Surveys across Western Canada have found two main pathogens responsible for root rots in pulses. Fusarium species are widely distributed, with F. avenaceum and F. solani among the most virulent root rot species that can cause yield loss. Aphanomyces euteiches, first reported in Saskatchewan in 2012, is a more recent concern. 

Aphanomyces root rot is most common under good soil moisture conditions. The pathogen is a water mould that depends on moisture for the zoospores to move in the soil and infect plant roots. Infection can occur at any time during the growing season, and spores can persist in the soil for many years. Root rots may still show up in drier growing conditions and may or may not be Aphanomyces root rot. 

The seedling stage appears to be the most susceptible to Fusarium root rot, but symptoms typically do not become visible until late flower. In drier years, root rot symptoms appearing later in the season may be caused by one of many pathogens. 

Aphanomyces root rot is very difficult to identify and isolate with conventional methods and requires a DNA test for confirmation. For fields with a history of root rot, growers are advised to test their fields for A. euteiches to implement practices to manage the disease if it is present. 

Several labs in Western Canada can test for the Aphanomyces root rot pathogen. These labs may analyze either root tissue or a soil sample. 

While each lab has its own sampling and submission protocol, the following are general recommendations for soil and plant sampling: Soil analysis can be performed by direct soil extraction or by a bait test. A soil bait test, offered by several commercial labs, utilizes germinating seedlings of an Aphanomyces host crop that are planted into the soil sample to induce Aphanomyces oospore germination. This test method has been shown to provide the most consistent results when testing soil for Aphanomyces. One challenge that still exists, however, is determining Aphanomyces levels in dry, heavier-textured soils, which, under current analysis techniques, are more likely to yield false-negative results.  

To address this issue, Saskatchewan Pulse Growers (SPG) collected soil samples from 12 lentil fields in Saskatchewan at in-crop and post-harvest times, across three landscape positions (hilltop, midslope, and depression) in 2022. This project aimed to identify differences in Aphanomyces (quantitative) and Fusarium spp. (qualitative) disease pressure at these landscape positions. Samples were analyzed using commercially available growers’ Aphanomyces oospore detection methods (direct soil extraction, bait test, and plant tissue extraction from in-crop plant samples) to determine which method produces the most consistent and accurate results. SPG also added a 28-day bait test method with an extended incubation period for post-harvest samples to determine whether longer periods of saturation improve the detection of Aphanomyces and Fusarium species in dry, drought-ridden soils. The goal of this project was to evaluate which sample-collection timing, landscape position, and laboratory testing method are optimal for growers to assess infection risk in future pea or lentil crops.  

Each sample was screened for Aphanomyces eutieches, F. avenaceum, F. oxysporum, F. redolens, and F. solani using quantitative polymerase chain reaction (qPCR). As expected, the 28-day bait tests showed higher Aphanomyces levels in the tissue than the 7-day bait tests. In comparison, the direct soil extractions did not consistently detect Aphanomyces present in the soil. Soil bait testing is currently the best method for detecting Aphanomyces oospores. Longer incubation periods beyond seven days, targeting 10–21 days, produce the most consistent Aphanomyces DNA results to date. When soil bait tests were conducted for 28 days, some host pea plants began to die from root rot around 21 days after planting. In these cases, the incubation had to be terminated early to conduct the DNA extraction. The most consistent results came from the 28-day bait test, in which all samples tested positive for Aphanomyces DNA. Compared with the post-harvest 7-day soil bait test, in-crop soil bait and plant tissue extraction detected Aphanomyces in 75–83% of the samples. Both direct soil DNA extractions (no saturation period and no host plant present) produced the worst results, only detecting Aphanomyces DNA in 50–58% of the samples.  

Figure 1. Percent incidence, samples testing positive (n=12), for Aphanomyces eutieches under different laboratory analysis methods (soil bait test vs. direct soil extraction vs. plant tissue extraction) at two sampling times (in-crop vs. post-harvest) from Saskatchewan lentil fields in 2022.

Aphanomyces was detected at all landscape positions in all samples by all laboratory methods except direct soil extraction at post-harvest (Figure 2). When comparing landscape positions and Aphanomyces incidence, we found the highest Aphanomyces incidence in depressions and a surprisingly high incidence in the midslope position as well (Figure 2). Although Aphanomyces was detected at all landscape positions, the infection severity is not reflected in Figure 2. Root rot infections were significantly worse across the landscape gradient, with depression samples most severely infected, followed by intermediate disease severity at the midslope and mild infection levels at the hilltop.

Figure 2. Percent incidence of Aphanomyces eutieches (n=12) under different laboratory analysis methods (soil bait test vs. direct soil extraction vs. plant tissue extraction) at two sampling times (in-crop vs. post-harvest) collected from three landscape positions in Saskatchewan lentil fields in 2022.

When determining root rot infection severity and risk, it is important to determine the last time a host crop (pea or lentil) was grown in a particular field and the moisture conditions that year. Figure 3 illustrates the gradient of disease severity across the landscape positions of two different fields in Saskatchewan during the summer of 2022. Both fields had lentils grown three times since 2011. Field a) was seeded to durum in 2016, while field b) was seeded to lentils. As shown in Figure 3, the plants from field b) had more severe disease infections than those from field a), illustrating the impact of environmental conditions on compounding the risk of Aphanomyces root rot in future years.

Figure 3. Aphanomyces eutieches and other root rot pathogen infection severity depicted by plant samples collected from three landscape positions (hilltop, midslope, and depression) in two lentil fields in Saskatchewan in 2022, with the same lentil frequency, a) durum grown in 2016 vs. b) lentils grown in 2016.

Aphanomyces eutieches infections do not often occur alone but are often found in conjunction with other root rot pathogens, particularly Fusarium species. The Fusarium species of greatest concern in pulses are F. avenaceum, F. oxysporum, F. redolens, and F. solani. Plant tissue tests and the 28-day soil bait test consistently detected Fusarium spp. infections (Figure 4). Incidence of Fusarium infections were not impacted by landscape position (Figure 4), however, similar disease severity to Aphanomcyes infections was observed where disease severity was worst in the depressions > midslope > hilltops.

Figure 4. Incidence of Fusarium species detected by different lab testing methods (7-day soil bait test, 28-day soil bait test, plant tissue extraction) in Saskatchewan lentil fields (n=12) collected at in-crop and post-harvest timing in 2022.

Overall, we determined that longer incubation periods (10-21 days) for soil analysis to detect root rot pathogens are recommended when soils are dry, particularly for fall-collected samples and for dry, heavier-textured soils. If a lab is unable to conduct a longer incubation period with their current soil bait testing method, conducting the 7-day soil bait test is the next most reliable method for determining the presence of Aphanomyces in soil. Landscape position correlates with disease incidence and severity, with the worst infections occurring in depressions, followed by midslopes, and then hilltops. Fusarium spp. incidence does not consistently correspond to landscape position, and the best detection method is plant tissue testing, followed by longer-incubation soil-bait testing.

Sampling Methods

Soil

Plant Tissue

What The Results Mean

Figure 1. Healthy seedlings (left) vs root rot infected seedlings(right).

The results from a lab test in the fall can mean several things depending on the reporting lab. The first is positive or negative. This simply means that the pathogen is present in the sample, but does not provide a number for the amount of spores per gram of soil or the level of infection of the root tissue.

Some labs take the positive/negative test one step further in their reporting, indicating that a positive result indicates the pathogen is present at levels capable of causing disease. A negative result cannot guarantee that the pathogen is absent in the field; it only indicates that it is absent in the soil sample.

Finally, some labs provide quantitative results reporting the number of spores per gram of soil or the level of risk for root rots. Previous research by Agriculture and Agri-Food Canada had suggested a higher risk of A. euteiches in fields when levels are above 100 oospores per gram of soil in dark brown soils and 750 oospores per gram in brown and black soils. However, the presence of Fusarium spp., particularly in Brown soils, increases disease severity. Because Fusarium spp. are so widespread on the Prairies, the risk threshold for A. euteiches has been adjusted. The number of A. euteiches oospores, at which the pathogen may begin to affect the crop, has been set at 100 oospores per gram of soil for all soil types.

If A. euteiches is confirmed in a field, growers should follow recommended management practices, including rotating to non-susceptible crops or more tolerant pulse crops such as faba beans, chickpeas, or soybeans, and maintaining a minimum of six to eight years between susceptible hosts such as peas, lentils, and alfalfa. Growers and agronomists are encouraged to sample across the landscape, particularly targeting high-risk areas (depressions), and to pair root rot disease incidence and severity assessments on plant samples with soil bait test results, cropping history, and historical weather data when evaluating future Aphanomyces and root rot infection risks.

Labs Offering Soil and/or Plant Specimen Analysis for Root Rot Pathogens