Anaerobic Soil Disinfestation to Control Soilborne Pathogen Rhizoctonia solani in Vermont Field Conditions

Progress report for ONE19-343

Project Type: Partnership
Funds awarded in 2019: $30,000.00
Projected End Date: 12/31/2021
Grant Recipient: University of Vermont
Region: Northeast
State: Vermont
Project Leader:
Dr. Deborah Neher, PhD
University of Vermont
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Project Information

Project Objectives:

This project will test whether Anaerobic Soil Disinfestation (ASD) can be used to control soilborne pathogen R. solani in Vermont field conditions. There are three components: 1) To provide multiple potential management options, we will test multiple carbon sources (compost, poultry manure, and cover crop) that are available and already used by organic farmers against a non-amended control; 2) We will assess efficacy over two years to answer the farmer question “how often do I have to do this?”; and 3) To assess practical and financial viability, a cost benefit analysis will be performed at a micro-scale farm and a > 10 acre farm in collaboration with the farm partners.

If the proposed project demonstrates that ASD successfully controls R. solani in field-grown crops over multiple years at multiple farms, it will offer robust evidence to growers that ASD can be used within existing management strategies to control soilborne pathogens. It would provide justification for investigation of ASD in high tunnels and greenhouse soils. Further, it will enable growers to make informed financial cost benefit decisions about the use of this practice on their farm. Finally, it provides a method to manage a persistent soilborne pathogen that meets organic certification regulations.


Rhizoctonia solani is an aggressive pathogen and a saprophyte that can survive as sclerotia under adverse environmental conditions. Up to 70% crop losses on lettuce is caused by R. solani on field-grown lettuce in the US. Control is difficult due to its extremely wide range of plant hosts including Solanaceae, Fabaceae, Asteraceae, and Brassicaceae. Bottom rot of lettuce, caused by R. solani, is a recurring problem for vegetable growers in Vermont, reducing field lettuce yields by 10-50%, and up to 80-90% for lettuce in over-wintered high tunnels. It is a problem exacerbated by increasingly warm and wet fall conditions.

Organic farmers lack proven and effective fungicides to manage the disease and a limited toolbox of management practices such as crop rotation and increasing airflow around plants is relied upon to prevent damage. There is minimal genetic resistance to R. solani and a limited choice of seed varieties that meet the organic certification standards of seed production and pelleting in New York and Vermont. 

Market farms on the micro-scale are increasing in popularity. These farms rely on quick succession of high margin leafy crops such as lettuce to be profitable with a limited land base. Crop rotation is difficult because crop groups are limited and space is less likely to be rotated into a non-host crop or fallowed. Small scale growers often extend the season into the early spring and late fall, overwintering greens in tunnels. This combination of factors (limited rotation, extended season, succession of lettuces, higher humidity in tunnels) is prime opportunity for colonization by R. solani, making new growers at this scale a potentially vulnerable population.

Anaerobic soil disinfestation (ASD) is a treatment to reduce R. solani pressure in soil. ASD is implemented through addition of an easily degradable organic matter (labile C) followed by irrigation saturation and covering with an oxygen-impermeable tarp. Soil microbes consume available oxygen and anoxia shifts the balance toward fermentation and facultative anaerobes. Most pathogens die from oxygen deprivation, but others are sensitive to volatile organic compounds produced by facultative or obligate anaerobic microorganisms. To our knowledge, the proposed study will be the first field test of ASD on soilborne pathogens of vegetables crops in the northeastern US.  If ASD works as an effective control in northeast growing conditions, it would be a low-cost option that could be easily integrating into existing management strategies that include the practice of tarping.

Installing the silage tarp for the Anaerobic Soil Disinfestation (ASD) treatment (June 2020)


Click linked name(s) to expand
  • Dave Marchant
  • Bruce Kaufman


Materials and methods:

The experiment will use a randomized complete block design with four blocks at each of two farms. There is a history of bottom rot of lettuce identified by both grower and researcher at each farm. Each block will contain 1 plot of each treatment arranged randomly for a total of 32 samples per year (3 treatments + 1 control x 4 planting blocks x 2 farms). Plots will be a 3.05m (10’) length of bed (containing 3 rows of plants, with 0.305 m (12”) between plants, and 30 to 41 cm between rows.

Block location within the field was based on grower and researcher observation of disease incidence and severity in August of 2019.

Treatments will include commercial compost (Black Dirt, Stannard, Vermont), poultry pellets, and chopped rye cover crop all compared to an untreated control.

We completed an on farm assessment in 2019 at the originally proposed farms, Riverside and GoodHeart, to confirm ‘hot spots’ of Rhizoctonia solani to identify the locations for experimental block establishment in summer 2020. The pathogen at GoodHeart was identified as Pythium spp. rather than R. solani. Therefore, we replaced GoodHeart with River Berry Farm where we confirmed the pathogen of focus. Riverside Farm has agreed to grow a winter rye cover crop that provides sufficient material for both farms. Dataloggers with sensors were installed at each farm to measure soil temperature, water potential, and redox potential. We lost some sensor data in 2020 due to battery failure but the problem has been corrected for 2021.

We planned to quantify pre-treatment disease assessment by planting radish seed 1 to 2 cm (0.5 to 1”) seed spacing with rows 30 cm (12”) apart in 2019. However, we were unable to isolate Rhizoctonia solani from one farm and had to replace that farm with another one. Environmental conditions were unfavorable for disease establishment by the time we completed site identification. Instead, we postponed the pre-treatment assessment to summer 2020 prior to application of treatments. We completed a mapping of the pathogen at both farms in 2020 prior to performing the ASD treatment.

Research results and discussion:

We originally planned to use a chopped winter rye cover crop for one of our carbon treatments. However, due to the pandemic, we were unable to establish the cover crop in 2020. Therefore, we replaced that treatment with cracked corn which has a similar carbon to nitrogen ratio. We discovered an unanticipated problem with cracked corn. Upon removal of the silage tarp at the end of the ASD treatment, we witnessed a plume of Aspergillus spores arising from the soil, a fungus capable of inciting a respiratory ailment called aspergillosis . A subsequent controlled experiment confirmed the fungus was originating from the corn itself which affirms are intent to disband use of cracked corn and revert to our original plan of using a cover crop in 2021. We transplanted lettuce into the treated soil 1-2 days after tarp removal. Unfortunately, the lettuce experienced transplant shock because the plants had not been hardened off sufficiently. Fortunately, the lettuce recovered within a few days and developed into a productive crop. We will make sure plants are hardened off before transplanting in 2021.

Disease incidence and severity varied by treatment and farm. Incidence and severity of bottom rot was greatest for the cracked corn treatment at both farms. Disease severity was decreased in the treatment receiving compost compared to the untreated control at one farm. No differences in disease severity occurred between poultry pellet and untreated control treatments. Crop yield was inversely related to disease severity.

Rating lettuce for disease severity.
Participation Summary
2 Farmers participating in research

Education & Outreach Activities and Participation Summary

Participation Summary

Education/outreach description:

These will be completed in the next phase of the project.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.