Management of soilborne diseases in small farms with eco-friendly treatment options

Project Overview

Project Type: Partnership
Funds awarded in 2015: $14,792.00
Projected End Date: 12/31/2017
Region: Northeast
State: West Virginia
Project Leader:
Dr. Mahfuz Rahman
West Virginia University

Annual Reports

Information Products


  • Vegetables: tomatoes


  • Education and Training: demonstration, extension, farmer to farmer, on-farm/ranch research
  • Pest Management: biofumigation, biological control, biorational pesticides, integrated pest management
  • Production Systems: organic agriculture
  • Soil Management: soil quality/health

    Proposal abstract:

    The purpose of this project is to find sustainable management options for soilborne diseases through on-farm trials of biofumigants and biological antagonists in grower collaborators’ farms. West Virginia is dominated by small scale vegetable growers with strong local ties who like to grow their own food or sell in the local farmers markets. Due to the restricted farm size, they have to grow similar vegetable crops in the same area without an effective rotation scheme. As a result, soil borne pathogen population builds up over time causing significant disease problem. Data collected from small farms over last two years indicated that tomato growers incurred heavy losses due to Bacterial and Verticillium wilt. Biofumigation and/or biologically based options for managing these pathogens are critical needs to these small predominantly organic growers due to the unavailability of custom applicators of chemicals or close proximity of farms to the homesteads. Crop failure in grower collaborators farms of this project have been linked with soilborne pathogens. Recent research has shown successful suppression of soilborne pathogens if biofumigants are incorporated properly in the soil. The grower cooperators have shown strong interest in conducting trials in their farms to find best biologically based treatment options. They are willing to share the results with other growers, participate in field days and talk at farmers’ market association. Additional outreach activities by PIs will include state IPM conference, annual small farm conference, Mid Atlantic Fruit and Vegetable Convention, articles in IPM chronicle and farm bureau updates

    Project objectives from proposal:

    For the soilborne disease problem that we identified previously, our primary objective is to determine efficacy of organically acceptable products and disseminate technical information to support rapid adoption.

    Specifically, our objectives are to:

    1. Identify wilt causing organisms up to race/pathovar level to better understand population structure in WV that should help matching resistant variety;
    2. Assess the efficacy of soil treatment with bio-fumigants and biological antagonists in mitigating soilborne disease severity;
    3. Assess the usefulness of grafted tomato in managing wilt disease;
    4. Measure yield advantage due to treatment of soil with potential bio-fumigant and biological antagonists;
    5. Disseminate the technology to organic growers and small farmers through individual communication, grower meetings and conferences, annual field day events, newsletters and cooperative county extension programming.
    6. Problem description. Soilborne diseases have caused serious losses to vegetable growers in West Virginia for last few years, especially tomato growers experienced total crop loss in many counties of the state due to Verticillium and/or Bacterial wilt. Soilborne pathogen Rhizoctonia and Fusarium were also identified as major problems on Snap beans and Cucurbits, respectively. WVU Extension Horticulturist Lewis Jett and Plant Pathologist Mahfuz Rahman visited many small farms and identified the problems related to soilborne pathogens. However, further analysis of the pathogen to determine race or pathovar would take additional work to recommend resistant variety or grafted plants on resistant rootstocks to the growers. This project will enable us to perform analysis of these organisms to determine the prevalent races of Verticillium in West Virginia. For example, two races of Verticillium dahliae cause wilt on tomatoes and some varieties possessing Ve gene are resistant against race 1 but not race 2. Small farm holders in most cases attempt growing tomatoes despite perceived risks posed by soilborne pathogens. These growers do not have enough acreage to rotate their crop or leave infested area fallow for a few years. Some growers are interested in fumigating their lands but find it very difficult to hire custom applicators that can do the job for them. Although we have documented the problems of soilborne diseases in many small farms, no effective control methods are available to the organic growers and those who are not interested in using chemicals. Most growers prefer organically acceptable products especially those can be applied with composts for managing diseases. The number of organic growers has been growing steadily over years. Predominant soil texture in WV farms is clay. Efficacy of biofumigation and biologically based products for managing soilborne pathogens in clay soils have not been researched sufficiently. There is a critical need for conducting on-farm trials with known infestation levels to determine the efficacy of potential biofumigants and organic seed/transplant treatments. Vegetable growers in many cases find it very difficult to link soilborne pathogen problems with foliar symptoms they observe.

      Proposed solution. Our general recommendations for managing soilborne pathogens are to rotate fields and use resistant variety. However, sometime growers’ preference for a special variety and unavailability of suitable land areas to rotate, makes multi tactics based IPM methods more practical and useful. For the soilborne disease problem that we identified previously, our primary objective is to determine efficacy of organically acceptable products and disseminate technical information to support rapid adoption.
      Specifically, our objectives are to:
      1. Identify wilt causing organisms up to race/pathovar level to better understand population structure in WV that should help matching resistant variety;
      2. Assess the efficacy of soil treatment with bio-fumigants and biological antagonists in mitigating soilborne disease severity;
      3. Assess the usefulness of grafted tomato in managing wilt disease;
      4. Measure yield advantage due to treatment of soil with potential bio-fumigant and biological antagonists;
      5. Disseminate the technology to organic growers and small farmers through individual communication, grower meetings and conferences, annual field day events, newsletters and cooperative county extension programming.

      Assessing population structure of Ralstonia and Verticillium (wilt causing pathogen-relates to our objective 1). Our approach is to better understand and characterize the population of soilborne pathogens that cause root infection and wilting of tomatoes in WV. Plants with wilt symptom from un-treated check plots of the proposed trials will be collected in four replicates during 2015 growing season. The tissue samples will be surface sterilized with 10% bleach, rinsed and homogenized with sterile distilled water. Then, the homogenized sample will be serially diluted with double-distilled water (DDW) up to 10-5. Dilution series made for each suspension will be placed onto 2, 3, 5-triphenyltetrazolium chloride (TTC) medium (1% peptone, 0.1% trypticase, 0.5% glucose, 1.8% agar and 0.05% 2,3,5-triphenyltetrazo- lium chloride) to isolate R. solanacearum (Kelman 1954) and cultured at (30 1)° C for 48 h. Based on the colony morphology of R. solanacearum on TTC medium, the viable colonies will be counted for each sample. The isolated R. solanacearum will be confirmed for strain ID by PCR with repetitive primers: 5′-CAGCAGAACCCGCGCCTGATCCAG-3′(pehA#6, upstream fragment) and 5′-ATCGGACTTGATGCGCAGGCCGTT-3′(pehA#3, downstream fragment), according to Gillings et al. (1993). For delineating race structure of Verticillium, isolates will be collected from infected plants and analyzed following the method described by Dylan et al (2014). We selected the primer pair, VdR2F-VdR2R for our study that consistently yielded a 256-bp amplicon in all race 2 isolates when used in the study by Dylan et al. Previously published primer pairs Tr1 and Tr2 (Maruthachalam et al. 2010) specific to race 1 will be used to identify race 1 isolates. PCR based method will substantially reduce time to identify these isolates up to race level compared to traditional pathogenicity assay on hosts carrying gene resistance against one or the other race.

      Determining efficacy of soil treatment with bio-fumigant and biological antagonists (relates to objective 2). We will conduct two on-farm trials with six different treatments that will inlcude1) Caliente mustard cover crop incorporated in the soil; 2) Dominus (bio-fumigant); 3) Serenade soil (QST 713 strain of Bacillus subtilis); 4) Prestop (Gliocladium catenulatum); 5) Grafted tomatoes and 6) Non-treated control. Treatments will be replicated four times in a randomized complete block design with each replicate plot consisting of 30 ft long and 5 ft wide plastic mulched drip irrigated row. Treated plots will be separated by a 5 ft length of nontreated bed within the bed and single nontreated beds between beds. Vascular wilt susceptible tomato (Solanum lycopersicum) cv (cherry) will be included in the study. Approximately one month old seedlings will be transplanted in the field plots on June 15, 2015. Plots receiving “Caliente” cover crop will be seeded during first week of April and incorporated in the soil end of May followed by covering with VIF plastic mulch. Dominus bio-fumigant will be applied through the drip tape under plastic mulch 15 days before planting. Serenade soil and Prestop will initially be mixed with soil mix that will be used to raise seedlings. These products will also be applied in the holes in the field before transplanting seedlings. Susceptible tomato seedling will be grafted on bacterial wilt resistant rootstock RST-04-105T/DP-105 for location 1 and Verticillium wilt resistant rootstock Maxifort for location 2. Dates of grafting will be adjusted accordingly so that grafted plants become available by June 15, 2015. Each plot will have 8 plants at the row center 4 ft apart from plant to plant. Foliar applications of fixed copper will be made as needed to suppress foliar diseases. Plants will be scouted by grower cooperators for wilt symptom or any stunting and foliar symptom for Verticillium infections. We will collect suspected samples and get isolates and characterize as described earlier.

      Data collection and analysis. Data will be collected on the incidence and severity of wilt in the middle and end of the season. Severity of Verticillium wilt will be measured on a 0-5 scale where 0=no disease symptom; 1 = 1 to 5% leaves with V shaped symptom; 2 = 6 to 10% leaves with V shaped symptom; 3 = 11 to 25% leaves with V shaped symptom; 4 = 26 to 50% leaves with V shaped symptom and some wilting of the plant; 5 = 51 to 100% of leaves with V shaped symptom and totally wilted plant. Disease index for each replicate plot will be calculated from number of plants with symptom and recorded severity on each plant. We anticipate Bacterial wilt will cause total plant wilting and only number of affected plants will be counted and converted as percent infected plants and compared for differences among treatments. The linear mixed model will be used to conduct the analysis of variance in SAS (SAS institute, Cary NC). Treatment will be considered as a fixed effect, and block will be considered as a random effect. Percent data will be transformed using angular transformation (arcsine of square-rooted value) prior to the analysis.

      Measuring yield advantage and economic analyses. Grower cooperators will be asked to keep record of fruit harvest from four plants at the center of each plot. Cumulative yield per plant will be compared for significant differences among treatments. For yield record, only fruits that mature up to ripening will be considered. We will calculate treatment cost for each proposed treatment compared with un-treated check for the additional yield obtained due to each treatment and convert it to equivalent dollar amount.

      Gillings M, Fahy P, Davies C. 1993. Restriction analysis of an amplified polygalacturonase gene fragment differentiates strains of the phytopathogenic bacterium Pseudomonas solanacearum. Lett Appl Microbiol 17:44–48.
      Kelman A. 1954. The relationship of pathogenicity in Pseudomonas solanacearum to colony appearance on a tetrazolium medium. Phytopathology 44:693–695.
      Maruthachalam et al. 2010. Molecular variation among isolates of Verticillium dahlia and polymerase chain reaction-based differentiation of races. Phytopathology 100:1222-1230.
      Short, D. P. G. et al. 2014. Verticillium dahliae race 2. Phytopathology 104:779-785.

      Vascular wilt diseases caused by soil-borne pathogens are among the most devastating plant diseases worldwide (Tjamos and Beckman, 1989). In many cases where crop rotation was not an option, application of methyl bromide would control fungi, bacteria, nematodes and weeds. As methyl bromide was phased out, many alternatives have been used with variable success although organic growers and small growers who can’t use chemical fumigants due to new regulations or lack of the availability of custom applicators left with few options. Biofumigation with isothiocyanates (ICTs) producing plants especially some mustard varieties have shown promising results (Hansen and Keinath, 2013) although inconsistency in the system and disease suppression has restricted its widespread adoption (Motisi et al., 2010). Among the variables, study conditions (e.g. site of the study) and stage of crop incorporation in the soil followed by covering with plastic can have profound effect on level of disease suppression (Matthiessen and Kirkegaard, 2006). Edaphic factors can also greatly influence the soilborne disease control from biofumigation (Gimsing et al., 2009) creating the need of site specific testing. Sarwar and Kirkegaard (1998) reported that glucosinolate (GSLs) concentration was highest at the bud-raised growth stage prior to flowering and higher in spring-versus fall-seeded brassicas. Seed treatment or augmenting beneficial microbial population in soil was also found to reduce seedling mortality from soilborne diseases (Rahman and Punja, 2005). Use of resistant variety may be ineffective if prevalent race of an organism in a geographic region is not known (Hall and Kimble, 1972).

      Gimsing, A.L., Sorensen, J.C., Strobel, B.W., Hansen, H.C.B., 2007. Adsorption of glucosinolates to metal oxides, clay minerals and humic acid. Applied Clay Science 35: 212-217.
      Hall. D. H. and Kimble, K. A. (1972). An isolate of Verticillium found pathogenic to wilt-resistant tomatoes. California Agriculture 26 (9): 3
      Hansen, Z.R. and Keinath, A.P. 2013. Increased pepper yields following incorporation of biofumigation cover crops and the effects on soilborne pathogen populations and pepper diseases. Applied Soil Ecology 63: 67-77.
      Matthiessen, J.N. and Kirkegaard, J.A., 2006. Biofumigation and enhanced biodegrada-tion: opportunity and challenge in soilborne pest and disease management. Crit. Rev. Plant Sci. 25, 235–265
      Motisi, N., Doré, T., Lucas, P. and Montfort, F. 2010. Dealing with the variability in biofumigation ef ficacy through an epidemiological framework. Soil Biology & Biochemistry 42: 2044-2057.
      Rahman, M., and Punja, Z. K. 2007. Biological control of ginseng seedling diseases by Gliocladium catenulatum. Can J. Plant Pathol. 29: 203-207.
      Sarwar, M., Kirkegaard, J.A., 1998. Biofumigation. Plant Soil 201: 91–101.
      Tjamos E.C. and Beckman C.H. 1989. Vascular Wilt Diseases of Plants: Basic Studies and Control. NATO ASI Series H: Cell Biology. Springer-Verlag, Berlin, Germany.

      Spring 2015
      As we have already identified infested farms, this project will move forward very smoothly starting early April 2015 with seeding of the “Caliente” mustard seed for biofumigation cover crop. Sarah Alexandropoulos with the help of seasonal labor will perform this job. PI and Co-PI will also be present to help with plot layout and consultation with grower collaborators in both locations. Tomato seedlings and resistant rootstocks will be raised at the WVU Evansdale greenhouse early May 2015 by Sarah Alexandropoulos. PI and Co-PI will do the grafting to have at least 64 grafted plants ready by June 15, 2015. Soil mix will be pre-inoculated with Prestop (Gliocladium) and Serenade (Bacillus) at the time of seeding in flats for 32 seedlings in each category.
      Summer 2015
      Mustard plants incorporation with the soil followed by covering with plastics, application of Dominus, bed preparation and mulching will be done during last week of May by the student and seasonal help together with PIs and farmer cooperators. Planting will be done on June 15th 2015 by PIs and student help. Disease scouting, watering, fixed copper applications and any other intercultural operations if needed will be performed by grower collaborators.
      July-August 2015: Disease sample collection, pathogen isolation and short-term preservation of isolates by student and PI depending on the appearance of disease.
      August-September 2015: All harvesting and yield record will be kept by the cooperators with the help of student during Disease rating will also be done by PI during these two months. County agent Dr. William Shockey will organize field days in consultation with grower cooperators to demonstrate results to potential growers. PIs will be present to explain how these treatments work to control soilborne pathogens and provide yield advantage. Proper incorporation of biofumigants will also be discussed.
      Fall 2015
      Molecular analysis of the isolates will be performed during October-December 2015 by PI with the help from student. Data analysis will also be completed by the end of the year 2015 and preliminary report will be produced to present in extension meetings.
      Winter 2015
      PIs will attend various conferences (WVUES annual meeting, State master gardeners annual meeting, Mid Atlantic Fruit and Vegetable convention) and present the results.
      Spring 2016
      In the beginning of 2016, we will publish material from the field season distribute them to relevant extension workers and the farmers, as well as any conference attendees who wanted follow-up information. Final report on the project will be prepared by the end of March 2015 and uploaded to SARE reporting system.

      This project is a collaborative effort among WVU Extension Service Specialists, County Agent with Davis college of Agriculture. Dr. Dylan Short who designed primers for discriminating race 1 and race 2 of Verticillium dahliae will provide technical support to characterize isolates from field sites of this project. During our work with small scale vegetable growers last few years, we identified many growers in the state who experienced problem with soilborne diseases and have been looking for solutions. We selected two farms (Shafer Heritage Farms and Vested Heirs Farm) where we diagnosed the disease and marked the areas with uniformly distributed high population of wilt causing organisms. WVU Extension horticulturist Dr. Lewis Jett has been working with these farmers for a long time and developed good rapport. These farmers agreed to cooperate with the project (please see support letter). Vested heirs farm has been in existence for 80 years and new generation is trying their best to introduce best management practice in the farm from pest management to food safety to marketing. They have commitment to get involved in the community and want to continue the agricultural stewardship. As the name implies, they have love for the land passed down from one generation to the next. This farm is a good source of fresh produce in the area and local farmers market. Shafer heritage farm located near Bruceton Mills, WV has also been a popular place for the community to find fresh picked produce. Joyce Shafer, the owner of the farm has been working with WVU Extension Service to find new opportunities and science based solution in farm management. This farm is considered as a small farm that needs intensive management to keep it productive. As WVU extension service is committed to bring science based solutions of farm problems to growers, this project will create opportunities to foster partnership with Davis College scientists, growers and county personnel.

      This project is an expansion of PIs ongoing efforts for helping growers finding appropriate technology to better manage plant problems including soilborne pathogens. Dr. Mahfuz Rahman is an extension plant pathologist who is involved with research in vegetables and small fruits. He is also the director of WVU Plant Diagnostic Clinic and keeps track of major disease problems in farmers’ field, sends AgAlert to county agents, crop consultants and growers in case of an immediate danger of disease outbreak. WVU plant diagnostic clinic is equipped with PCR, real-time PCR and all essential molecular reagents to perform molecular analysis by the PI. This lab also has facilities for long term preservation of isolates. PI is well trained in molecular methods to conduct such study. In addition, PI is involved in conducting field trials with conventional and organic disease control products on a regular basis and has extensive experience in evaluating efficacy of products by collecting data on disease incidence and severity. Dr. Rahman has been collaborating with Dr. Lewis Jett on improvement of soil health and nutrient cycling with cover crop project since 2012. He also has also been implementing collaborative Extension IPM project with WVU Extension Service (WVUES) entomologist, weed scientist and WV state university horticulturist Dr. Barbara Liedl. Co-PI of the project Dr. Lewis Jett is a WVU-ES Horticulturist who has been conducting on-farm trials on many different aspects of vegetable production, season extension technology with high tunnels for last 15 years. He has been working with vegetable and small fruit growers all over the state and is familiar with problems and prospects of vegetable farming in small scale farms. He has a “Rain-Flo 2500 Raised Bed Plastic Mulch Layer” that will be used in preparing beds and laying plastic in the proposed study at site 1. He also has nutrient injector for the drip irrigation system that will be used for the application of biofumigant “Dominus”. Grower collaborator at site 2 already has all these facilities on site. Preston County agent Dr. William Shockey has been involved with assisting with implementation of many similar projects with growers in the county and has agreed to organize growers training and field day on managing soilborne diseases. He will also help grower collaborators scouting for disease incidence, collecting sample and send it to PIs for further analysis. Sara Alexandropoulos is an undergraduate student technician working with PI. She is expected to graduate in the spring of 2015 with Horticulture major and pursue graduate study in the area of sustainable agriculture.
      The principal target audience for this project is current and potential or transitioning small organic vegetable growers and members of WV Farmers Market Association. Major objective of the research and outreach is to connect with above mentioned clientele by conducting trials in their farms which will enable them to witness and evaluate the effect of treatments and thereby accelerating adoption of technology. Along with conferences and field days, we will follow through with the farmers with research updates. The major incentive for this work is that the farmers are eager to see some treatments in the study work to their expectation. Although the target audience for this outreach is small scale organic growers, this practice may be applicable to conventional commercial growers. We anticipate that mustard cover crop and biological antagonists of soilborne pathogens will be welcome by most growers as sustainable means of disease control and soil health improvement. The main output generated from these on-farm trials will be a long term science-based sustainable solution for soilborne diseases to small farm operators. We will develop web-based publications (bulletins, fact sheets, etc.) on non-chemical means for management of soilborne pathogens and share those with farmers through different list serves and links with WVU Small farm center and IPM sites. Results will be presented at WVU organic farm (certified) field day together with demonstration of soil treatments with biofumigants and mustard cover crop. In addition, we will offer training sessions in concert with other programs such as the WV Small Farm Conference, NE SAREPDP training opportunities, State Master Gardeners’ annual meeting and as requested by grower groups. Workshop on grafting tomatoes on rootstocks resistant to soilborne pathogens will also be offered concurrently during Small Farm Conference and Organic Farm Field days.

    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.