Disease management

1. Introduction

Over 100 diseases of soybean have been recorded world-wide. In Australia the most prominent diseases of soybean crops are a range of fungal and bacterial diseases. Good crop rotational practices, careful varietal selection, destruction of soybean volunteers and weeds and thorough decomposition and incorporation of crop residues will minimise disease occurrences. Avoid planting soybean after other broadleaf crops.

2. Principles of disease management

Integrated disease management (IDM) can be defined as the use of a range of control measures to reduce the impact of plant diseases. Used alone, an individual management practice may not reduce the level of disease to an acceptable level, whereas the additive effect of several practices will. 

A plant pathogen is a broad term used to describe an organism, such as fungi, bacteria, nematodes, protists and viruses, that causes plant disease. Plant pathogens will only cause disease on specific plant species. When this occurs, the host is considered susceptible to the pathogen and the pathogen is described as being virulent on that host. When a virulent pathogen comes into contact with a susceptible host and the environmental conditions are suitable, a disease develops in the host and the characteristic symptoms of that disease are produced.

The disease triangle (Figure 1) depicts the interactions between host, pathogen and the environment, the latter having the major impact on the severity of the disease outbreak. A plant disease will occur when a susceptible host, the pathogen, and favourable environmental conditions are present. Although a pathogen may be present, if the weather conditions are not conducive the disease will not develop on a host. IDM strategies aim to disrupt one or more of these interactions. 

3. Integrated disease management

Effective Integrated Disease Management (IDM) should be on the whole farm level. Basic strategies should be implemented regardless of whether or not a significant disease exists. Prevention and minimisation of the disease risk is the key to effective IDM.

3.1 Best practice strategies

• Staff training: educate staff on possible disease incursions and encourage pro-active feedback on unusual symptoms and plant growth habits.

• Farm hygiene: minimise movement of pathogens between paddocks and between farms. Many pathogens can easily be transferred on tyres, machinery, boots or plant matter such as hay.

• Developing a sound crop rotation strategy: repeated plantings of soybeans will lead to the build-up of soil borne pathogens. A good understanding of the host range of major pathogens of soybean is vital.

• Paddock selection: a thorough knowledge of the disease history of paddocks and of the biology of major soybean pathogens will help in paddock selection.

• Management of crop residues and weeds: to minimise carryover and build-up of pathogens, for example nearly all weeds host Sclerotinia.

• High quality seed: use high germination and vigour, disease-free seed to ensure rapid germination and to reduce the risk of seedling diseases. A fungicide seed dressing will also help to minimize risk.

• Resistant varieties: use whenever available. Source information on the resistances of varieties to pathogens and select a variety with the highest resistance to the major disease(s) in your area.

• Crop nutrition: a healthy crop is more able to express its resistance/tolerance than a crop under stress.

• Disease awareness: ensure you have up-to-date information on the incidence and biology of current disease outbreaks and whether or not the incidence/severity of outbreaks is increasing each season.

• Regular crop monitoring: regularly check your crops for anything out of the ordinary. Walk through the crop in a W pattern – this will minimise the risk of missing disease hotspots and allow you to gauge any possible edge effects or disease gradients.

• Foliar fungicides: spray registered/permitted fungicides in a timely manner using good application techniques to minimise damage from foliar fungal pathogens.

4. Steps to effective disease management

4.1 Risk assessment

Assessment of disease risk relies on a grower’s/adviser’s knowledge of paddock history, confidence in forecasts of the weather and possible price, willingness to educate themselves about pathogen biology, and their tolerance for accepting risk.

Some disease management decisions can be made pre-planting.

Other disease management risk factors involve both pre- and post-planting decisions.

Each crop/disease risk analysis will:

Identify the factors that determine risk

• Pathogen: Pathogenicity, survival, transmission and infection mechanism, availability of control measures, is it widespread or sporadic?

• Host: vulnerability, varietal reactions, availability of resistant varieties, host range of major diseases and seed dressings.

• Agronomy: row spacing, soil conditions, cultural practices, plant residues, nutritional interactions, irrigation or dryland, herbicides used, time of planting.

• Weather: weather forecasts including possible temperature variation, rainfall and relative humidity. Climatic conditions affect both plant growth and the pathogen’s biological activities. A stressed plant is more vulnerable to disease outbreaks.

• Risk management: access levels of risk, contemplate ease of implementing management plan, assess cost of implementation, and assess value of possible returns over known risk factors.

Analyse risk levels of the factors

• Pathogen: level of inoculums in air/soil/seed, aggressiveness of isolate, known paddock history, alternative weed hosts for either pathogen or its vector.

• Host: susceptibility to pathogen, stress reactions to herbicides, nutritional disorders.

• Agronomy: time of planting, effectiveness of cultural control methods prior to planting, herbicide history, availability of spray equipment, irrigation.

• Weather: water storage in profile, long term forecast for rain or abnormal conditions, potential for water stress during growing season.

• Risk management: ensure strategy is flexible and adjust as necessary.

Acknowledge your own acceptable risk level

• Low: crop failure would impact seriously on the farm economic situation, not necessarily a good time to try new and untried cropping options. 

• High: grower is prepared to accept substantial yield loss as potential returns are high and financial situation sound; crop failure will not impact on rotation or other components of farming system.

5. Providing accurate diagnosis

Not so easy: diagnosing a plant disorder is not always quick or easy. Unlike insect pests, which are relatively easy to identify, the accurate diagnosis of plant diseases requires patience and at times, a microscope.

Different pathogens can produce similar and confusing symptoms, so the diagnostician needs to keep an open mind until all aspects of the host/pathogen interaction are considered. Several casual agents could be involved in the expression of symptoms.

However, some pathogens cause characteristic symptoms and with experience, a network of other specialists and suitable reference materials, a quick diagnosis can be achieved. There is no substitute for having hands-on approach to soybean disease management – each season will bring its own unique mysteries to solve.

• Be observant: note the range of symptoms you observe in the crop.

• Make a list: list all possible culprits as you observe symptoms. Most will be discounted as you progress through your diagnostic analysis.

• Study healthy plants: compare healthy plants with affected plants to understand the effects that a pathogen has had on the plants.

• Check all parts of the plant: symptoms on leaves can be the result of infection by foliar, root or vascular pathogens.

• Look for patterns of affected plants:

  • • • Are affected plants scattered across the crop, in groups or at the edge of a crop? 

      • Do the affected plants follow the row or are they randomly distributed across the paddock? Wilted plants along a row can be the result of mechanical damage during cultivation methods. Plants randomly distributed across the paddock are more likely to indicate a soil borne pathogen.

      • Are the symptoms widespread across the paddock – if so, are there any abiotic (non-living) reasons why the crop would be uniformly affected. Was a particular herbicide used in the previous rotation that may not have broken down quickly as expected due to weather conditions: was the appropriate rate of fertiliser applied or could the symptoms indicate a nutritional disorder; was a chemical applied off-label or in a mix that caused phytotoxicity; could spray drift be a factor?

Widespread symptoms can indicate abiotic factors such as: 

• • • • Soil conditions – deficiencies, toxicities, pH, excess salt in irrigation water

      • Adverse climatic conditions – hail, drought, flooding, cold or heatwaves

      • Toxic chemical – inappropriate chemical usage, experimental products, growth regulators

      • Human error

• Is there a disease gradient into the paddock – if so, has a neighbouring paddock or laneway had a chemical applied that may be phytotoxic to your crop or is a weed growing alongside your crop that may be a host for vector for the disease.

• Pathogens take time to build up in a crop – regular monitoring for both insects, diseases and weed hosts will decrease the chances of unpleasant surprises later in the season.

• Check for distinctive visual or odour symptoms – is there ooze or an unpleasant odour?

• Is the problem restricted to this paddock? Or is it across several varieties? Are the plants at different growth stages? Did the previous crop exhibit any symptoms?

• Geographical distribution – some pathogens are more suited to certain growing regions. For example, rust is virulent particularly on coastal soybeans and legumes.

• Know your pathogens – understanding the life cycles of the pathogens can help with obtaining an accurate diagnosis.

• Check watering schedules – herbicides can accumulate in tail ditches of paddocks – is there a gradient of symptoms up from the end of the paddock? Could these plants be waterlogged? Water logging can lead to nutritional disorders and increase plant susceptibility to disease.

• Symptom variability – can lead to improper diagnosis. Environmental conditions, varietal differences and multiple pathogens infecting the one plant can cause symptom variability. Inspect a number of plants and note common irregularities. If in doubt, get a second opinion.

• Check soil compaction – compacted soil and plough pans will often lead to “right angle root syndrome”. Roots are unable to penetrate through the impacted layers resulting in poor root development, which can lead to water stress, nutritional disorders and herbicide damage.

• Ask questions – the more information you can gather about a site and affected crop, the better – crop rotational history, variety, herbicide, insecticide and fungicide applications for both this crop and the previous crops, fertiliser applications, chemical applications in nearby crops.

• Be aware – many disease outbreaks occur in tandem with outbreaks in other cropping areas. Be aware of changes in environmental conditions, which could lead to potential disease outbreaks.

• Ask for help – do not hesitate to contact other specialists. Working together will enhance the chances of an accurate diagnosis and will also improve your knowledge of potential diseases.

6. Tools of the trade

Reference materials: even specialists who work with plant diseases on a daily basis need reference material. Important reference materials include the Mungbean & Soybean Disorders: The UteGuide (out of print), Compendium of Soybean Diseases 5th edition (APS Press), and the internet.

Hand lens, magnifiers: essential when looking for fruiting bodies in lesions; small digital magnifiers such as Dinolite® are very useful.

Knife or secateurs: invaluable for checking damage to the interior of roots and stems.

Camera: record a range of symptoms and send to a specialist. Sometimes, a few good images is enough for the diagnostician to make a tentative diagnosis.

Paper and plastic bags: place samples in a plastic bag and keep them cool until lab testing can be completed. If the sample has to be posted, ensure overnight delivery or the sample may rot in a plastic bag. If in doubt, use both plastic and paper bags. Send plants displaying a range of symptoms and also include one or two healthy plants.

Esky and cooler bricks: preferably, carry an esky and cooler bricks to keep samples cool before they are sent to a specialist.

GPS: provides an accurate location for data, monitoring outbreaks and disease spread.

Felt pens: ideal for labelling plastic and/or paper bags.

Clipboard and sample information sheets: use a clipboard or notebook to record all the information so it can be recalled and reviewed at a later date if required. 

7. Soybean diseases

7.1 Fungal diseases

Fungicides are very expensive, so consider this option carefully before using them.

Soybean crops may be affected by the following fungal diseases:

• Seedling root rots

• Charcoal rot

• Phytophthora root rot

• Sclerotinia stem rot

• Sclerotium base rot

• Pod and stem blight

• Rhizoctonia root rot

• Rust

• Downy mildew

• Purple seed stain

• Powdery mildew

• Target spot

• Anthracnose

• Black leaf blight

The incidence of the different fungal diseases in the major soybean cropping regions throughout Queensland and New South Wales are displayed in Table 1.

Seedling root rots (Rhizoctonia solani, Phytophthora sojae, Fusarium and Pythium species)

Seedling diseases, also known as damping off, are caused by a group of fungi that act independently or together to cause seeds to rot in the ground, or death of young seedlings after emergence. Infected seedlings often display water-soaked, brown or reddish coloured lesions on the roots and along the lower stem near ground level. Diseased seedlings are often weak and less vigorous and poor stands may be the first obvious symptom of a significant infection.

These seedling diseases may be referred to as either pre-emergence or post-emergence disease. Seedlings that become diseased prior to emerging above the ground have pre-emergence disease, whereas those that emerge and then become diseased have post-emergence seedling disease Pythium, Phytophthora, Fusarium, and Rhizoctonia species are associated with seedling diseases in soybean. These fungi may be soil or seed borne. 

Seedling diseases are often associated with plant stress, such as cool and wet soil, planting too deep, herbicide injury, and poor seed quality. Outbreaks of Pythium and Phytophthora are most likely under cool, wet conditions. Species of Pythium and Phytophthora survive for a long time in soils as thick-walled oospores. Oospores are able to survive extreme environmental conditions in the absence of a soybean crop. During saturated soil conditions and in the presence of soybean root exudates, oospores germinate to produce sporangia, in which motile (mobile) zoospores develop. These zoospores need water to then swim towards the roots, where they encyst and later germinate. The germ tubes then invade the roots, which start to rot. 

Outbreaks of Rhizoctonia and Fusarium are favoured by rainfall followed by warm weather. Rhizoctonia survives in soils as sclerotia and in infected stubble as mycelium, so soybeans growing through soybean or other stubble are at high risk. Fusarium species survive in the stubble of a wide range of hosts as mycelium and for a long time in soils as chlamydospores. Infection by Fusarium occurs when the soybean seeds or roots come into contact with spores or mycelium. 

Seedlings usually become infected within the first 14 days following planting and tend to be more common in compacted and poorly drained soils. To minimise losses:

• Avoid sowing deeper than 50 mm.

• Use high-quality seed.

• Plant a variety with higher tolerance to Phytophthora. Most newer varieties have good tolerance or resistance to Phytophthora.

• Minimise the amount of stubble in the vicinity of the sowing line.

• Use crop rotation.

• Do not expose the seedlings to herbicide.

Fungicidal seed dressings containing thiram or metalaxyl may be worth considering. Apply these fungicides to the seed and allow to dry before inoculating with soybean rhizobia. Metalaxyl will control seedling losses only from Phytophthora and Pythium, but infection by Phytophthora is possible later in the growing season.

Charcoal rot (Macrophomina phaseolina)

This pathogen can be found in all agricultural soils in Australia. Symptoms usually appear from pod-fill to maturity with affected plants dying prematurely, but seedlings can die when there is hot, dry weather during emergence. The disease is associated with plant stress. Crops under severe moisture or heat stress are particularly susceptible and even irrigated crops can be badly affected. Waterlogging can also predispose plants to infection by M. phaseolina.

Leaves on infected plants often yellow, wilt and die before any external lesions or discolouration is visible on the stem. However, in most cases the stems of wilted plants turn light tan and later dark brown, and when the bark is peeled away the inner stem will be orange-brown rather than the normal white to light-green colour.

Once the plant has died the external surface of the lower stem and taproot turns a charcoal colour. Internally there is often a grey staining pattern. Affected stems contain minute, black fungal bodies called microsclerotia, which can survive in the soil and crop trash and spread on seed. Macrophomina phaseolina has a wide host range, including most summer crops and weeds. Evidence suggests that infection of soybean plants occur during the early seedling stages and remain latent until the plants are stressed.

Since the disease is associated with plant stress, to minimise losses:

• Irrigate to avoid moisture stress.

• Rotate soybeans with poor hosts such as winter cereal crops for at least 2 years.

• Control weeds.

• Fertilise appropriately to minimise stress.

• Plant lower plant populations in soils with a higher risk of drought stress.

• Manage insect pests that may cause additional stress to plants.

There are no known resistant varieties and no reliable chemical control options for charcoal rot. 

Phytophthora stem and root rot (Phytophthora sojae)

This pathogen attacks soybean plants at all stages of growth, causing pre-emergence and post-emergence damping off and later wilting and death of older plants.

As P. sojae needs free water for spore development, movement and infection, diseased plants will usually occur in patches in poorly drained areas of the paddock and at the tail ditch end of irrigated crops. Infected plants may be later found throughout the field. On older plants the first symptom is wilting and interveinal chlorosis (yellowing) of the lower leaves. However, the diagnostic feature of this disease is a sunken, brown-reddish lesion advancing up the stem, with a distinct margin between the lesion and the green, healthy part of the stem.

Infected lateral and branch roots are almost completely destroyed and infested taproots turn dark brown. Infected plants usually die, and withered leaves can remain on the plant for a week or more.

Phytophthora root rot is found throughout all growing regions, and is most severe on heavy, poorly drained soils where soybeans have been grown continuously for several years. As the fungus can survive for many years as thick-walled oospores in soil, avoid planting susceptible varieties where there is a history of the disease in the paddock. The fungus is specific to soybeans and does not occur in other crops or weeds.

Seventeen (17) races (strains, pathotypes) of P. sojae have been identified in Australia to date. Current varieties have good levels of resistance to the main races.

Another species of Phytophthora, P. macrochlamydospora has been found on soybeans only in the coastal growing areas of northern NSW. It causes a root rot without the presence of the typical stem lesion caused by P. sojae. Local native legumes are susceptible to the pathogen, so it appears that this fungus is indigenous to Australia. The disease generally appears after a crop has been waterlogged or flooded. There is no known resistance to P. macrochlamydospora.

To minimise the risk of Phytophthora stem and root rot developing:

• Plant tolerant varieties in well-drained soils. Restrict the sowing of susceptible varieties to well-drained paddocks with a history of no Phytophthora. Older varieties may only have tolerance to selected Phytophthora races. Newer varieties have good tolerance to the main races.

• Use crop rotation. Avoid planting soybeans in the same paddock year after year.

• Fungicides containing Metalaxyl may be considered to minimise the risk of seedling infection.

• Avoid excess irrigation and waterlogging.

• Consider management practises that improve soil drainage, such as tillage.

• Practise good farm hygiene. Clean machinery of soil prior to entering farm. Harvest known infected paddocks last to prevent further spread of the pathogen. Avoid movement through infected paddocks.

Sclerotinia stem rot (Sclerotinia sclerotiorum, S. minor)

Stem rot in soybeans can be caused by the two species, Sclerotinia sclerotiorum and S. minor. Symptoms are usually not evident until canopy closure. The first sign of the disease is often wilting or dead leaves at the top of individual plants scattered though the crop. 

Plants infected with S. sclerotiorum develop a white, cottony growth on the stems, leaves or pods followed by the formation of large (commonly 4–10 mm long), black sclerotia (resting bodies of the fungus) of varying shapes. Lesions develop on the plant stems, which soften and appear bleached and sometimes shredded due to advanced decay. the plant parts above the lesion dies. Sclerotes may also form in the pith where they are more uniform and cylindrical in shape. Seeds in diseased pods are typically shrivelled, may be infected by the fungus, or replaced by sclerotia. Seed harvested from a diseased crop is often contaminated with sclerotia. Plants infected with S. minor typically develop a white, cottony growth on stems at ground level and produce smaller (<4 mm long) sclerotes.

The pathogens survive for long periods in soils or plant debris primarily as sclerotia. The disease has a wide host range and often occurs where soybeans are grown following susceptible crops such as sunflower, mungbean, cotton, peanuts and crucifers. Many broadleaf weeds are also hosts of Sclerotinia. 

During wet weather, sclerotes of both species, but more typically S. minor, may germinate to produce fungal strands (hyphae) that infect the bases of nearby soybean plants. Cool, humid weather conditions, tall, dense crops and overhead spray irrigation or rainfall during flowering favour the disease caused by S. sclerotiorum. Under these conditions sclerotes of S. sclerotiorum on or just below the soil surface germinate to produce a small mushroom-like structure on which spores develop. These airborne spores firstly colonise dead flower petals and leaves and later stems and other aboveground tissues. 

Regularly inspect the lower canopy of plants after flowering for signs of the disease. No fungicides are currently registered for the control of sclerotinia stem rot.

To minimise the risk of developing Sclerotinia:

• Avoid planting into paddocks where Sclerotinia has been observed on any host within the last 4 years.

• Plant disease-free seed. Avoid planting seed harvested from an infected crop.

• Use crop rotation. Do not grow soybeans in paddocks known to be infested with Sclerotinia for at least 4 years after the last affected crop and rotate with grass crops such as sorghum, sugarcane, maize and winter cereals.

• Control weeds. 

• Avoid overhead irrigation. Avoid irrigation during flowering.

• Plant in wider rows or lower plant populations to increase air flow and reduce humidity.

• Consider tillage practises in paddocks with a long history of disease.

• Practise good farm hygiene. Clean machinery of soil and crop debris prior to entering farm. Harvest known infected paddocks last to prevent further spread of the pathogen. Avoid movement through infected paddocks.

Sclerotium base rot (Sclerotium rolfsii)

This disease causes yellowing, wilting and death usually on isolated plants of all ages, but in some situations plant losses can be significant. A brown lesion develops on stems at ground level and a white fan-like mat of fungal strands (mycelium) develops on the lesion and sometimes on the ground and plant residues around the affected stem. As nutrients deplete, round, light tan or brown sclerotia, 1–2 mm in diameter, usually form in the fungal mat. 

The pathogen survives for long periods of time in soils as sclerotia or in infected plant residues. During warm, wet conditions the sclerotia germinate and invade nearby soybean plants just below or above the soil surface. The disease occurs during hot (25°C to 35°C) weather often after drought conditions and when soil moisture levels are high. Therefore, the disease is more common in areas such as central Queensland. 

Planting into partly decomposed plant residues increases the risk from infection. Sclerotium rolfsii has a wide host range, infecting many crop and weed species. 

Losses due to Sclerotium base rot can be minimised by:

• Rotate with poor hosts such as sorghum, maize and wheat for at least 2 years.

• Control weeds that may host the disease.

• Consider tillage practises in paddocks with a long history of disease.

• Practise good farm hygiene. Clean machinery of soil and crop debris prior to entering farm. Harvest known infected paddocks last to prevent further spread of the pathogen. Avoid movement through infected paddocks.

Phomopsis pod and stem blight, stem canker and seed decay (several Phomopsis/Diaporthe species)

Plants with pod and stem blight may be infected early in the season but only express symptoms during the pod-filling stage. Infected plants usually do not display any symptoms of infection until plant death. A slightly sunken brown lesion may develop at the base of a branch or a leaf stalk. After plant death, small black fruiting bodies (pycnidia) develop on stems and pods. Symptoms of pod and stem blight may be confused with anthracnose or charcoal rot, however in the advanced disease stage a distinct difference is the presence of small black fruiting bodies arranged in rows on the infected tissues of a plant with pod and stem blight. On stems, the fruiting bodies tend to develop in rows, whilst on pods the pycnidia are scattered. Infected plants may also develop dark grey zone lines on the lower stem. 

Plants infected with stem canker develop grey or brown lesions with a reddish-brown margin and sunken cankers at the nodes of stems after flowering. Leaves from plants infected with stem canker or pod and stem blight may wilt, yellow, and develop interveinal chlorosis and necrosis. 

Seed decay can occur when seeds are infected. Infected seeds are usually dull, discoloured and covered by a white cottony fungal growth. Other symptoms include shrivelling, cracking, and splitting of the seed coat. Affected seeds have low vigour, are susceptible to seed decay, and seedlings growing from such seeds usually die.

Phomopsis pod and stem blight and seed decay tend to occur more commonly in coastal areas of Queensland and northern New South Wales where warm, wet weather is conducive for disease development. Warm, humid weather close to crop maturity increases the risk of disease. Seed infection occurs during periods of prolonged rainfall during late pod formation. Delaying harvest after wet weather can lead to high infection levels. 

Infected crop residues and seed are the main modes of survival from season to season. Spores, which ooze out of the fruiting bodies, are spread from plant to plant by rain splash. Wounds, such as those caused by insect damage, stem breakage or hail, allow the pathogens to invade and infect plants. 

Losses due to pod and stem blight, stem canker, and seed decay can be minimised by:

• Use disease-free seed. Avoid planting seed from a known infected crop.

• Avoid planting soybean and other legumes in the same paddock for at least 2 years. Rotate soybean with non-host crops, such as maize, sorghum or sugarcane. 

• Plant a weathering tolerant variety and avoid delaying harvest.

• Consider tillage practises in paddocks with a history of disease.

• Fertilise appropriately. High nitrogen levels and low potassium have been associated with a higher incidence of disease.

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Rhizoctonia root rot (Rhizoctonia solani)

As well as causing seedling damping off, R. solani can also cause root rot in older plants. The first sign of infection is stunted plants, which usually occur in patches across the paddock. There is often a clear boundary between the stunted and healthy plants. The crown and tap roots of affected plants have a reddish-brown discoloration, and the lateral roots are short and stubby. Foliar symptoms may include yellowing or wilting of leaves.

Disease outbreaks are favoured by heavy soils and rainfall followed by cool then warm conditions. Rhizoctonia root rot is most common in southern New South Wales and Victorian soybean crops. The pathogen survives in soils as sclerotia or resting mycelium. The pathogen also has the ability to saprophytically colonise all types of plant residue. No Australian varieties have resistance to R. solani.

Losses due to Rhizoctonia root rot can be minimised by:

• Use crop rotation. Avoid planting soybean in paddocks with a history of disease

• Use high-quality seed

• Consider tillage practises in paddocks with a history of disease

• Avoid or reduce plant stress, such as herbicide injury

Rust (Phakopsora pachyrhizi)

Soybean rust is present in most Australian soybean growing regions and can infect the crop at any stage in its development although it is usually found late in the season. Rust typically occurs on coastal crops with an outbreak occurring every four to five years, but rust has been recorded in inland areas in mild, wet summers. Extended periods of wet, humid weather and mild temperatures (22°C to 28°C) favours disease development. Under ideal conditions pod formation and seed size are affected, often reducing yields by 10% or more.

The disease is favoured by showery weather. Once infected, plants will develop small yellow lesions on the upper-leaf surface. Light grey to brownish-red pustules develop in the lesions on the underside of leaves, which break open to release masses of wind-borne spores. Initially, the lesions will usually appear on the lower leaves, but may later spread rapidly over the entire plant, leading to yellowing and premature defoliation.

In Australia, soybean rust also infects some native legumes. The pathogen is an obligate parasite and requires a living host for survival, so between cropping seasons it survives on volunteer soybean plants or alternative hosts. 

Losses due to rust can be minimised by:

• Sow varieties with rust resistance, such as Gwydir, in high-risk seasons or regions.

• Consider fungicide applications to manage disease. Although mancozeb is registered (as various products) for the control of rust, it is a protectant fungicide that is most effective when applied before the disease appears. Several applications should be made, 14 days apart. Overseas, systemic fungicides are applied at the first appearance of the disease. In most years there is little advantage in applying these fungicides during the crop’s vegetative stage unless rust levels are high. Early pod formation is the most critical time for systemic fungicide application if rust is present, and a follow-up spray 2 weeks later is recommended. These systemic fungicides are not to be applied after the R5 stage due to residue concerns. Check the APVMA website for fungicides under permit for rust control.

Downy mildew (Peronospora manshurica)

Downy mildew appears on the upper surfaces of leaves as pale green to light yellow spots expanding to pale to bright yellow lesions of varying shape. On the lower leaf surfaces, a whitish grey downy growth appears opposite the discoloured lesions and under severe conditions premature leaf drop may occur. Downy mildew can occur on plants at all stages of growth, although the disease is more common after flowering. Young leaves are most susceptible to infection. While this disease is often widespread during mild, wet seasons, yield loss is insignificant. However, the disease can reduce the quality of the harvested seed due to a white crust (consisting of oospores) on the seed coat. The pathogen survives as oospores in infected leaves and on seed. Disease development is favoured by high humidity and mild temperatures (20°C to 24°C). 

The resistance of current varieties is not well known due to the sporadic nature of the disease. New South Wales coastal varieties may be more resistant than other varieties because the disease is more common in this region, but the low incidence and relatively nominal impact of the disease on yield, make this a low priority when selecting varieties.

Losses due to downy mildew can be minimised by:

• Use disease-free seed. Downy mildew can be transmitted by seed and can reduce germination and establishment.

• Use crop rotation. Avoid planting soybean following soybean or another bean crop.

Purple seed stain (Cercospora kikuchii)

Seeds affected by C. kikuchii have a diffuse purple discoloration of the seed coat, which may extend to part or all of the seed coat. The disease is favoured by warm wet weather during which airborne spores developed on infested stubble infect stems, leaves and pods. Cercospora kikuchii does not reduce yields and is not considered detrimental to the quality of beans as the purple colour disappears upon heating. Avoid using infected seed for planting as it can reduce establishment and crop vigour.

Powdery mildew (Erysiphe diffusa)

Powdery mildew is characterised by white, powdery patches occurring on the upper and lower surface of leaves. Initially the disease infects older leaves but will quickly spread up the plant to the younger, upper leaves during favourable conditions. Under severe infection, all aboveground parts of the plant can be infected, which may lead to significant yield reductions. 

Cool, humid conditions are ideal for powdery mildew. Spores, which develop on the white powdery growth, spread many kilometres in the wind. The soybean powdery mildew pathogen is thought to survive from season to season on volunteer soybean plants and perhaps on alternative hosts, but little is known about the host range of this fungus. The pathogen will not survive in soils, crop residues or in seed. Some Australian soybean varieties are more susceptible to Erysiphe diffusa than others. 

To minimise losses due to powdery mildew:

• Plant resistant varieties, such as Moonbi, Richmond, Gwydir or Hayman.

• Control volunteer soybeans. 

Target spot (Corynespora cassiicola)

Target spot is a foliar disease, primarily affecting soybean leaves, stems, petioles and pods. Lesions on leaves are reddish-brown, round to irregular in shape, and vary from specks to larger spots up to 15 mm in diameter. Leaf spots are often surrounded by a yellowish-green halo. Older leaf lesions may have concentric rings with varying shades of brown, hence the name target spot. Lesions start in the lower canopy and move upward as the disease progresses. Severe infection can lead to leaf defoliation. Lesions on stems are petioles are dark brown and range in size from specks to elongated lesions. Lesions on pods are generally small (1 mm in diameter), circular dark brown or purplish spots. In some cases, infected seed may have small black or brown lesions. Seedlings can also be infected during cool temperatures (15°C to 18°C) and develop root lesions. Symptoms are most obvious after canopy closure.

Extended periods of warm temperatures (23°C to 29°C) combined with high humidity (over 80%) and/or rainfall are conducive for disease development. Dry weather will suppress the development of the disease. Crops grown in coastal regions have a greater risk of developing disease due to higher rainfall conditions. 

Corynespora cassiicola has a wide host range, infecting over 500 plant species. Recent studies indicate that some C. cassiicola isolates are host-specific while others can cause disease in different hosts. The impact of C. cassiicola isolates infecting soybean in Australia on other hosts is poorly understood. 

The pathogen survives in infected crop debris and soils for several years. The fungal spores erupt from leaf lesions and are spread via wind and rain-splash to infect nearby healthy plants. 

To minimise losses due to target spot:

• Use crop rotation and manage volunteer soybeans. Avoid planting soybean in the same paddock for at least 2 years. Avoid rotating with other legumes or cotton that may host the disease.

• Use disease-free seed.

• Consider tillage to manage crop residues in paddocks with a history of high disease levels.

• Practise good farm hygiene. Clean machinery of soil and crop debris prior to entering farm. Harvest known infected paddocks last to prevent further spread of the pathogen. Avoid movement through infected paddocks.

Anthracnose (Colletotrichum species)

Anthracnose in soybean is caused by several Colletotrichum species and can infect plants at any stage of growth. Foliar symptoms may include necrosis of leaf veins, leaf rolling, petiole cankering and premature defoliation. During the soybean reproductive stages, symptoms may develop on stems, petioles and pods as irregularly shaped, brown lesions. Affected plants may senesce prematurely. Plant tissues can also be infected and not present any obvious symptoms until a stress occurs. Closer to plant maturity, infected tissues are covered in small black fungal fruiting bodies. The black fruiting bodies (acervuli) produce black spines (setae) and are a distinguishable character for preliminary identification of the pathogen. Symptoms of anthracnose may be confused with pod and stem blight, however the latter produces fruiting bodies in rows and lack setae. During pod infection, the pathogens can infect seeds and lead to poor germination and damping off in seedlings. 

Extended periods of warm, humid, wet weather are conducive for disease development. Infection may occur when leaf wetness exceeds 12 hours per day. Crops grown in coastal regions that regularly endure wet weather are at a higher risk of this disease. 

The pathogens survive between seasons in infected crop residues and in seeds. Spores in infected tissues spread to healthy plants via wind and rain-splash. Seedlings may become infected and only express disease symptoms at crop maturity. The species causing anthracnose in soybean are thought to have wide host ranges. 

Losses due to anthracnose can be minimised by:

• Use crop rotation with non-hosts such as maize, sorghum or sugarcane. Avoid planting soybean in the same paddock for at least 2 years. Avoid rotating with other legumes that may host the disease.

• Use disease-free seed.

• Consider tillage to manage crop residues in paddocks with a history of high disease levels.

• Practise good farm hygiene. Clean machinery of soil and crop debris prior to entering farm. Harvest known infected paddocks last to prevent further spread of the pathogen. Avoid movement through infected paddocks.

• Consider fungicide applications to help manage the disease. Consult the APVMA website for chemical registrations and permits. 

Black leaf blight (Arkoola nigra) 

Black leaf blight in soybean is caused by the fungus, Arkoola nigra. The pathogen was first reported in New South Wales crops in 1982 but has not been recorded in any other soybean growing regions of Australia. Plants infected with black leaf blight have spots and blighting of leaves, stems and pods. Leaf spots are circular or oval in shape, 1–10mm in diameter, and brown or grey in colour with a distinct dark brown margin. Leaf spots are present on both leaf surfaces and may have a yellow border. The spots coalesce to form larger necrotic, blighted regions that tear easily. Darker brown oval to elongated spots form on the stems and pods of infected plants. Severely infected pods are shrunken and may contain discoloured seed. Infected leaves and pods may defoliate. Webs of dark fungal mycelium develop on infected plants and fallen plant tissues. 

The black leaf blight pathogen survives between cropping seasons on infected crop debris and in seed. Seeds infected with the pathogen do not germinate. The disease is typically not seen in crops until after flowering when the canopy closes. The disease is most severe in crop maturing during wet weather. 

Losses due to black leaf blight can be minimised by:

• Avoid planting soybean in the same paddock for at least 2 years. Avoid rotating with other legumes that may host the disease.

• Use disease-free seed.

• Consider tillage to manage crop residues in paddocks with a history of high disease levels.

• Control weeds and volunteer soybeans that may host the disease.

• Consider fungicide applications to help manage the disease. Consult the APVMA website for chemical registrations and permits. 

• Avoid overhead irrigation. Avoid irrigation during flowering.

• Plant in wider rows or lower plant populations to increase air flow and reduce humidity.

7.2 Bacterial diseases

The pathogens responsible for the major bacterial diseases of soybean survive on un-decomposed crop residues, alternate hosts and volunteer soybean plants and infected seed. Once established in a crop, the bacteria can rapidly spread during wet, windy weather. Seed infection can occur during harvesting of a diseased crop. The major bacterial diseases of soybean in Australia include:

• Bacterial blight

• Bacterial pustule

• Wildfire

The incidence of bacterial diseases throughout Queensland and New South Wales are shown in Table 2. 

Bacterial blight (Pseudomonas savastanoi pv. glycinea)

Bacterial blight causes water-soaked brown, angular spots, which join to form dark-brown, dead areas with yellow margins on the leaves. These areas frequently tear, giving the leaves a ragged appearance. Spots may also occur on the stems, petioles and pods.

The bacterium spreads from infected tissues through rain-splash and wind-blown rain. Warm (21°C to 27°C), wet, windy weather is ideal for disease development. While bacterial blight is a common disease in most crops it is never severe (<1% of the leaf affected), causing little or no economic loss. 

Losses due to bacterial blight can be minimised by:

• Use disease-free seed.

• Consider tillage practices to encourage the breakdown of crop residues.

• Use crop rotation. Avoid planting soybean in the same paddock for at least 2 years. Avoid rotating with other legumes that may host the disease. Control weeds and volunteer soybeans.

• Practise good farm hygiene. Clean machinery of crop debris prior to entering farm. Harvest known infected paddocks last to prevent further spread of the pathogen. Avoid movement through infected paddocks, especially when wet. 

Bacterial pustule (Xanthomonas axonopodis pv. glycines)

This disease causes small, yellow or pale green spots with light-brown centres on leaves. Later, a tan coloured, raised pustule develops at the centre of each spot, usually on the lower leaf surface. The raised pustule collapses with age leaving a brown spot with a bright-yellow margin that coalesce to form larger necrotic areas. The lesions can vary in size from small specks to larger, irregularly shaped lesions. Pustules may also develop on stems and pods. 

It is difficult to distinguish this disease from rust when both diseases are at an early stage of development. Symptoms of bacterial pustule may also resemble bacterial blight, though the latter has water-soaked lesions and does not have raised pustules. 

The disease is favoured by warm (29°C to 33°C), wet weather and spreads via rain-splash and wind-blown rain. The pathogen survives between seasons in infected crop residues and in seed. While not generally regarded as an important disease, it can be a problem in coastal regions, especially under wetter, more humid seasonal conditions with extended cloud cover. 

Losses due to bacterial pustule can be minimised by:

• Use disease-free seed.

• Consider tillage practices to encourage the breakdown of crop residues.

• Use crop rotation. Avoid planting soybean in the same paddock for at least 2 years. Avoid rotating with other legumes that may host the disease. Control weeds and volunteer soybeans.

• Practise good farm hygiene. Clean machinery of crop debris prior to entering farm. Harvest known infected paddocks last to prevent further spread of the pathogen. Avoid movement through infected paddocks, especially when wet. 

Wildfire (Pseudomonas syringae pv. tabaci)

Wildfire is distinguished by brown, dead areas of variable size and shape surrounded by wide, yellow haloes with very distinct margins on plant leaves. The spots may join as the disease progresses. Affected leaves fall readily.

Wildfire generally occurs only after bacterial pustule infection. A bacterial pustule, or a remnant of one, is usually found near the centre of each wildfire spot. Disease resistance developed through the plant breeding program and field screening is the only practical means of control. Wildfire is a rare disease. The same management strategies to control bacterial blight and pustule should be followed to minimise losses due to wildfire. 

8. Other diseases and disorders

Other diseases and disorders include phytoplasma and viruses.

8.1 Phytoplasma (also called big bud, witch’s broom and little leaf)

Phytoplasmas are responsible for this disease, which causes a proliferation of branching, replacement of flower petals with short leafy shoots and small leaflets. These pathogens are a form of specialised bacteria that infect phloem cells and are transmitted by leaf hoppers. Plants affected by phytoplasmas are generally found at a very low incidence in most soybean crops where they tend to be more common at the edges of crops. However, in recent years since about 2015, there have been multiple crops with moderate levels of phytoplasma and occasionally at high incidence, causing significant losses. In particular, severe epidemics in multiple soybean and mungbean crops were observed on the eastern Downs in 2016. Weeds are the main alternative hosts for phytoplasmas. While leafhoppers may be partially controlled using insecticides, there is no clear evidence that it will reduce phytoplasma infection in mung bean crops and is likely to compromise other integrated pest management strategies. Good crop and farm hygiene are recommended to reduce the inoculum near crops and limit the spread of disease. 

8.2 Viruses

Several viruses potentially affect soybeans in Australia. These include, roughly in order of importance, cowpea mild mottle virus (CPMMV), tobacco streak virus (TSV), soybean mosaic virus (SMV), peanut mottle virus (PMV) and alfalfa mosaic virus (AMV). 

The incidence of viruses throughout Queensland and New South Wales are shown in Table 3 above.

Cowpea mild mottle virus (CPMMV) 

CPMMV was first detected in Australia in 2016 and has been found in several soybean crops in the SE-QLD, Bundaberg and Ayr production regions. It causes symptoms varying in severity depending on the strain of the virus and the variety of soybean affected, ranging from mild chlorotic mottle to severe distortion and blistering of leaves. To date, CPMMV has mostly been found at very low incidence in Australian soybean but has caused significant damage in other crops (French beans). It is reported to be one of the most damaging of all soybean diseases in south America, so caution is warranted to monitor CPMMV in Australian soybean. It is transmitted by whitefly and is relatively common in alternative weed hosts such as siratro and glycine. It may be seed transmitted in some hosts but research to date in Australia has found no seed transmission in several lines of soybean and French beans. Good crop hygiene is recommended to avoid planting next to weedy areas. If CPMMV is affecting crops and whiteflies are present, selective control sprays may be warranted to reduce within crop spread but particular attention should be paid to possible sources of infection outside the crop. If CPMMV becomes a production issue in Australian soybean, resistant varieties may provide adequate control. 

Tobacco streak virus (TSV) 

TSV has been found occasionally in soybean in central QLD (central highlands region) and causes mild chlorotic mottle and some terminal necrosis and bud blight. It has been reported to cause up to 100% yield losses in Brazil but to date, no significant damage has been reported in Australian soybean. TSV is restricted to the central highlands region and while soybean remains a minor crop in this region, there will be little risk of widespread damage. TSV should not pose a risk to other regions unless the major alternative host, parthenium weed is accidentally moved outside of CQ. TSV is moved in infected pollen from weeds into nearby crops and requires that pollen, in combination with feeding action of thrips to cause transmission. There are some reports of TSV seed transmission in soybean from other countries but is not known if this may happen soybean in Australia with the strain of TSV present. It has been shown to be highly seed transmitted in parthenium and crownbeard and these pose the greatest risk for accidental movement to new regions. If growing soybean in the central highlands region, avoid planting nearby, and particularly downwind of areas infested with parthenium. If this is not possible, control flowering parthenium nearby to crops by spraying out or slashing prior to planting crops as they are most susceptible as seedlings. Spraying for thrips is unlikely to provide reduced TSV transmission which is continuously moving into crops from outside.

Soybean mosaic virus (SMV), peanut mottle virus (PMV) and alfalfa mosaic virus (AMV)

While SMV, PMV and AMV are found on rare occasions, they are not economically important. SMV causes a light green-dark green mosaic, vein clearing, rugosity and stunting of leaves, with symptoms are being reduced above 25°C and masked above 30°C. On varieties with seeds that have brown or black hila, infected seeds will display brown or black streaks extending from the hilum. Symptoms of PMV on leaves are similar to those caused by SMV, but line or ring patterns may appear on leaves. PMV is more common when soybean crops are grown near peanuts. AMV is often common in forage legumes (e.g. lucerne) and rarely infects soybean. There may be an increased risk if soybean is grown next to perennial lucerne crops. The low occurrence and incidence of these aphid borne viruses means that management through insect control or other practices is not needed.

8.3 Nematodes 

Root knot nematodes (RKN, caused by Meliodogyne species) and root lesion nematodes (RLN, caused by Pratylenchus species) have wide host ranges. On soybeans these nematodes cause stunting, yellowing, poor growth and wilting during hot, dry weather. The diagnostic feature of root knot nematode infection is the presence of galls or knots of various sizes on the roots of affected plants. Root lesion nematodes cause dark lesions on lateral roots. Root knot nematodes are more severe on light sandy soil, whereas RLNs are more common in heavier soils. Different species of Meliodogyne and Pratylenchus have different host ranges, so knowledge of the species affecting soybean crops in a particular paddock is needed before effective rotations can be developed.

8.4 Sunburn

Sunburn damage results in small, interveinal brick red spots on the underside of leaves but in more severe cases the entire leaf surface may have a diffuse reddish colour. Sometimes the spots develop dead centres and can be colonised by saprophytic fungi and bacteria.

9. Further reading and references

• Mungbean & Soybean Disorders; The Ute Guide. Grains Research Development Corporation and Queensland Department of Primary Industries.

• Compendium of Soybean Diseases, 5th edition (2015). (Ed: G.L. Hartman, J.C. Rupe, E.J. Sikora, L.L. Domier, J.A. Davis and K.L. Steffey). APS Press, St. Paul MN, USA.

• Moore, N., and Ryley, M. (2010). Soybean Leaf Rust. GRDC Factsheet.

• DAF website https://www.daf.qld.gov.au 

• NSW DPI website https://www.dpi.nsw.gov.au 

• Soy Australia website www.soyaustralia.com