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Evaluating IPM Methods to Control Apple Replant Disease

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Tianna DuPont, Washington State University Extension; Mark Mazzola, USDA-ARS; Shashika Hewavitharana, California Polytechnic University. January 26, 2021.
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 When apple replant disease occurs, it can cost orchardists $70,000 to $150,000 in reduced returns during just the first four years of production. Washington growers generally fumigate using 1-3 Dichloroproprene, Chloropicrin to try to prevent the complex of pathogens which cause replant. But fumigation generally only provides short term benefits. Growers asked for alternatives that may provide longer term benefits and higher returns allowing them to maintain their organic status.

Current study

In 2017 we initiated three studies looking at anaerobic soil disinfestation and bio-renovation using Brassica seed meal treatments that have worked well at a small scale and in field applications in strawberries.  To see if these treatments are ready for field application, we used large field plots of one to twelve-acres where we could look at variability across a field and use field scale equipment. Studies were conducted in three locations with 4 to 5 replications.

Bio-renovation using mustard seed meals releases volatile compounds produced by the interaction between the mustard plant compound glucosinolate with a plant enzyme (myrosinase). Volatiles suppress soil-borne disease organisms and can select for beneficial microorganisms that directly parasitize plant pathogens and induce plant defense. See Figure 1.

Anaerobic soil disinfestation (ASD) is a process where organic carbon sources are added to the soil and then the soil is flooded using irrigation and covered by a gas impermeable plastic film. During anaerobic decomposition, microbes release volatile compounds which are toxic to plant parasites and pathogens. See Figure 2.

A fumigated control (1,3-Dichloropropene, Chloropicrin) and a no-treatment control were included in each site.

We planted trees the spring following summer/fall soil treatments. Orchards were planted to cv WA 38 on G41 in Othello (spring 2018), cv TC2 on Bud 10 Rootstock in  Tonasket and cv WA 38 on G41 and M9.337 in Rock Island (spring 2019).

Figure 1. Steps to Brassica seed meal bio-renovation.

Step 1. Apple Brassica seed meal when soils are warm.

Pescadero Gold Mustard meal (1:1 formulation of B. junco and S. alba) was applied using a Whatcom spreader at 0.4 lb per ft2 to the 4 ft wide tree row (3.5 tons/orchard A).

Step 2. Incorporate mixing well.

image shows a tractor pulling a rototiller attachment making individual tilled rows.
Material was incorporated using a rototiller to 10 in.

Step 3. Totally impermeable film.

image shows a tractor with the film spool applicator laying down the barrier following behind the rototiller tractor.
Totally impermeable film (TIF; 1.2 ml) was laid within 30 min of incorporating to trap volatile gases. Plastic should be tight to soil.

Step 4. Treatments for 3 weeks.

Leave TIF in place for 3 weeks.

Step 5. Aerate soil 3 weeks or more.

Remove TIF and allow soil to aerate. Volatile compounds from bio-renovation are phytotoxic. Bio-renovation was performed the fall before planting.

Figure 2. Methods for anaerobic soil disinfestation (AASD) employed at three field sites in WA.

Step 1. Carbon source from grass cover crop or hay 8 to 10 ton per acre.

Tractor shown mowing triticale in rows.
At Othello, the carbon source was triticale seeded at 100 lbs/A with a seed drill. Triticale was terminated at anthesis. Standing biomass of 3.5 ton/A was cut and windowed to form 10 t/A applied biomass.
Image shows Tianna and Shashika hand applying hay in rows.
At Rock Island and Tonasket sites, timothy hay was applied at 8 ton/A to the 4 ft wide tree row.

Step 2. Chop carbon material into small pieces.

Three-panel image: First image is close-up of the flail mower attachment in action; second image shows grower kneeling down and golding up a handful of the resulting chopped material; third image shows the tractor with flail mower moving down the row.
Material was chopped with multiple passes of flail mower to form small bioavailable pieces.

Step 3. Incorporate.

Tractor with rototiller attachment going down a row.
Biomass was incorporated using a rototiller to 10 in.

Step 4. Tarp with TIF.

tractor with spool attachment laying down film in rows.
Rows were tapped with totally impermeable oil (TIF)1.2 ml black or clear.

Step 5. Maintain soil moisture.

Image shows person shoveling soil along edges of tarp to seal following tractor as it lays tarp in row.
Soil moisture was bought up to and maintained above 30% VWC using a double drip line under TIF.

Step 6. Remove TIF and aerate.

Soil was allowed to aerate 3 weeks. Compounds released during anaerobic conditions can be phytotoxic.

New Findings

Did treatments change the soil biology?

Bio-renovation treatments can initiate successive changes to the soil microbiome. For example, during ASD when the soil goes anaerobic bacterial communities generally progress from dominance by Bacillus and Paenibacilus groups to dominance by anaerobic bacteria including Clostridium. Clostridium produce a variety of chemistries such as volatile fatty acids which inhibit fungi and dimethyl disulfide which is nematocidal and fungicidal. Volatile compounds reduce the numbers of pathogens in the soil and ideally the shift in the soil microbiome is more stable than that observed in response to fumigation where communities often quickly revert to high parasite/pathogen levels.

We measured the soil biology three weeks after soil treatments using Terminal restriction fragment length polymorphism (T-RFLP) analysis. The soil bacterial and fungal communities in the Brassica seed meal treatment were different than the no-treatment control and the fumigated control in all three sites. In the anaerobic soil disinfestation treatment bacterial and fungal populations were different than in the no-treatment control in Rock Island and Tonasket but not in Othello. Lack of soil biology transformation in Othello ASD treatments was likely because those soils did not stay wet enough to become anaerobic when we used sprinkler irrigation. When treatments were performed again in Othello using drip vs sprinkler irrigation application microbial communities did shift in ASD. We looked at microbial communities again the fall after trees were planted using high-throughput DNA sequencing of soil in the root rhizosphere (Figure 3). A year after treatment bacterial communities were still different in Brassica seed meal treated soil compared to non-treated soil in Tonasket and Rock Island as well as two years later in Othello.

Images shows a gloved hand dangling a root mass with small clods of soil attached.
Figure 3. Rhizosphere soil is the soil directly influencing plant roots. See the small clods of soil adhered to and tangled in fine plant roots above.
Image shows the orchard test site with researchers spread out amongst the trees sampling the soil at the base of trees.
Figure 4. Researchers sampling rhizosphere soil 1 year after planting in anaerobic soil disinfestation (right) and Brassica seed meal (left) treatments in Rock Island, WA.
Bar graph comparing treatments at all sites.
Figure 5. Effect of replant management strategies on tree growth 1 year after treatment. Brassica seed meal bio-renovation (BSM), Anaerobic soil disinfestation (ASD), fumigated control (FUM), no-treatment control (NTC).
Impacts on tree growth  

Cost-benefit over the first five years will tell us whether treatments were successful. To give you a sneak peek let’s look at initial tree growth. Tree growth in Brassica seed meal treatments was greater than or equal to tree growth in fumigated plots at all sites during first year growth as well as in second year growth in Othello (Figure 5). The anaerobic soil disinfestation treatment was more variable. In Tonasket, anaerobic soil disinfestation tree growth was greater than the no-treatment control but less than the fumigated control. In Rock Island anaerobic soil disinfestation tree growth on M.9 and G.41was as good as the fumigated control and greater than the no-treatment control. In Othello, the anaerobic treatment was fumigated in order to avoid risking four acres of grower trees after anaerobicity was not achieved and thus impacts are not reported here.

Tips for Growers

Brassica seed meal bio-renovation is looking promising as an alternative to fumigating with 1,3-Dichloropropene, Chloropicrin. If you are considering this option keep in mind that not all brassica seed meals are equal. The seed meal used here was a 1:1 formulation of B. juncea and S. alba (Mazzola 2015). Seed meals are often processed at different temperatures and with different grinding methods which affect the quantity of active chemistry that is released. Tests should be conducted to determine the type and quantity of glucosinolate contained in the seed meal that you intend to use. To date in the US, the Brassica seed meal we used is labeled only as a fertilizer. Until products have the appropriate labels as a soil fungicide/nematicide, application for this use is not legal. Remember that soil temperature and moisture are important. These are biological processes where moisture and temperature affect the activity of soil biology and the movement through the soil of the compounds they produce. For Brassica seed meal, treatment soil should be warm (above 70° C) and moist. Last, application rate is important.

Anaerobic soil disinfestation resulted in significant changes in composition of the rhizosphere microbiome and tree growth that was better than the no-treatment control in three of four experiments but not always greater than the fumigated control.  It will be essential to keep soil wet (above 30% moisture) and reach anaerobic conditions for success. In sites with high pratylenchus nematode populations, higher carbon inputs and longer incubation times might be necessary for success.

Next steps

We plan to follow these plots for at least three more seasons to have five years of tree growth and three years of harvest data. Returns from packed fruit over the long-term compared to costs will let us track success. Additional work is also needed to further improve the practical application of treatments.

For further information

DuPont, S. T, Hewavitharana, S.S., Mazzola, M. Field scale application of Brassica seed meal and anaerobic soil disinfestation for the control of replant disease. Applied Soil Ecology (submitted Sept 2020).

Wang, L., and Mazzola, M. 2019. Field evaluation of reduced rate Brassicaceae seed meal amendment and rootstock genotype on the microbiome and control of apple replant disease. Phytopathology 109:1378-1391.

Mazzola, M., Hewavitharana, S. and Strauss, S. L. 2015. Brassica seed meal soil amendments transform the rhizosphere microbiome and improve apple production through resistance to pathogen re-infestation. Phytopathology 105:460-469.

Mazzola, M., Muramoto, J., Shennan, C., 2018. Anaerobic disinfestation induced changes to the soil microbiome, disease incidence and strawberry fruit yields in California field trials. Appl. Soil Ecol. 127, 74-86.

Hewavitharana, S.S., Mazzola, M., 2016. Carbon source dependent effects of anaerobic soil disinfestation on soil microbiome suppression of Rhizoctonia solani AG-5 and Pratylenchus penetrans. Phytopathology 106, 1015–1028.

Hewavitharana, S.S., Reed, A.J., Leisso, R., Poirier, B., Honaas, L., Rudell, D.R., Mazzola, M., 2019. Temporal dynamics of the soil metabolome and microbiome during simulated anaerobic soil disinfestation. Front. Microbiol. 10, 2365.

Funding Sources & Acknowledgements

 This project was supported by grants from the Washington State Tree Fruit Research Commission grant # 10211000 and the USDA Crop Protection grant # 2017-70006-27267. Thank you to in-kind support from Progen Seed, Trident Ag Products, Farm Fuel Inc and generous support of labor, materials, and equipment from orchardists Mike Robinson, Jim Baird, and Sam Godwin.


Table 1. Field Operations Othello, WA
Anaerobic soil disinfestation application
Operation Implement/Equipment Details Date
Fertilize April 2017
Tillage John Deere 7200/ 15 ft disc April 2017
Seed triticale John Deere 7200/ Great Plains seed drill 95 lbs per acre April 19, 2017
Irrigation Hand lines (R33 sprinklers) 6 gal per min, 0.26 inch per hr May-June 2017
Cut and swath John Deere 7200 R450/ swather 4 ft windrow June 28 2017
Chop Pak flail 0.7 mph July 3, 2017
Incorporation John Deere 7200/ Celli rototiller 8 inch depth July 4, 2017
Tarping Kubota M8540/ Mulch layer Mechanical Transplanter Co Model 90 July 7, 2017
Brassica seed meal application
Operation Implement/Equipment Details Date
Pre-irrigation Hand lines (R33 sprinklers) 6 gal per min, 0.26 in per hr July 15, 2017
Mustard meal application John Deere 5083/ Whatcom mulch spreader Settings: 4 low, 1700 rpm, belt 5, floor 4, gate 12.5 inch July 19, 2017
Incorporation John Deere 7200/ Celli rototiller 8 inch depth July 19, 2017
Tarping Kubota M8540/ Mulch layer Mechanical Transplanter Co Model 90 N/A July 19, 2017


Table 2. Filed Operations Rock Island, WA
Anaerobic soil disinfestation application
Operation Implement/Equipment Details Date
Pre-Irrigation Sprinkler system (R5 sprinklers)/ Big gun system (8mm nozzle) 1.5 acre-inch applied July 2-4, 2018
Hay distribution By hand 8 ton per acre July 4, 2018
Hay chopping Falail mower July 4, 2018
Incorporation Mascchio Rototiller 8 inch depth July 5, 2018
Tarping Mechanical Transplanter N/A July 5, 2018
Saturation Drip irrigation to flood soil 0.44 acre-inches per hr July 6-27, 2018
Brassica seed meal application
Operation Implement/Equipment Details Date
Mustard meal application Whatcom compost spreader 750 Settings: 2  floor, 2  belt July 6, 2018
Incorporation Mascchio Rototiller 8 inch depth July 6, 2018
Tarping Mulch layer Mechanical Transplanter Co Model 90 Within 20 min of mustard incorporation July 6, 2018


Table 3. Field Operations Tonasket, WA
Anaerobic soil disinfestation application
Operation Implement/Equipment Details Date
Pre-Irrigation Big gun system (8mm nozzle) 5 acre-inch applied in 12 hr sets Aug 2-6, 2018
Hay distribution By hand 8 ton per acre Aug 8, 2018
Hay chopping Falail mower Aug 8, 2018
Incorporation Mascchio Rototiller 8 inch depth Aug 8, 2018
Tarping Mulch layer Mechanical Transplanter Co Model 90 N/A Aug 8, 2018
Saturation Drip irrigation to flood soil 0.44 acre-inches per hr Aug 8-29, 2018
Brassica seed meal application
Operation Implement/Equipment Details Date
Mustard meal application Mill Creek mulch spreader 1.7 lbs per tree row ft
Settings: 4 floor, 4 belt
Aug 9, 2018
Incorporation Mascchio Rototiller 8 inch depth Aug 9, 2018
Tarping Mulch layer Mechanical Transplanter Co Model 90 Within 20 min of mustard incorporation Aug 9, 2018


Table 4. Treatment Costs
Anaerobic Soil Disinfestation (ASD) – Carbon grown in place.
Field Activity hrs/A $/hr $/A
Tillage 0.25 $40 $10
move irrigation triticale 4.0 $13 $52
seeding triticale 0.25 $40 $10
cut and swath triticale custom $50
flail 1 $40 $40
hay rake custom $7
hand rake 2.8 $13 $36
move irrigation for ASD 4.0 $13 $52
lay plastic 2.0 $40 $80
Supplies $/unit unit unit/A $/A
triticale seed 0.32 lb   100 $32
Totally impermeable film 0.06 ft 4200 $252
Equipment equip yrs amortized A/yr $/A
hand lines   $650 10 50 $1.30
flail $4,000 10 50 $8
plastic layer $2.300 10 50 $5
seed drill
Total cost $635
Anaerobic Soil Disinfestation (ASD) – Hay carbon source
Field Activity hrs/A $/hr $/A
pre-irrigate 3 $14 $41
apple hay 16 $14 $213
flail hay to chop 1 $40 $40
place drip lines 5.25 $14 $71
lay plastic 2 $40 $80
Supplies $/unit unit unit/A $/A
hay $100 ton 8 $800
hay shipping $500 ea 1 $500
drip line $0.07 ft 8400 $546
drip couplings $3.63 ea 20 $73
Totally impermeable film $0.06 ft 4200 $267
Equipment equip yrs amortized A/yr $/A
flail $4,000 10 50 $8
plastic layer $2,300 10 50 $5
Total cost $2,642
Brassica seed meal bio-renovation
Field Activity hrs/A $/hr $/A
irrigation 4 $13 $52
mustard meal application 2 $13 426
incorporation 2 $13 $26
tarping 2 $13 $26
Supplies $/unit unit unit/A $/A
mustard meal* $0.85 lb 6720 $5,712
Totally impermeable film $0.06 ft 4200 $267
Equipment equip yrs amortized A/yr $/A
mulch spreader $22,000 10 100 $22
plastic layer  $2,300 10  50 $5
Total cost $6,135
Field Activity hrs/A $/hr $/A
Total cost custom $900

*1.6 lbs per tree-row-foot for 4 foot wide tree strips.


Tianna DuPontImg1380

WSU Extension Specialist, Tree Fruit

(509) 663-8181 ext 211 articles may only be republished with prior author permission © Washington State University. Republished articles with permission must include: “Originally published by Washington State Tree Fruit Extension Fruit Matters at” along with author(s) name, and a link to the original article.

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