Source: PURDUE UNIVERSITY submitted to NRP
HARNESSING THE POWER OF SUPPRESSIVE SOILS TO MANAGE ROOT-KNOT NEMATODES IN ORGANIC VEGETABLE PRODUCTION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1032802
Grant No.
2024-51106-43054
Cumulative Award Amt.
$998,987.00
Proposal No.
2024-03996
Multistate No.
(N/A)
Project Start Date
Sep 1, 2024
Project End Date
Aug 31, 2027
Grant Year
2024
Program Code
[112.E]- Organic Transitions
Recipient Organization
PURDUE UNIVERSITY
(N/A)
WEST LAFAYETTE,IN 47907
Performing Department
(N/A)
Non Technical Summary
The increasing demand for organic foods in the US is creating an opportunity for conventional vegetable growers to transition to organic production. However, pests and diseases are major barriers for transitioning growers since chemical pesticides are no longer options for pest management on transitioning and organic farms. Root-knot nematodes (RKN; Meloidogyne spp.) are among the critical yield-limiting pests of conventional and organic vegetable production in the US and around the world. When RKN populations reach damaging levels in fields, effective management approaches become imperative. However, as RKN continues to spread under the changing climate and emerging virulent RKN populations overcome host resistance, lack of effective methods for managing RKN post a significant barrier during transition to organic vegetable farming. This project focuses on research and extension activities to explore suppressive soils as a resource for growers to manage RKN in organic vegetable farming by (1) identifying suppressive soils against RKN at organic vegetable farms in Indiana and Kentucky and assessing the impacts of soil management practices on suppression via closely working with growers; (2) investigating microbial communities of representative suppressive soils to identify groups of microbes associated with RKN-suppressiveness. The microbes identified may serve as bioindicators of RKN suppressiveness of soils; (3) developing grower-friendly procedures to create RKN-suppressive soils by scaling up the identified suppressive soils or through de novo methods; (4) developing a new method for managing RKN in organic vegetable farming by transplantation with suppressive soils; (5) creating a knowledge-generating and sharing platform as a hub to guide growers for effective RKN management. With the collaborations between Purdue University, University of Kentucky, growers, conservation groups, organic industry, and other stakeholders, the multidisciplinary team aims to provide vital assistance to transitioning and organic vegetable growers with effective RKN management strategies and practices to facilitate smooth transition and successful organic vegetable production.
Animal Health Component
40%
Research Effort Categories
Basic
30%
Applied
40%
Developmental
30%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2123130112050%
1010110107050%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 101 - Appraisal of Soil Resources;

Subject Of Investigation
3130 - Nematodes; 0110 - Soil;

Field Of Science
1120 - Nematology; 1070 - Ecology;
Goals / Objectives
The long-term goal of the project is to manage root-knot nematodes (RKN) by optimizing soil management in transitioning and organic vegetable farming. This project will conduct both research and extension activities to discover suppressive soils against RKN and explore suppressive soils as a resource for growers to manage RKN in organic vegetable production. Specific objectives include: 1. Exploring suppressive soils against RKN at organic vegetable farms and assessing the impacts of soil management practices on suppression; 2. Investigating microbial communities of suppressive soils to identify groups of microbes associated with RKN-suppressiveness; 3. Creating RKN-suppressive soils by scaling up the identified suppressive soils and through de novo methods; 4. Developing a new method for managing RKN in organic vegetable production by transplanting with suppressive soils; and 5. Creating a knowledge-generating and sharing platform among organic vegetable growers and the scientific community.
Project Methods
Objective 1: Exploring suppressive soils against RKN at organic vegetable farms and assessing the impacts of soil management practices on suppression. We aim to collect soil samples on ~ 100 organic and transitioning vegetable farms, including open fields and high tunnels, in Indiana and Kentucky, approximately 50 farms in each state to identify soils with natural suppression against RKN in Year 1. In Years 2 and 3, representative farms with suppressive soils identified in Year 1 will be followed up to monitor the changes in soil suppression efficacy against RKN. The presence of RKN species and population density will also be checked and documented for each soil sample collected. We will collect and analyze soil properties and farm management information. We aim to identify soil properties and/or management practices that are significantly correlated with soil suppressiveness to RKN. The plant-parasitic nematode report and results of soil suppressiveness against RKN will be shared to each participating grower. Objective 2: We aim to identify core groups of microbes associated with RKN suppressive soils. These core microbe groups will be used as indicators of soil suppressiveness on RKN during this project. We will select 18 representative suppressive soils identified in Obj. 1 based on efficacy on RKN suppression, soil texture, and years the soils have been in organic management. Similar criteria except for RKN suppressiveness will be used to select 6 conducive soils as controls for microbiome analysis. For each soil or nematode sample, DNA will be extracted and 16S and ITS-amplicon metagenomic sequencing will be carried out o to study bacterial and fungal communities, respectively. Alpha and Beta diversity analyses, and comparative analyses, including differential abundance and core microbiome analysis to identify the groups of bacteria and/or fungi that are specifically present or highly associated with the suppressive soil samples. We will study the dynamic changes of microbiome in suppressive soils in Year-2 and 3 to confirm the association of core microbes identified with RKN suppressiveness. Objective 3: We propose to create RKN-suppressive soils by scaling up the identified suppressive soils (Obj. 3.1) and through de novo methods (Obj. 3.2). Obj. 3.1: based on the preliminary data, our hypothesis is that by mixing identified suppressive soils from organic farms with the widely available conducive soils on organic farms and nurturing the microbial growth in the mix, the mixed soil can develop suppressiveness and increase in volumes of suppressive soils. We will test the effects of factors, including soil mix ratio, moisture, temperature, incubation timing and organic matter amendments, on scale-up of RKN suppressive soils. Obj. 3.2: We aim to learn from organic vegetable growers who have successfully built suppressive soils against RKN and translate their knowledge to optimized protocols, which will help more transitioning and organic growers to manage RKN. We will learn from farmers and apply results generated from Obj. 1 to develop 2-3 protocols representing typical organic vegetable farming scenarios (open-field vegetable production, monoculture high tunnel tomato production and four-season high tunnel production, etc.). We will follow the protocols and test the effectiveness of converting conductive soils to suppressive soils. The experiment will be conducted at Purdue SWPAC organic field, organic or transitional vegetable farms with RKN-conductive soils in Indiana. The two procedures, scaling-up and de no creation, will provide transitioning and organic vegetable growers ways to develop suppressive soils to manage RKN and potentially other plant-parasitic nematodes on their farms. Objective 4: We propose to develop and validate a new method for managing RKN in organic vegetable production by transplanting with suppressive soils. The vertical distributions of RKN in soil were mainly found in the top 30-cm soils in fields during growing seasons. Our hypothesis is that providing a protective zone to vegetable plant roots in this depth by transplanting with suppressive soils can reduce RKN infection of roots and therefore yield losses. In addition, plant roots grown laterally out of the protective zones may be protected by the beneficial rhizomicrobes originally in the suppressive soils which can propagate along developing roots to the outside of the suppressive soil zone. We will test the hypotheses by conducting experiments in greenhouse at Purdue University to optimize the transplanting method and further conducting on-farm trials in Kentucky to validate the efficacies of the methods on reducing RKN infection and alleviating yield losses. We expect that the optimized vegetable seedling transplanting with suppressive soil can provide effective protection of vegetable plants from RKN infections. Objective 5: Creating a knowledge-generating and sharing platform among organic vegetable growers and the scientific community. This project aims to enhance the understanding and utilization of natural suppressive soils in the management of RKN. Organic vegetable growers play pivotal roles in advancing this knowledge and will be encouraged to join the Extension members of the team to facilitate the dissemination of project findings to a broader audience. The project outcomes will be communicated to the broader farming community through various Extension platforms, including field days, presentations at farmers' conferences, articles in Extension newsletters and popular media. Additionally, we will produce videos and audio content and contribute to both existing and newly developed farmers' webinars and podcasts. The Purdue Nematology Lab website (https://ag.purdue.edu/department/btny/labs/zhang/index.html) will serve as the central information hub for this project, providing timely updates on project activities and disseminating new findings.Evaluation Plan: Research performance of the project will be evaluated by publishing research findings as peer-reviewed journal articles, extension publications and informative articles on websites. The number of times that the information is accessed or downloaded, and citations of journal articles will be monitored. For Obj.1, we will monitor the number of growers interacted and soil samples collected, and suppressive soils against RKN identified during the project. Obj. 2, we will monitor the number of suppressive soils included in the soil microbiome analysis, and the diversity and core microbes identified in representative suppressive soils. Obj. 3, the success rates of creating suppressive soils by scale-up and de novo methods will be closely monitored, and optimizations will be made when necessary. Obj. 4, efficacies of RKN management by vegetable transplanting with suppressive soils will be monitored. We will actively involve growers and stakeholders in the four research objectives to build connections which are important for the extension activities we will conduct.

Progress 09/01/24 to 08/31/25

Outputs
Target Audience: The target audience for this project includes organic and transitioning vegetable growers, vegetable growers implementing organic practices, conventional growers, agricultural professionals and scientists, and Extension County educators. We also shared the project findings with undergraduate and graduate students through lectures and laboratory sessions in the College of Agriculture at Purdue University. Changes/Problems:We are currently conducting experiments in controlled environment conditions to test and determine which suppressive soils or on-site made composts function effectively in the transplanting experiment. The information will be useful to better design the field trials. Therefore, we decided to conduct field trials in 2026 and 2027, so the team can refine the experimental design and enhance the potential efficacy of RKN suppression in soil transplanting field trials. What opportunities for training and professional development has the project provided?The project provided comprehensive training to two graduate students and one postdoc. The two graduate students have been working on this project since the beginning of this reporting period and are deeply involved in the research and outreach activities. Both students have learned and contributed to soil sampling, various tests including soil-plant based assay to identify RKN-suppressive soils. The graduate student at Purdue got trained and contributed to soil sample preparation, DNA extraction and data analysis of the amplicon sequencing of suppressive and conducive soils for microbiome studies. The postdoc started working on the SWPAC field trial in 2025 and got trained on field experimental design and evaluated the initial soil conduciveness to RKN on the organic field. Participation in regional conferences and field events allowed both graduate students, postdoc to network with growers and industrial professions and presented their research. The project has provided training to at least ten agricultural professionals. These include county Extension educators who assisted in disseminating project findings to farmers, as well as professionals who participated in the field day and project presentations. They learned about RKN infection identification and management strategies. How have the results been disseminated to communities of interest?Growers in Indiana and Kentucky who participated in soil sampling (18 farms in Indiana and 19 farms in Kentucky) received field-specific reports and recommendations. These included soil chemical and physical properties, the identity and density of plant-parasitic nematodes, and an assessment of whether their soil was suppressive or conducive to RKN. Communications were conducted through on-farm visits, phone calls, and emails. In addition, our team presented updated project results at the 2025 Indiana Small Farm Conference in March 2025 through both an oral presentation and a poster session, reaching more than 250 farmers and agricultural professionals. The project was also highlighted at the 2025 Southwest Purdue Agricultural Center Field Day in June 2025, which drew approximately 70 farmers and agricultural professionals. Project updates were disseminated through newsletter articles and posted on the Purdue Nematology Lab website (https://ag.purdue.edu/department/btny/labs/zhang/index.html). The project was additionally discussed at the "ABC of Organic Agriculture" workshop organized by one of our collaborating farmers. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, we will continue soil sampling on organic vegetable farms, with a focus on follow-up visits to the six farms where RKN-suppressive soils were previously identified. The long-term soil monitoring will enhance our knowledge on how environmental factors and management practices may contribute to soil's suppressiveness to RKN. Concurrently, we will evaluate the two on-farm-produced composts from Indiana growers, along with several commercially available organic composts, to assess their effects on suppressing RKN infection and reproduction on tomato when mixed with conducive soils. Results from these tests may identify compost-based amendments capable of generating RKN-suppressive soils using commercially accessible products. We will further refine and optimize soil transplanting procedures under controlled-environment conditions to identify soils or composts that effectively protect tomato against RKN. Findings will guide the selection of materials and methods for the upcoming high-tunnel field transplanting trials. Additionally, we will continue the ongoing field trial at SWPAC to explore the development of RKN-suppressive soils through different soil and crop management practices. The project team will also continue analyzing the amplicon sequencing datasets to identify microbial groups correlated with, or potentially responsible for, soil suppressiveness to RKN. Throughout the next reporting period, we will maintain active engagement with advisory board members and expand outreach efforts to share project progress and findings with a broader audience.

Impacts
What was accomplished under these goals? The long-term goal of this project is to develop effective root-knot nematode (RKN) management strategies by optimizing soil management practices in transitioning and organic vegetable production systems. The specific aim of the project is to discover and explore RKN-suppressive soils as a resource for growers to manage RKN in organic vegetable production. To identify RKN-suppressive soils (Obj. 1), we took advantage of our connections to organic vegetable growers and county agents in Indiana and Kentucky, also used news releases via Morning Ag Clips, Purdue Pest & Crop Newsletter, Vegetable Crops Hotline, Purdue Nematology Lab website, etc. to recruit growers to participate in the research. Between September and November in 2024, we visited 37 vegetables farms. A total of 73 soil samples were collected from both high tunnel and open field vegetable production settings. The identity and density of plant-parasitic nematodes, including RKN, in each soil samples were identified and recorded. RKN was identified in nearly 50% of soil samples. The chemical and physical properties of each soil sample, along with the soil management practices used on each farm, were also documented. We reported back to the participating growers the results of our soil sampling, including presence and density of RKN and the species identified. Recommendations of management were also provided to the growers. Furthermore, we selected 32 soil samples (with RKN density less than 20 per 100 cc soil) as candidate suppressive soils. Six suppressive soils (3 from Indiana and 3 from Kentucky) were identified using a soil-plant based screening of the 32 selected soil samples. The RKN suppressiveness of the 6 soils was confirmed by repeating the test one more time. The reproduction factor (Rf, number of eggs at harvest/number of eggs inoculated) of Meloidogyne incognita was between 3 and 4 in the six RKN-suppressive soils, significantly less than the conducive soil control where Rf reached to 10 or higher. In addition, compared to the conducive soil control, the number of eggs per gram of tomato roots were reduced by from 45% to 82% in the 6 suppressive soils identified. Analysis of soil properties revealed a negative correlation between soil organic matter (OM) content and RKN density, highlighting the importance of soil quality in suppressing RKN. Through discussions with growers, we learned that two Indiana farms with RKN-suppressive soils identified regularly applied on-site-produced composts. These composts may contribute to the development of RKN suppressiveness. In addition to evaluating their field and high-tunnel soils, we will further investigate the suppressive effects of these composts on RKN. We prepared samples for bacterial and fungal community analyses of the six RKN-suppressive soils and four selected conducive soils (controls; two from Indiana and two from Kentucky) to conduct amplicon sequencing (Obj. 2). For each soil, three sample types were collected for sequencing: bulk soil, rhizosphere soil, and M. incognita egg masses recovered from the soil. Four to five biological replicates were collected for each sample type. Genomic DNA was extracted and assessed for quality, and all samples were submitted to Novogene Inc. for 16S (bacterial) and ITS1 (fungal) amplicon sequencing. High-quality raw sequencing data have been received, and we are currently analyzing the amplicon datasets. To develop protocols for creating RKN-suppressive soils, we consulted with organic vegetable growers whose farms had been identified as having RKN-suppressive soils. After gathering detailed information on farm management and soil practices, we began testing these strategies on a certified organic land at the Southwest Purdue Agricultural Center (SWPAC). This site was originally identified as conducive to RKN. We established side-by-side comparisons of different soil management approaches. On the targeted suppressive-soil side, our plan is to implement mixed cover crop plantings, no-till practices, and organic compost amendments. On the control side, we will maintain organic practices but follow a typical annual vegetable production system (Obj. 3). Beginning in August 2025, we collected additional soil samples from the six vegetable farms where suppressive soils had been identified. We initiated soil transplant experiments under controlled conditions to assess whether these suppressive soils provide protection to tomato plants (Obj. 4). Two on-farm-produced organic composts from Indiana growers were also included to evaluate their potential contributions to RKN suppressiveness in the transplanting assay. Findings from these experiments will guide the design of future soil transplant trials in organic vegetable systems. An advisory board, comprising organic vegetable growers, organic agriculture extension specialists, and a scientist from the biopesticides industry, was established to support project development (Obj. 5). A meeting with the advisory board and the project team was held on May 20, 2025, to present project goals and initial data and to discuss research plans.

Publications