Alternative control of apple replant disease

Is fumigation the only option? By Anna Mouton.

Apple orchards have a limited lifespan, and sites for apple orchards are finite, so new apple orchards are regularly established where old ones have been removed. These new orchards are at risk of apple replant disease, which will prevent them from reaching their full potential. Control of apple replant relies on protecting trees from the outset. Fresh Quarterly spoke to two experts about alternative strategies for managing the disease.

Are there alternative chemical options?

Fumigation is the only reliable method for replant control in South Africa, according to Prof. Adéle McLeod of the Department of Plant Pathology at Stellenbosch University, but alternatives are needed. “There’s international market resistance to fumigation, especially because the chemicals are broad-spectrum. Many people see it as the destruction of the organisms in the soil.”

McLeod points out that research has shown the effects of fumigation to be short-lived — the population of organisms in fumigated soil is indistinguishable from that in unfumigated soil within two years of fumigation. She believes that this is because soil organisms in the unfumigated work row are able to recolonise the fumigated tree row.

One reason why fumigation works so well is that it targets a wide range of disease-causing organisms. There are several organisms that can contribute to apple replant disease, and there’s no easy way to know which ones are going to cause problems on a given site. Treatments that are too specific may miss the mark.

“What we found on this side of the world, was that sometimes when we used a less broad-spectrum chemistry that merely targeted the oomycetes, we ended up with more disease caused by fungi,” relates Dr Mark Mazzola, a plant pathologist affiliated with the United States Department of Agriculture in Washington State, as well as with the Department of Plant Pathology at Stellenbosch University.

Mazzola explains that when two disease-causing organisms occupy the same niche, controlling one gives the other an opening to dominate. “So I think there are opportunities to utilise some more selective chemistries, but you really have to know what the most important factor in your replant setting is that you need to control.”

A recent study by Mazzola, McLeod, and co-workers looked at the efficacy of standard fumigants and semi-selective chemicals in managing apple replant disease in orchards in Grabouw, the Witzenberg Valley, and the Koue Bokkeveld. They compared an untreated control to standard fumigation with two different formulations of chloropicrin and 1,3-dichloropropene; treatment with a cocktail of semi-selective chemicals; fumigation combined with treatment with semi-selective chemicals; and methyl bromide fumigation.

The semi-selective chemicals in the study were fenamiphos, imidacloprid, metalaxyl, and potassium phosphonate. The first three chemicals were applied together as a soil drench after planting, and the potassium phosphonate was applied as a foliar spray or trunk paint. Phosphonates were applied regularly for three years after planting.

Trees showed similar growth performance 3–4 years after planting regardless of the treatment that was used, and all treatments resulted in significantly better growth than no treatment.

The researchers also measured yields, and concluded that fumigation with a product containing a higher percentage of chloropicrin is more effective than using a formulation with a lower chloropicrin content. Their results — see figure 1 — showed that a formulation containing 57% chloropicrin and 38% 1,3-dichloropropene gave better results than a formulation containing 33% chloropicrin and 61% 1,3-dichloropropene. The researchers concluded that the 57% chloropicrin fumigant can be as effective as methyl bromide.

Treatment with the 57% chloropicrin fumigant appeared to be less effective in the Witzenberg orchard. McLeod believes that this was probably due to incomplete removal of old tree roots, and to replanting the orchard too soon. “It is important to keep in mind that the fumigants that replaced methyl bromide are less forgiving regarding bad fumigation practices.” Combining fumigation with semi-selective chemicals may be useful in such cases.

Employing the combined effect of semi-selective chemicals and fumigation may also help to address the introduction of disease-causing agents in nursery stock. However, the semi-selective chemical used against nematodes in this trial, fenamiphos, is likely to become unavailable to South African growers in the near future.

McLeod is currently involved in another project that includes investigation of alternatives to fenamiphos. The project is still ongoing, and so far the researchers have established greenhouse trials.

Beyond chemical control

When asked what the important questions are about apple replant disease, McLeod replies, “We need to know how to control it in an environment-friendly, cost-effective manner.”

“Our growers in Washington State are interested in developing alternative approaches to soil fumigation, just because we know the fumigation effect is so short-term,” says Mazzola. “In the state of California, which has very different environmental regulations, they’re moving into a non-fumigation methodology for regulatory reasons.”

Mazzola has been working on the use of mustard-seed meals to control apple replant disease for two decades. “We’ve developed a formulation that’s capable of suppressing all of the target pathogens that we’re aware of.” The formulation is a mix of seed meals from a brown- and a white-mustard cultivar. Mustards are brassicas, and the seed meal is usually a by-product of oil extraction for biodiesel production.

A recent trial compared seed-meal amendment to standard chloropicrin-1,3-dichloropropene fumigation for control of apple replant disease in Washington State. Seed meal was applied to the tree row only, incorporated to a depth of 15–20 centimetres, and covered with plastic. The plastic is removed two weeks after treatment.

Soil application of the mustard-seed meal formulation was as effective in controlling apple replant disease as fumigation, and also suppressed weed growth. An application rate of 4.4 tonnes of seed meal per hectare gave the best results.

“In our work, a major advantage of either the seed meal or the anaerobic soil disinfestation treatment is that we achieve excellent weed control,” observes Mazzola, “whereas we achieved no weed control with the chloropicrin-1,3-dichloropropene fumigant.”

The researchers found that the mustard-seed meal changed the microbial population of the soil for as long as two years after application, whereas the microbial population in the fumigated soil was the same as that of untreated soil within a year after treatment. An added bonus of seed-meal amendment was the increase in bacteria and fungi that inhibit various fungi, oomycetes, and nematodes that attack plants.

“Whereas soil fumigation may suppress the lesion nematode for maybe the first growing season, depending on which fumigant you use, we see that in our seed-meal soil we get two or three years of extended suppression,” says Mazzola. “And that’s because of the transformation in that soil microbiome.”

One downside of mustard-seed meal soil amendment is the cost. In the United States, the application of seed meals is likely to cost about twice as much as conventional fumigation.

Anaerobic soil disinfestation

Anaerobic soil disinfestation is a complicated name for a simple process that has shown promise in controlling apple replant disease. The idea is to remove oxygen from the soil, thereby choking disease-causing organisms while boosting some of their competitors. Oxygen levels are dropped by adding organic matter and letting it rot while excluding air.

In trials conducted in Washington State, anaerobic disinfestation was compared to standard chloropicrin-1,3-dichloropropene fumigation. For the anaerobic disinfestation method, organic matter was either produced on site by growing cover crops, or brought in as hay. When cover crops are grown on site, anaerobic disinfestation has the advantage of being less expensive than fumigation.

The organic material was mowed into small pieces and incorporated into the soil to a depth of 15–20 centimetres. Planting rows were covered with plastic. The soil was then irrigated to ensure that soil moisture remains above 30% field water capacity. After three weeks, the plastic was removed, and after another three weeks, trees were introduced.

Preliminary results showed that anaerobic disinfestation can control apple replant disease as well as fumigation does, provided that soil moisture levels remain above 30% field water capacity. More research on anaerobic soil disinfestation is needed, especially relating to its use in different soil types.

When it comes to soil amendment with organic material more broadly, McLeod and Mazzola agree that this isn’t a solution for apple replant disease. “Not all composts are generated from the same material, so you can get some different outcomes, depending on what type of compost you utilise,” cautions Mazzola. “Sometimes you actually exacerbate the disease.”

Rooting out replant

“I think host genetics is a huge part of replant control,” says Mazzola. He describes the ongoing efforts of the rootstock breeding programme in Geneva, New York State, to achieve resistance to apple replant disease.

“They’ve identified genotypes that are more tolerant to the disease phenomenon. But even though they outperform some of the historic rootstocks, like some of the Malling rootstocks, they’re probably going to have to be integrated with another disease control mechanism because they’re only tolerant, not resistant.”

Hortgro recognises the importance of genetics in combatting replant, and has funded research projects to evaluate rootstock tolerance to the disease. Recently, a project to evaluate rootstocks was initiated under the leadership of McLeod, Dr Iwan Labuschagne of specialist cultivar-evaluation company Provar, and Dr Xolani Siboza of the Department of Horticultural Science at Stellenbosch University. The first trees are due to be planted this spring.

Another new project, led by McLeod, is specifically investigating rootstock tolerance to root and crown rots. She will screen thirteen apple rootstocks in a greenhouse trial by challenging them with laboratory-grown Phytophthora cactorum. This project is also set to start this year.

Mazzola believes that new technologies will revolutionise our understanding of apple replant disease, and speed up the development of control measures. For example, he is part of a team that used genome sequencing to explore the microbial communities associated with replant-tolerant and -susceptible rootstocks grown on replant soils amended with mustard-seed meal.

The researchers found that tolerant rootstocks had higher numbers of microbes that protect against apple replant disease, whereas susceptible rootstocks harboured disease-causing microbes. “The variables that need to be considered are not only the microbial community in a soil, and the soil type, but also the genetics of the tree itself,” says Mazzola. “There are certain rootstock genotypes that might be more efficient at putting up with a certain pathogen complex than other rootstock genotypes.”

For now, fumigation remains the mainstay of apple-replant-disease control in South Africa. But Mazzola is confident that change is coming. “From a research standpoint, it’s an amazing time to be working in soil microbiology. But from a grower’s standpoint, these new technologies are definitely down the road going to influence the productivity of their systems.”

Image: Mustard-seed meal is incorporated into the soil by rotovation.

Supplied by Mark Mazzola.