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Another root rot

There’s another root rot pathogen in the neighbourhood. It’s called Aphanomyces euteiches. It loves peas, lentils and waterlogged soils. And it’s tough to deal with because its resting spores can survive in the soil for many years. Although Aphanomyces has been present in Manitoba since the late 1970s, researchers only recently identified it in Saskatchewan and Alberta. Now they are at work on some new strategies for managing it.

Aphanomyces euteiches is an oomycete, or water mould, which is a fungus-like organism. It produces one generation in a season. “The oospores are the primary inoculum left behind in the soil or decaying host tissue. They are thick-walled, very resistant resting structures. Reports in the literature indicate they can survive in the soil from five to upwards of 20 years, depending on weather conditions,” explains Syama Chatterton, a plant pathologist with Agriculture and Agri-Food Canada (AAFC) in Lethbridge, Alta.

“A susceptible host plant releases root exudates and signals into the soil. Oospores respond to those signals and germinate. Through a complicated germination process, they eventually produce zoospores, which are single cells with two flagella that help them swim.” They swim in soil water films to the host root and attach themselves to it.

“Then they produce hyphae, the fungal strands that penetrate into the root, and very rapidly begin colonizing it.” They break down the root tissues, feeding on the nutrients. Once they have used up all the nutrients in the root, they form oospores.

The whole life cycle can be completed in about three weeks if temperature and moisture conditions are ideal. Infection can occur at any stage of the host’s development, with the timing depending on the environmental conditions.

Soggy, warm conditions are ideal for infection. “Aphanomyces often occurs in a complex with other root rot pathogens, like Fusarium, Pythium and Rhizoctonia. They all like moist conditions, but the oomycetes – Pythium and Aphanomyces – do even better with excess moisture,” says Faye Bouchard, provincial plant disease specialist with the Saskatchewan Ministry of Agriculture. On the Prairies, optimal soil temperatures for Aphanomyces infection (22 to 27 C) are typically reached by about July (see Table 1).

Chatterton has done Aphanomyces host range work with Sabine Banniza at the University of Saskatchewan. They have found that peas and lentils are both highly susceptible, whereas dry beans, fababeans, chickpeas and soybeans all have pretty good resistance. Alfalfa is somewhat susceptible, but some alfalfa cultivars are resistant. In 2015, Chatterton surveyed alfalfa crops grown on fields that have had peas in the rotation and found that the alfalfa roots were very healthy, suggesting that Aphanomyces is probably not a big concern for alfalfa.

Why now?
Aphanomyces has been around in Canada since the 1930s. But we just found it in Saskatchewan in 2012 in peas,” Bouchard notes. “Then we started doing more surveys for it, and Alberta started looking for it [and found it in 2013].” These surveys show the pathogen is fairly widespread in both provinces.

So why has Aphanomyces root rot suddenly become an issue? “My hypothesis comes down to three reasons that have all come together in a perfect storm,” Chatterton says.

“The first reason is that we’re reaching the point where most places in Alberta and Saskatchewan have had a good 25-year cropping history of either peas or lentils. So, if producers are using good rotational practices with a pea or lentil crop once in every four to five years, then some fields would have had a pea or lentil crop six to seven times, or more often if they have tighter rotations. If a field started with a low inoculum level…the amount of inoculum would gradually build up every time a susceptible host crop was planted because the oospores can survive for a long time. It would take about six to seven cropping cycles to reach a threshold level of inoculum where it is more widespread throughout the field and can cause visible damage,” she explains.

“The second reason is that we had several really wet springs in a row, and Aphanomyces is dependent on having saturated soils in order to infect. So you get increased infections because the environmental conditions are right, and the inoculum load in the soil increases quite quickly.”

And the third reason is a detection issue. “In previous root rot surveys, they were taking pieces of roots and plating them out on agar to determine the causal agent. But usually Fusarium over-grows Aphanomyces on the culture, so it can be really hard to confirm Aphanomyces. I think it was Sabina Banniza who decided in 2012 to do a PCR test [which uses DNA markers specific to Aphanomyces euteiches]. That was the first time we were able to confirm Aphanomyces in [a Saskatchewan sample]. For our Alberta surveys in 2013 and onwards, we’ve expanded to using that PCR test. It has definitely improved detection of Aphanomyces.”

In Chatterton’s root rot surveys for 2013, 2014 and 2015, root rot was found in about 70 per cent of the surveyed fields each year, but disease severity varied greatly from year to year. The highest root rot levels occurred in 2014 because it was a particularly wet year. Chatterton says, “In 2014, we found that root rot was common and widespread throughout Alberta. The results from the PCR tests showed Aphanomyces was present in about 44 per cent of all fields in Alberta and in 60 per cent of fields that had root rot symptoms.”  

The PCR analysis of the 2015 Alberta samples is not yet complete, but the field surveys showed root rot severity was definitely lower than in 2014, due to the very dry conditions in 2015.

The Alberta surveys also show that “Aphanomyces-positive fields are more common in the Black and Gray soil zones that are more typical of central Alberta. I think that is because they have had a pretty long history of pea production there, and those areas tend to be wetter than southern Alberta,” Chatterton notes. “In southern Alberta’s Brown soil zone in 2014, only about 18 per cent of the fields were positive.”

Although Saskatchewan didn’t do a formal root rot survey in 2015, the dry conditions in the spring and early summer likely reduced the amount of disease. Bouchard didn’t see as much root rot in the field, she didn’t get as many inquiries about it from growers, and fewer samples were submitted to the ministry’s Crop Protection Lab.

Difficult to diagnose in the field
Trying to figure out which root rot pathogens you have in your field isn’t easy. Aboveground, they share the same symptoms, like poor emergence, wilting, yellowing and stunting. The belowground symptoms are usually a confusing mix caused by a complex of pathogens.

In the lab, if you infect plants with only Aphanomyces, the symptoms are distinctive. “The whole root system will have a honey-caramel discoloration. And the classical symptomology is that the epicotyl, which is the portion between the point of seed attachment and the green stem, becomes very tightly constricted and has that same honey-brown colour, which stops abruptly right at the green stem,” Chatterton explains. “Also, because the disease causes decay of the entire root cortex but not the vascular system, oftentimes if you pull up the plant from the soil, only the white vascular bundle is left and the rest of the roots are gone.”

In the field, Fusarium species tend to colonize tissue that Aphanomyces has already started to infect, producing mixed symptoms. “The roots will look black and will be pruned away; Fusarium causes pruning of the roots. So you get an ugly mess of a black taproot and brown decaying lateral roots,” Chatterton says. “A good way to check for Fusarium is that it causes red colouring in the vascular system.”

When a root rot infection is advanced, it is especially difficult to figure out the original cause. “Not only are the roots rotting and the plant dying, but there could be multiple root rot pathogens as well as saprophytes, which are fungal organisms that live on the decaying and dead plant material,” Bouchard says.

She adds, “The other difficulty is that it is hard to separate out the damage that excess moisture causes to the crop, even without any pathogens present. Lentils and especially peas don’t like wet feet, when the plant is sitting in too much water. Those conditions alone will mean that the roots won’t develop as well and probably won’t form nodules as nicely, and the above-ground plant parts will probably be yellowing, stunting and wilting. But those wet conditions stress the plant, so if a pathogen is present, it will probably cause even more damage because of the stress.”

The best way to tell which root rot pathogens are present is to send samples to a diagnostic lab, such as Saskatchewan’s Crop Protection Lab, Discovery Seed Labs or BioVision Seed Labs.

root-rot table1 feb16

Seeking more management options
Researchers in Alberta and Saskatchewan are tackling Aphanomyces from several angles. For example, at the University of Saskatchewan, they are working on developing resistant lines of peas and lentils.

To assess various Aphanomyces management practices in field peas, Chatterton initiated a large study in 2015. The study is taking place at Drumheller, Brooks, Taber, Lethbridge, Saskatoon, and two sites in the Red Deer-Lacombe area. Collaborating with Chatterton are Mike Harding and Robyne Bowness at Alberta Agriculture and Forestry, and Bruce Gossen at AAFC in Saskatoon. The Alberta Crop Industry Development Fund, Alberta Pulse Growers and AAFC, through the Growing Forward 2 Pulse Cluster, are funding the study.

At each site, the study is evaluating seed treatments, cultivar resistance and soil amendments. All sites are in producers’ fields. Six of the seven sites were selected because the fields had a high risk for Aphanomyces root rot; the Lethbridge site only had Fusarium root rot.

The seed treatment trials include different combinations of various products with activity against Fusarium, Pythium, Rhizoctonia and Aphanomyces. The seed treatment for Aphanomyces is ethaboxam (Intego Solo) – a new option that was given emergency use registration on field peas in Alberta, Saskatchewan and Manitoba in 2015.

The cultivar trials involve 20 pea cultivars, including some currently popular cultivars as well as some that are just about to be released.

The soil amendment trials are comparing three possibilities. “We searched the literature for any instance of something that might have some effect against Aphanomyces,” Chatterton explains. One treatment uses calcium, involving spent lime from the sugar beet industry; calcium has reduced zoospore production in greenhouse tests. Another treatment is Phostrol, a phosphite-based product, which has activity against oomycetes and provided some suppression of Aphanomyces in peas in the Pacific Northwest. The third treatment is the herbicide Edge (ethalfluralin), which showed Aphanomyces suppression in some preliminary work a few decades ago.

In the study’s first year, all the cultivars were susceptible to Aphanomyces root rot, as expected from previous greenhouse testing at the University of Saskatchewan.

“The seed treatments and soil amendments gave some promising results early in the season. By about five to six weeks, we could see some nice visual differences in root rot severity between some of the treatments,” Chatterton says. “But by the end of the growing season, the root rots were pretty similar across the board. Some treatments definitely yielded better than others, but we didn’t find any statistically significant differences between treatments.”

With only one year of data in an unusually dry year, it’s too soon to draw any conclusions. Also, Chatterton points to a key challenge with trying to do these types of field trials. “Because the distribution [of Aphanomyces] can be very patchy in fields, we had to choose sites with very high levels of Aphanomyces root rots. I think the inoculum load at some of these sites is too high, and at that level, disease management strategies often aren’t going to work. We could try to find sites that have a lower level of Aphanomyces, but then we won’t be certain that the inoculum has spread throughout the soil [so some plots might have different levels of inoculum].”

The researchers will be repeating the trials in 2016. Then, Chatterton hopes to get continued funding for several more years to determine how low the inoculum levels need to be for the practices to be effective.

In a project funded by the Saskatchewan Pulse Growers, Chatterton and Banniza are determining how much Aphanomyces inoculum is needed to cause different levels of the disease. “Right now, you can submit samples to a lab to find out if Aphanomyces is present or absent, but the lab can’t determine if you have a low or high risk of getting Aphanomyces root rot,” Chatterton says.

“So we want to determine the amount of inoculum needed in the Brown, Dark Brown and Black soil zones to get low, medium or high disease levels. The idea is that interested testing labs could then offer a DNA quantification service for Aphanomyces and be able to use the DNA levels to determine if a field has a low, moderate or high level of Aphanomyces. That should help inform decisions on the length of time peas or lentils might need to be out of the rotation, or whether the grower could look at seed treatments or maybe a soil amendment treatment.”

Advice for growers
At present, the best strategy is to submit plant or soil samples to a diagnostic lab to determine which root rots are causing problems in your fields, and if Aphanomyces is an issue, then use that information in your management decisions.

For fields that are highly infested with Aphanomyces, Bouchard and Chatterton advise waiting at least six years before planting peas or lentils again. Bouchard says, “Hopefully growers won’t have to do that on a permanent basis because there should be more options available as more research is done. One seed treatment, called Intego Solo, is available now, and there are potentially other treatment options coming down the pipeline. And hopefully we’ll get some resistant varieties.”

In the meantime, Chatterton suggests, “If you want to grow a pulse crop [on a field that is heavily infested with Aphanomyces], then fababeans are a really good option because they are really resistant to Aphanomyces.“

For fields with low to moderate Aphanomyces infestations, Chatterton recommends extending pea or lentil rotations from three or four years to perhaps five or six years. She adds, “Those are good fields for possibly using a seed treatment with activity against all the pathogens in the root rot complex, and that should help to boost your crop and keep it healthier.”

 


February 17, 2016
By Carolyn King

Topics
Classical Aphanomyces root rot symptoms include honey-brown discoloration of the roots There’s another root rot pathogen in the neighbourhood. It’s called Aphanomyces euteiches. It loves peas