Identification, assessment and management of soil-borne plant pathogens in vegetable production systems in the Northeast

Final Report for LNE10-296

Project Type: Research and Education
Funds awarded in 2010: $124,851.00
Projected End Date: 12/31/2014
Region: Northeast
State: New York
Project Leader:
Beth Gugino
The Pennsylvania State University
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Project Information


Root diseases affect a wide array of vegetable crops grown throughout the Northeast region, significantly impacting the quality and quantity of marketable yield annually. Among the major root pathogens causing damage to vegetables are Phytophthora, Pythium, Rhizoctonia, Fusarium, Sclerotinia, Thielaviopsis, Verticillium, and Phoma. Not only can these pathogens incite disease individually, but they can also interact with other soilborne pathogen(s) and non-pathogenic organisms and cause more severe and damaging disease complexes. They are also frequently associated with poor soil health. Diagnosis of the root disease(s) and its causal pathogen(s) is critical in designing long-term effective integrated pest management strategies either to prevent or reduce soilborne pathogen populations while improving soil health.

Through five full-day workshops, our project team trained a total of 117 growers, county extension educators and other agriculture service providers in the diagnosing the symptoms and signs of soilborne pathogens and diseases as well as understanding their biology, learning how to assess their prevalence and discussing sustainable management strategies. The interactive nature of the workshop promoted networking and sharing of disease management strategies. Equipping growers and ag service providers with research-based knowledge about soilborne pathogens and skills through these hands-on trainings helped to expand the IPM toolbox of each participant and promote integrated crop management across the Northeast region.

Based on the 42% of participants (30 of 72 surveyed) who returned the follow-up impact survey, a reported 926 growers plus another 810 new Master Gardeners have benefited from subsequent contact with trained extension educators and ag stakeholders through various outreach activities including one-on-one interactions and meeting presentations. The growers, extension educators and other ag service providers continue to use the electronic and hardcopy resources to make on-farm decisions and disseminate information to other farmers and stakeholders. Several growers have already used their acquired knowledge and skills to diagnosis soilborne disease issues on their farms and are adjusting their current production practices to use include the use of more cover well as biofumigant crops, lengthening their crop rotations between susceptible crops, selecting resistance cultivars as well as using seed treatments. These new practices are benefiting the growers will improved plant health and reductions in losses resulting from soilborne pathogens and their resultant diseases.


Root diseases are a problem potentially affecting 100% of the vegetable acreage in the Northeast (USDA Crop Profiles, 2007).  These diseases will become more difficult and critical to manage with the intensification of vegetable production and the adoption of reduced tillage systems. Affected crops include beans, peas, carrots, lettuce, onion, tomatoes, potatoes, cabbage, cucumber, beets peppers, sweet corn, and others (Sherf and MacNab, 1986). Even though in a given year only 10-15% of fields will actually be affected, growers must carefully plan cropping sequences (main cash crops, cover crops and soil-building crops) to manage existing root disease problems as well as proactively manage soils and cropping sequences to prevent root diseases from becoming an economical problem. The lack of a “silver bullet” for managing soilborne pathogens further emphasizes the importance of preventative management. In a 2006 soil health survey mailed to vegetable growers in New York by the Cornell Soil Health Work Team, 64% of respondents (n=170) indicated that soilborne pathogens and diseases affect both yield and profitability on their farm (B. Gugino, personal communication). 

In addition, the increasing use of high tunnels for intensive vegetable production and season extension has led to an observed increase in the incidence and the severity of root diseases incited by Fusarium and Verticillium species in tomatoes and brought out the economic constraints of rotating to non-cash crops in these production systems. Steve Groff, a PA grower, received two consecutive NE-SARE farmer grants (FNE08-636 and FNE09-658) to try grafting tomatoes as a way to overcome soilborne pathogens in high tunnel production. Another example is the significant increase in occurrence and damage of Rhizoctonia-incited diseases on vegetables grown in NY (beets, carrots, cabbage, beans and possibly others). This increased disease is in part due to reduced tillage systems that leave infected crop residue on the surface and to genetic variation in the population of the pathogen (Ohkura et al., 2009; Olaya and Abawi, 1994). Phytophthora blight caused by P. capsici is also of increasing concern because of the long lived nature of the overwintering oospore and the ease with which it is dispersed via contaminated irrigation water and run-off both within and between fields (Hausbeck and Lamour, 2004). Once thought to predominately be a problem in New Jersey and Long Island, growers and extension educators have expressed increasing concerned about Phytophthora blight caused by P. capsici in PA. Phytophthora has been a recurring problem on peppers and cucurbits in the Connecticut River Valley and was recently discovered affecting beans in Connecticut (LaMondia et al., 2010) and on Long Island, NY (McGrath, 2009).

In addition to the pathogens mentioned above (Fusarium, Verticillium, Rhizoctonia and Phytophthora), several other root pathogens including Pythium, Sclerotinia, Thielaviopsis, Plasmodiophora, Streptomyces, Phoma, are also known to cause serious diseases on several vegetables or groups of related vegetable crops (Sherf and MacNab, 1986: Abawi, et al., 1985; Abawi, et al., 1986). These pathogens may interact with each other or with diverse combinations of other pathogens, pests and/or saprophytic soil microorganisms in causing root diseases of complex etiology and increased damage (Abawi and Chen, 1998). Often root diseases are most severe and damaging to vegetables when soil conditions are poor. Thus, root pathogens and root disease management options have to be compatible and be managed as a component of overall sustainable soil health practices.  Healthy soils are characterized as having diverse and active beneficial microbial communities and low and/or inactive root pathogens and other pest communities (Gugino,, 2009; Magdoff and van Es, 2000; Doran et al., 1994).  Soil health management practices consist of various combinations and modifications of reduced tillage systems, crop rotations, cover crops, and soil amendments.  All these practices are well known to directly or indirectly to influence soil populations of root pathogens and the incidence and severity of their root diseases (Abawi and Widmer, 2000). Cover crops can be used as non-hosts to break-up the pathogen lifecycles and some including brassicas and sudan grasses can be used as biofumigants. Grafting crops such as tomato onto resistant rootstocks can be used for managing Verticillium wilt in intensive high-value production systems like single or multi-bay high tunnels. Once established, the persistence of Phytophthora capsici in the soil makes it particularly difficult to manage by means other than improving water management through changes in soil health and irrigation management.

Performance Target:

Through use of intensive discussions and hand-on trainings in NY, PA, CT/MA, VT/NH and ME, 200 growers, extension educators, NRCS, crop consultants, and other agriculture service providers will be trained in the diagnosis, assessment and management of soilborne fungal pathogens and their root diseases on vegetable crops. Of those, 100 will incorporate acquired knowledge in their programming and communications with growers and thus reach an additional 7,000 growers/stakeholders. In addition, 30 extension educators/ag service providers will actively work with growers to identify and address soilborne pathogen disease problems on their farms. An additional 20 grower participants will diagnosis a disease problem and implement a management solution. Several case studies will be developed to further document impact.


Click linked name(s) to expand/collapse or show everyone's info
  • George Abawi
  • James LaMondia


Research results and discussion:

Milestone 1.
Target beneficiaries attend and participate in one of seven soilborne disease management trainings that will be held in NY, PA, CT/MA, VT/NH, ME and NJ/DE/MD. Training sessions are designed to educate 25 to 30 people per session with a new group of participants attending in each location over the course of 19 months.

From winter 2011 through early spring 2013, five full-day interactive training sessions were held in Windsor, CT, Allentown, PA, Hershey, PA, Ballston Spa, NY and Geneva, NY. The workshop consisted of the following sessions divided by two breaks and lunch: 1) workshop overview and introductions, 2) biology and ecology of soilborne organisms, 3) symptoms and signs of soilborne pathogens and diseases common in vegetable production systems, 4) sampling and assessing plants and soil for soilborne pathogens, and 5) soilborne pathogen management – available options and strategies. The topics covered during the biology and ecology section of the training included: characteristics of healthy soil, losses attributed to soilborne diseases, plant disease triangle, characteristics of soilborne pathogens, pathogen survival, distribution in the soil and factors that affect infection and disease development. The signs and symptoms section focused on the types of damage caused by soilborne pathogens (damping-off, wilts, root rots, etc.) as well as symptoms specific to oomycetes, Fusarium, Rhizoctonia, Sclerotinia and Verticillium on specific crops and host families. Due to time constraints, pathogens covered during each workshop were based on local need, however all the information which covered a wider range of pathogens and disease complexes was made available in the resource binder. In the section on how-to assess for soilborne pathogens participants learned about disease foci and pathogen spread in the field, how-to collect and submit diseased plant samples for diagnosis, how-to sample and conduct the soil bioassay with snap bean and observe prepared pathogen cultures on selective media and slides to facilitate pathogen identification and disease diagnosis. Specific topics covered in the management section  included: selection of resistant/less susceptible cultivars and grafting, pathogen-free plant material, chemical and microbial seed treatments (how they work and how long do they last), mycorrhizal inoculants, transplant drenches, crop rotation/sequences, cover crops/biofumigant crops as well as products applied at planting and post-emergence/planting.

Hands-on demonstrations provided the participants the opportunity to see signs and symptoms of the select pathogens and diseases and also observe the diagnostic characteristics of plated cultures under the microscope. The demonstrations included examination of specimens of various stages of root rots on snap bean and pea, Rhizoctonia and Pythium on beets, Fusarium wilt on tomato, and root knot nematode on carrot, tomato and lettuce. In addition, demonstrations were prepared to show how to bait Thielaviopsis out on carrot disks, baiting of Phytophthora capsici out of water and soil using lemon leaves and green tomatoes as well as use Agdia immunological test kits for Phytophthora and Pythium.

A resource binder that contained the hardcopies of the workshop PowerPoint presentations, an array of relevant factsheets on soilborne pathogens and diseases, protocols on soil sampling and conducting soil bioassays for soilborne fungal and nematode pathogens was developed and has been refined based on participant feedback. All these resources as well as some additional factsheets were placed on a CD-ROM so participants can use the information in the future. Participants also received a trowel to emphasize the importance of digging up the root system when assessing for soilborne pathogens.

The workshops were announced via flyers that were distributed via various email listservs, newsletters and web postings as well as through personal communication with growers, extension educators and other ag stakeholders. Based on the post-workshop survey, the majority of participants learned about the workshop from newsletters (n=35), email listservs (n=29), directly from colleagues (n=21), web postings (n=18), and project leaders (9) as well as from the marketing materials for the 2013 Mid-Atlantic Fruit and Vegetable Convention (n=6).Although the grant covered the costs associated with the workshop, it was determined that a nominal $20 registration fee was needed to reduce the potential number of no-shows the day of the workshop. 

Milestone 2.
At the end of each training session, evaluation of hands-on training, supplemental materials, perceived change in knowledge and intention to use acquired knowledge and skills. 19 months.

A single pre/post workshop survey (PSU IRB #35301) was administered at the conclusion of each workshop to evaluate the hands-on training materials, perceived change in knowledge and intention to use the acquired knowledge and skills. 

Milestone 3. 
Extension educators and other ag service providers will incorporate acquired knowledge and skills into outreach programs and communications with growers. Growers will evaluate and diagnosis root disease problems on their farm and implement appropriate management strategies as needed. 24 months.

In the pre/post workshop survey administered at the end of the workshop, participants were specifically asked to indicate, using a categorical scale of not likely, somewhat likely, moderately likely and very likely, their intention to incorporate the knowledge and skills acquired during the training workshop on their farm or in their programming and outreach activities. To further document impact, participants were asked more specific questions about how and to what extent they have been able to incorporate the knowledge and skills acquired (i.e. one-on-one interactions with growers, newsletter articles, etc.) on a follow-up impact survey. Participants were also asked to what extent they have been able to 1) diagnose a soilborne pathogen problem(s); 2) assess a field for soilborne pathogen problems; and 3) implement targeted management practices.

Milestone 4.
Target beneficiaries and other stakeholders in the vegetable production industry access additional information as needed from the developed web-based resources. 24 months.

Some unforeseen challenges arose in the development of the web-based resources due to changes in the web platform at Penn State and compliance with accessibility that limits the posting of pdf files and requires text to accompany and audio files or voiced PowerPoint presentations. It is the PIs intentions to still make the workshop content available on the on-line but it has taken longer than expected.

Milestone 5.
Target beneficiaries complete an on-line (or hardcopy) evaluation one-year following attendance at a workshop to assess project behavioral impact among target beneficiaries and anticipated long-term impact of outreach to vegetable producers in NY, PA, CT/MA, VT/NH, and the Northeast region. 30 months.

A final follow-up impact survey (PSU IRB #35301) was administered to assess how the knowledge and skills acquired during the full-day workshop had been incorporated onto their farm or into the participants programming and/or outreach activities and communications with growers. This survey was administered using the web-based survey tool, SurveyMonkey. Slightly different questions were asked of growers and extension educators/ag service providers (non-grower) so the response to the first survey question directed the participant to the appropriate set of questions. Extension educators and other ag service providers answered questions 2 through 13 and growers answered questions 14 through 28 (see attached follow-up survey instrument).

Participation Summary


Educational approach:

As part of the resource notebook, participants received a CD-rom that contained electronic files of all the PowerPoint presentations, general nematode references, nematode fact sheets, soil sampling and bioassay protocols. A hardcopy of the workshop resource binder along with the resource CD has been submitted to the Northeast SARE office.

No milestones

Additional Project Outcomes

Project outcomes:

Impacts of Results/Outcomes

A total of 117 people from ten states attended one of five full-day training workshops titled ‘Identification, assessment and management of soilborne plant pathogens in vegetable production systems in the Northeast’ that were offered in three states in the Northeast region from winter 2011 to early spring 2013. Based on the pre/post-workshop survey (n=105), the breakdown of the target audience was as follows: growers (61%; n=64), extension educators and university personnel (16%; n=17), crop consultants (6%; n=6), government employee (5%, n=5) and self-described other (12%, n=13). Although we fell short of the target number of people, the majority of participants reflected our target audience of growers and based on the responses from the extension educators and other ag service providers (n=16) on the follow-up impact survey an additional 1426 growers and 810 new Master Gardeners were reached with new, useful information during the course of the project; an average of 102 people per participant (not including the Master Gardeners). Not surprisingly, the primary reason stated for attending the workshop was to learn and increase their knowledge or gain a better understanding about soilborne pathogens/diseases. Many of the participants had limited to no exposure to soilborne pathogens prior to the workshop or it had been many years since initially this topic was covered in school. With such a diverse audience and the numerous topics covered, it is also not surprising that the ratings of the usefulness of the information presented were variable. However, all the vast majority of participants rated the workshop as excellent (59%) or good (35%) with respect to the content. In fact the majority of the participants (57%, n=60) indicated an increase in knowledge in all four of the major topics covered (biology/ecology, symptoms, assessment and management) and an additional 21% (n=22) increased knowledge in three of the four major topic areas. By the end of the workshop, 86% (n=91) of participants had a strong to moderately strong intention of incorporating the knowledge and skills gained either on their farm or into their educational programming and outreach activities. Participants indicated that they planned to use the information in a number of ways ranging from increased scouting and digging up the roots to look for symptoms to paying more attention to good soil management practices to sharing information with fellow farms and submitting plant samples for accurate diagnosis.

Of the participants that completed the follow-up impact survey (42%, n=30 of 72 surveys administered via an on-line survey instrument), almost 100% of the participants have either used the knowledge acquired during the training with interactions with growers or used it to diagnosis and implement management practices for managing soilborne pathogens on their farm. Approximately 86% of participants have used the hardcopy and electronic resources subsequent to attending the workshop with the diagnostic photographs being most frequently used.

Sixty-four percent of the growers who responded to the follow-up survey (n=9) diagnosed a soilborne pathogen problem on their farm. The identified soilborne pathogens included Sclerotinia, Phytophthora, Fusarium and Verticillium on crops ranging from tomato to pumpkins to lettuce. In one case, Phytophthora blight and Fusarium root rot were identified in a 3A pumpkin field. The grower valued the loss at $6000 and decided to adjust his crop rotation and incorporate cover crops and biofumigant crops on 20 A at an estimated cost of $40/A. The grower observed improved soil health and reduced losses due to these diseases and valued economic gain as a result of the implementation of these practices at $10,000. Another small scale market grower identified Sclerotinia white mold and Phytophthora blight in her lettuce and peppers, respectively. The small scale nature of her farm (< 1A) limited her ability to adequately crop rotate. As a result of participation in the workshop, she began to incorporate cover crops into her rotation and rent another plot of land to facilitate a better cropping sequence on her farm. A third grower diagnosed Sclerotinia in a 0.5A pumpkin field and valued to losses at $200. This grower made provisions for better drainage in poorly drained portions of the field and is planning on augmenting his tillage practices to further reduce disease losses.

An extension educator from Pennsylvania worked with one high tunnel grower to diagnose Pythium root rot and has been working with him to reduce the frequency and amount of irrigation, plant on raised beds to facilitate drainage, utilize drenches of Trichoderma-based products in transplant production, and include biofumigant crops of Caliente mustard this past summer. The grower indicated that following the biofumigant crop this summer, his fall high tunnel carrot crop looked excellent. Additionally, another project that came out of this workshop was two years of on-farm demonstrations with mustard cover crops to reduce soilborne diseases. Summaries of this project are available at the Penn State Vegetable and Small Fruit Extension team website ( under research reports left-hand tab. Another extension educator in New York worked with a grower in slowing the spread of Phytophthora capsici in his fields as well as implement several management strategies. This educator also applied the knowledge and skills acquired to diagnose and manage root disease problems in strawberry (a crop not covered but affected by a similar complex of pathogens).

Below are examples of what several participants shared with us:

  • “This training provided specific tools and knowledge that have been useful for my extension work. It also has contributed to my overall professional development and ability to confidently address problems caused by soilborne pathogens and extrapolate the information to producers of other commodities.” - PA extension educator
  • “The biggest thing that I learned is not to rush to judgment. Root diseases are very complex and sometimes difficult to diagnose. I find it challenging to diagnose an entire field - unless it’s something relatively easy like Phytophthora capsici (Pcap).” - NY extension educator
  • This workshop “gave me a better understanding of what I am dealing with, what to look for and ideas how to work at making things better.” - PA Grower
  • “The notebook and CD are excellent. I thought it was well-organized and logically presented.” - PA Master Gardener
  • “I plan to present some of this information to growers in the growers association I’m involved in.” - WV grower
  • “Excellent overview of concepts preceding detailed discussions; all great photos and samples; outstanding group presentation - well prepared shows outstanding collaboration of knowledge.” - CT Master gardener
  • “I feel more able to identify and find resources to address future problems as they arise.” - CT grower

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.