under barley and wheat on sandy soils. | Inoculum is conserved on organic matter with little run down of inoculum | An early break will allow crops to establish before Rhizo ramps up – sow high risk cereal paddocks early. Later sown crops may benefit from a seed or soil fungicide for Rhizoctonia. |
Take-all | Likely limited infection in all but cereals grown in parts of the south east and EP. Mostly reduction in inoculum. | Any inoculum likely conserved as dry summer means very little antagonistic biological activity. | Take-all is unlikely to be an issue in 2025, except in areas that still had reasonable rainfall in 2024. If there’s an early deluge, these areas may still have take-all issues. Critical to control early weeds in these paddocks well before sowing. |
Root lesion nematode | Reduction in inoculum or maintenance of levels at worst. | Dry summer likely to conserve nematodes | An early break and good moisture will allow early infection and reproduction of RLN, which can have successive lifecycles within a season. |
Be on the lookout for unexplained poor performance in pulses in 2025 (Table 1). Root rots caused by Fusarium, Pythium, Rhizoctonia, Phytophthora and Aphanomyces are now known to be common in South Australia and increasingly look to be limiting yield. While the management options are only just being developed now, early signs suggest there will be crop, variety and seed treatments options for pulses.
Effective testing of root disease
If you are unsure about the root disease risk in any paddock or part paddock, then testing the soil prior to sowing is recommended. Predicta B is a DNA-based soil testing service provided by SARDI through accredited agronomists. The tests have been validated and disease risk categories defined through decades of research linked with industry collaborators. Most agronomists in SA are accredited, and new accreditation courses are run by SARDI annually to ensure the service is accessible to all growers, and to provide industry with root disease training and research updates. February–March is an ideal time to take soil samples, as it is close enough to sowing to be relevant, but also leave some time to make changes based on the results. It is important to collect samples according to a developed method, which is not the same as for nutrient testing – this includes adding in stubble so that diseases, such as crown rot, are well estimated.
Predicta B provides a disease risk category for crown rot, Rhizoctonia root rot, root lesion nematode, take-all, cereal cyst nematode, stem nematode, and also includes tests for other emerging pathogens.
Predicta B can also be used to evaluate the success of a management strategy over time, or diagnose possible issues observed last year. If you have previously tested a paddock some years ago, a follow-up Predicta B can be conducted to evaluate the efficacy of management.
Acknowledgements
The research undertaken as part of this project is made possible by the significant contributions of growers through both trial cooperation and the support of the GRDC, the authors would like to thank them for their continued support. Predicta B continues to be developed with significant input from collaborators from around Australia, particularly those associated with State agriculture departments. Current research presented here is being conducted in collaboration with NSWDPI, Agriculture Victoria, DPIRD, CSIRO and QDAF.
Useful resources
Predicta B (broadacre) (https://pir.sa.gov.au/research/services/molecular_diagnostics/predicta_b)
Root disease in pulses – cause of poor performance? (https://grdc.com.au/resources-and-publications/grdc-update-papers/tab-content/grdc-update-papers/2021/02/root-disease-in-pulses-cause-of-poor-performance)
The health report - emerging pulse root diseases (https://grdc.com.au/resources-and-publications/grdc-update-papers/tab-content/grdc-update-papers/2020/02/the-health-report-emerging-pulse-root-diseases)
GRDC GrowNote Rhizoctonia Southern region (https://grdc.com.au/__data/assets/pdf_file/0025/170386/grdc_tips_and_tactics_rhizoctonia_southern_web.pdf.pdf)
GRDC Crown rot – Southern fact sheet (https://grdc.com.au/__data/assets/pdf_file/0031/385645/GRDC_FS_CrownRotSouth_1902_13-002.pdf)
GRDC Root lesion nematode fact sheet (https://grdc.com.au/__data/assets/pdf_file/0025/385621/GRDC_FS_RootLeNematodesSouth_1902_12.pdf)
Contact details
Blake Gontar
Plant Research Centre, Waite Campus
Urrbrae SA 5064
0430 597 811
blake.gontar@sa.gov.au
GRDC Project Code: UOA2206-007RTX, DAW2206-006RTX,