Researchers trying to unlock root rot solutions

Field Choice 

A few years ago, Zakir Hossain began taking soil samples from pea and lentil fields in Saskatchewan.

The Agriculture Canada research biologist, who works at the research centre in Swift Current, was taking soil from specific areas of the field where root rot was particularly bad, and samples from parts of the field with minimal root rot.

That began Hossain’s quest to answer a basic question: what’s special about the soil where there was no root rot?

“There’s something protective about the soils in the healthy regions (of the field),” said Michelle Hubbard, an Ag Canada plant pathologist specializing in pulse crops.

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Root rot is a massive challenge for pea and lentil producers on the Prairies. The complex of root rot diseases, including aphanomyces, Pythium and fusarium, make it almost impossible to grow peas and lentils once the pathogens get established in the soil.

“Aphanomyces can infect peas, lentils, alfalfa, dry beans, and possibly some of the native weedy legume species,” says a document on root rot, produced by provincial pulse associations. “Faba bean and chickpea varieties with partial resistance can be used to maintain pulse crops in rotation. Soybeans are another option.”

Root rot causes poor emergence, stunting, a poorly developed root system and plant decay.

Scientists like Hubbard have been searching for a solution to root rot, but for now the only answer is a long break between susceptible crops. Six to eight years between peas or lentils.

“That’s the only proven option and people are looking at whole bunch of different things that don’t really work that well,” said Hubbard, who is also in Swift Current.

Hossain and Hubbard realized that patches within pea and lentil fields without root rot might offer a solution.

Hossain took the samples, collected in 2016 and 2017, and studied the bacteria and micro-organisms in the soil. After many hours in the laboratory, he isolated about 10,000 bacteria from the pea roots and another 10,000 from the lentils.

“That was an absolute massive amount of work,” Hubbard said.

He then narrowed it down to dozens of bacteria, by conducting experiments in petri dishes.

“Seeing if each individual bacteria could inhibit the growth of aphanomyces on a plate,” Hubbard said.

He reduced the search to about 70 species of soil microbes for peas and 35 for lentils, which could be effective against aphanomyces.

Next came greenhouse trials.

Some bacteria were effective, but not as effective as they were in the petri dish.

Last year, Hubbard and Hossain took the research to the field — kind of.

They grew peas in Rubbermaid containers and added the aphanomcyes-killing bacteria to the soil.

“It wasn’t truly in the field. But they were outside.”

Unfortunately, they didn’t get enough disease in the containers to reach a conclusion.

Wonder where the yellow came from?

Plant roots and nitrogen-fixing bacteria need oxygen. When the soil is saturated, roots function poorly, and rhizobia activity is reduced, resulting in yellow growth.

Cool conditions slow seedling metabolism and root growth. This also slows mineralization of nitrogen from organic matter.
Plants that are stressed or have low vigour are more susceptible to seedling diseases.
Seed treatments are ineffective past the seedling stage and foliar fungicides will not work on root diseases.
Root rots tend to be more severe under waterlogged conditions. However, root rots can occur even under ideal or drier moisture conditions.
Crops can also appear yellow and stunted due to wet feet regardless of pathogen pressure.

Source: SaskPulse

They will try again this year because Hubbard believes the approach still holds promise.

But many un-answered questions remain:

Why are beneficial soil microbes, which combat root rot, in one part of the field and not in other parts?

Is it possible to change agronomic practices, to create conditions where the beneficial bacteria will thrive?

Is it one soil bacteria that controls aphanomyces, or a bunch of microbes?

“There are big differences between the healthy and diseased sites, but I’m not at the point where I can say it’s this one species of bacteria (that’s controlling root rot),” Hubbard said.

Besides looking at individual species, Hubbard and her Swift Current colleagues are studying the microbiome of the soil. That’s the collection of micro-organisms within the soil that work together on functions like nutrient cycling and building soil aggregates.

“Continuing to analyze and hopefully publish work on the microbiome. See what we can make sense of,” Hubbard said.

Another opportunity is the metabolites, or chemicals produced by the soil bacteria.

Such metabolites are sometimes called bio-pesticides — natural chemicals that ward off plant diseases.

If they can pinpoint metabolites that are effective against aphanomyces and other root rot diseases, it could lead to a commercial product.

Hubbard cautioned that the research is in the early stages.

If they found a promising microbe, next week, it would take years to get a product to market.

“It’s a long road from identifying the bacteria… to figuring out how to scale it up, how to formulate it and how best to apply it.”

One question she really wants to answer is why root rot is a terrible problem in certain parts of a field and not others. Maybe producers could alter their agronomic practices and create soils that naturally fight root rot.

“That might be a more critical thing, if we could figure out why are some areas better than others,” Hubbard said. “I don’t have an answer for that, but that would be fantastic to know.”

Root rot risk reduction – what can be done?

Field choice

Lighter textured soils with good drainage
No peas/lentils for at least three years (four year rotation) and up to six years if aphanomyces was known to be present

Soil testing and fertility

Apply nutrients as needed

Starter nitrogen if soils have less than 15 lb./ac available nitrogen in top 12 inches
Phosphorus if seeding early into cool soils
Other nutrients as shown in a soil test

Know the seed

Use tested seed
Apply seed treatments as warranted for seed-borne disease or if planting early into cool soils. To combat risks of aphanomyces, ethaboxam (Inego Solo) can be applied, but needs to be mixed with other seed treatment modes of action to control any other diseases except pythium.
Root rot complex that includes botrytis, fusarium, pythium and rhizoctonia in cool conditions could have the following applied:

– Captan (Agrox FL)

– Fludoxnil, metalaxyl and thiabendazole (Apron Advance)

– Thiamethoxam, fludoxonil and metalaxyl (Cruiser Maxx Pulses)

– Penflufen, prothiconazole and metalaxyl (Everglo Energy)

– Metalaxyl, fluxapyroxad and pyraclostrobin (Insure Pulse)

– Thiram

– Trifloxystrobin and metalaxyl (Trilex AL)

– Trifloxystrobin and metalaxyl with penfluxfen (Trilex Everglo)

– Fludioxonil, metalaxyl and sedaxane (Vibrance Maxx)

– Carbathiin and thiram (Vitaflo)

Seeding decisions

Use appropriate inoculant and good application methods
Choose more resistant pulse crop options – faba bean, chickpea and soybean (only for aphanomyces)
Minimize seed damage and minimize airspeed of seeding tools
Seed into warm, moist soil – the quicker the emergence the more vigorous the seedlings

Post seeding