Impact of Commercial Fungal Inoculant on Tomato Yield and Disease Resistance in Deep Composted Raised Beds

Final report for FNC20-1237

Project Type: Farmer/Rancher
Funds awarded in 2020: $8,907.00
Projected End Date: 01/31/2022
Grant Recipient: Liberty Prairie Foundation
Region: North Central
State: Illinois
Project Coordinator:
Shannon McBride
Liberty Prairie Foundation
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Project Information

Description of operation:

Our farm is a certified organic vegetable farm, working towards no till. We grow on approximately 2 acres, but have 5 acres that are available for production. Our farm is the home of the Prairie Farm Corps, a high school job training program, where we use the farm to teach students how to navigate their first job and the importance of organic agriculture. The students are a part of all we do, and 5 students were actively a part of this research project. The farm itself is nestled within the Prairie Crossing Farm, which is 100 acres of certified organic farmland located within Chicago's heartland. Our larger farm is home to an anchor farm, Prairie Wind Family Farm, and a farm incubator program for beginning farmers. It has been running as an organic farm for over 20 years.


In the Midwest, climate change has increased the difficulty of growing tomatoes through more frequent precipitation events, colder, wetter Springs, and colder Falls. These conditions leave tomatoes more susceptible to disease and shorten the harvest season, resulting in less yield and profit.

Arbuscular mycorrhizas (AM) increase a plant’s ability to acquire nutrients from the soil, by increasing the plant roots’ absorptive surface area through hyphal extension (Cavagnaro et. al., 2014). If AM fungal partners are able to increase the nutrient absorption for plants, they may have a positive impact on disease resistance and yield.

Commercial fungal inoculants have become readily available as an option for sustainable farmers. Products are touted to improve nutrient efficiency, root system growth, and water absorption; however, limited research is available as to the impact of these products on tomato production.

Our study examined if commercial fungal inoculant can have an impact on yield or disease resistance in tomatoes. If fungal inoculants can impact the disease resistance and yield of tomatoes, farmers could further the ecological health of their farms by decreasing their fungicide usage, and increase their economic viability through increasing profits from their tomato harvests.

From our research, we were unable to determine conclusively if the inoculant had an impact. From the trial tomatoes, there was no significant impact on disease resistance or yield between the test and the control tomatoes. However, in early root colonization assays, it was determined that the AMF had not colonized the roots. This was likely caused by high levels of phosphorus available to the plant through the deep composted raised beds. It would be beneficial to analyze the inoculant in standard, tilled raised beds to determine its impact when phosphorus levels are not high, and it would be more beneficial to the plant to allow the colonization of AMF. 

However, from our application of deep composted raised beds through this experiment, we saw high increases in both yield and disease resistance in our tomatoes in 2020, and will continue this practice into the future. 

Project Objectives:
  1. Evaluate the impact of Arbuscular mycorrhizas (AM) fungal inoculant on yield and disease resistance on field tomatoes.
  2. Complete the project to the best of our ability despite COVID hindrances. 


Materials and methods:

The tomato trials were placed in a field that was tilled and bed shaped. Each bed was approximately 3’ across with 18” pathways. This field was chosen  because it had not had a tomato planting in over 4 years.  7 beds were prepared for tomato plants. Every other bed was set aside for the tomato trial, resulting in 4 beds. The remaining 3 beds were planted with standard field tomatoes, per our usual planting methods. These planting methods include transplants grown in Vermont Compost, a compost based potting mix, assumed to be fungally active. In the 4 experimental trial beds, 60 feet were reserved on both the west and east sides of the beds to represent field conditions across the entirety of the tomato field. In the middle of the two 60 foot sections of each bed a section of Sungold tomato plants were planted using our usual aforementioned planting methods. A buffer was applied on either side of the sungold tomatoes planted within the experimental beds. Only 43' of tomatoes were planted allowing for a 17' buffer between each planting of experimental tomatoes and the standard sungold tomatoes. 

Therefore we had 8 60' trial beds for the experiment.

Prior to planting any tomatoes, 4 inches of purchased, OMRI certified organic compost was laid on top of the beds. After the initial compost application and bed shaping, these beds will not be tilled again, and so we call these beds, "permanent raised beds". We'll be applying this method of bed preparation to the entirety of our farm, and therefore wanted to analyze the tomatoes under these conditions. This method of growing is also becoming increasingly popular for small farms, and for this reason it was also of interest. 

Within the experimental trial beds, 2 test conditions were implemented within the field: Permanent Raised Beds, with or without AMF inoculation.

The following tests were performed once the beds were established:

  • Midwestern Bio Ag Soil Test (1 sample from each of the 8 beds).
  • Phospholipid Fatty Acid Analysis & Neutral Lipid Fatty Acid Analysis (PLFA/NLFA), performed by Ward labs.
  • Root Colonization Assays, performed on farm. 

Black landscape fabric was applied for mulch and drip irrigation was installed for watering. No additional inputs were applied using the drip tapes. The fabric was laid to cover both the bed and the pathways. All tomatoes were trellised, and an initial pruning was performed to prevent bottom leaves from touching the soil level.

Transplants were grown in Miracle Grow Performance Organics All Purpose Container Mix within 50 plug trays. The potting mix was chosen because it was OMRI certified and because it was manure based for fertility rather than compost based. A compost based mixture hypothetically would have higher fungal populations than a manure based mix. The trays were bleached using Lysol disinfectant spray and water prior to filling with soil to remove any residues of fungi that might have been remaining from previous uses of the trays. The inoculation rate was a quarter cup of inoculant was added to 16 quarts of Container Mix. A 50 plug tray of seedlings for each variety of tomatoes was seeded with the inoculated soil mixture. Then an additional 50 plug tray of seedlings was seeded with a non-inoculated soil mixture.  The inoculant utilized was MycoApply® EndoMaxx  produced and provided for by Valent Biosciences, LLC.  Tomato varieties were chosen according to our market needs and durability under field conditions. The three varieties are Marnero, Margold, and New Girl.

During the growing, the inoculated trays showed stress, through yellowed leaves and stunted growth. To accomodate for this, they were moved throughout the greenhouse to ensure they were in a sunny spot. Our team was quarantined for one week, during which time a fellow crew of farmers watered our plants. They did not notice the inoculated tomatoes, and they did not receive water for two days. After this period of dehydration, they looked significantly worse than their uninoculated counterparts and they were no longer considerable as comparable experimental conditions. Therefore, we inoculated at transplant and planted fewer tomatoes only using the healthier uninoculated transplants for both types of experimental beds. 

Inoculation rate at transplant is recommended at approximately 1 teaspoon/transplant. To inoculate, we dug a hole for the transplant, placed 1 teaspoon of inoculant in the hole and placed the plant on top. We then covered the root ball with soil. 

Initially at transplant,  plants were pulled and their roots were harvested to utilize in root colonization analysis. These initial pulled transplants were not able to be examined due to an overstaining of the roots, making it difficult to see through the roots. Additional plants were pulled at the end of the 2nd week from transplant for a second attempt at examining root colonization by the mycorrhizal fungi. The root colonization technique was one that was designed by Valent Biosciences. They supplied the materials needed and the protocol, and we performed the root staining on farm in our kitchen. We then would look at the stained roots to determine what percentage of the roots were colonized by AMF. The initial plan was for Valent to assist in this process, but this had to change as their labs were closed to most of their employees, due to COVID, and we were not allowed in their labs. We were able to get them the samples and they looked at them independently from us to help analyze percentage root colonization. 

Also at transplant, soil samples were taken using a soil corer. Two cups of soil was removed from each of the 8 trial beds to be utilized in both the Midwestern Bio Ag soil test for overall soil health, and additionally for the PLFA testing performed by Ward labs. Both batches of soil samples were taken and placed in the refrigerator to allow for sending the following day. The soil samples were taken after the compost was laid, and no compost was shifted or moved to allow for soil sampling, therefore a portion of compost was included in the soil sample. Most of the compost appeared to fall from the corer as it was lifted out of the soil, but varying levels of compost made it into the soil samples and this is likely shown through the varying levels of organic matter that showed up on the soil tests. 

The plant heights were measured during the 2nd week after transplant. 

Regular maintenance of the tomatoes was performed throughout the growing season. This included watering biweekly via drip irrigation and trellising with baler's twine to keep vines off the ground. 

Approximately biweekly, disease prevalence was recorded within the trial planting. This was calculated as an overall prevalence of disease as a percentage of leaf mass. As diseased leaves were found, they were pruned from the plant. 

Yield was measured at harvest each week, separating the harvests from the inoculated plants from the harvests of the non-inoculated plants. 

Further testing was planned for the soil at the end of the experiment. This included submitting an additional standard soil test to Midwest BioAg and an additional PLFA/NLFA test at Ward labs; however, due to COVID, our educational efforts in regards to this project were not possible, and the project leader also got married and moved on in her employment at the end of the 2020 growing season. Additionally, the initial soil tests for the PLFA/NLFA were not consistent or intelligible from soil sample to soil sample. So it was determined that his form of soil testing would not have been helpful to repeat in Spring. As you'll see in the results section, the tomatoes also did not fair well due to the setback from the team's absence of one week due to COVID. This, along with other COVID related factors delayed planting of the trial tomatoes until July, and they were significantly stunted. To achieve results in the experiment that were worthy of reporting, it would have been necessary to complete the experiment again in 2021; however, our organization did not have the staffing capacity to continue into 2021 with the project. 

Research results and discussion:

Tomato Yield and Disease Resistance

Our two main areas of analysis focused on tomato yield and disease resistance. 

Initially, within the first three weeks of growth, the inoculated tomatoes showed less disease prevalence than the non-inoculated tomatoes. This was exhibited in a difference of 5% disease prevalence on leaves in the inoculated tomatoes vs. 10% in the non-inoculated sections of the field. However, after the first three weeks, both the control and the trial tomatoes had similar disease prevalence. 

In regards to tomato yield, there was also no significant different in yield for the control vs. trial tomatoes. Each 60' section of tomatoes yielded between 5 and 10 lbs of tomatoes each week. Their yields, compared to the tomatoes planted earlier that were not part of the trail were significantly less. The field trail tomatoes were planted very late in the season, around mid-July. It is possible that the later planting date, did not allow the plants to grow significant enough leaf masses to allow for a plentiful harvest of tomatoes. Additionally the quality of the tomatoes out of the field trail was significantly different from the tomato plants planted earlier. The Marnero and Margold specifically resulted in small, stunted tomatoes with significant cracking. The New Girl tomatoes yielded more marketable tomatoes than the Marnero and Margold, but their harvest quantity was also low compared to the New Girl tomatoes planted earlier. Marnero and Margold are advertised as excellent alternatives to Cherokee Purple and Striped German tomatoes; however, both of these varieties produced much higher yields of marketable tomatoes in our field conditions with earlier planting dates. Marnero and Margold were also bred for greenhouse conditions. It is possible that either the late planting date, which is exceptionally late for tomatoes in the Midwest, or the Marnero and Margold not thriving in outdoor field condition presented such a significant difference in tomatoes we took to market; however, from the experimental results, our farm would not purchase Marnero and Margold seeds again, as they are expensive and not worth the risk from the results we observed in the field. 

From the yield and disease resistance data we gathered, the inoculant does not have a statistically significant impact on either factor of tomato production. 

However, the root colonization analysis and the results of the standard soil testing show that perhaps there were some factors that influenced our results, indicating that an additional study would be needed to determine if the inoculant had an impact. 

Soil Test Results and Root Colonization Analysis

The Midwestern BioAG soil test showed the P levels in the soil were very high. This makes sense as a large portion of the soil sample was compost. In the deep composted beds, approximately 4 inches of compost was applied to the entire bed, and at many points this quantity was closer to 6 inches. If phosphorous was readily available to the plant, it might have little to no incentive to open up it's roots to the localized AMF populations or to the inoculant. The decision to allow AMF to colonize roots is thought to be dependent on the plant's need for the relationship, or perhaps subsequently, the fungi's need for the plant roots. 

The root colonization supports this, as there was very little to no colonization evidenced in the samples. The roots evidenced very little root nodules, indicating that the AMF was not forming a relationship with the tomato plants analyzed. The first hypothesis of why this occurred is the reason outlined in the paragraph above. However, another hypothesis is that the roots were too young to have opened the door to colonization at the points in which we performed the sampling. 

In summary, the root colonization analysis indicated that the inoculant did not infect the host plants, during the first month of growth. 

Seedling growth

As mentioned in the methods, the seedlings that were inoculated were visibly stressed compared to the non-inoculated controls. The stress showed primarily in the form of yellowing leaves. Typically, yellowing is a sign of nitrogen deficiency. From qualitative observation, the potting mix was relatively woody. It was hypothesized that if the C:N ratio was high, degradation of the woody material by the AMF inoculant could use up the available nitrogen,  causing competition with the host plant, and resulting in nitrogen deficiency. This would be an interesting area for further study. Could the C:N ratios in both the potting mixes or soil systems in which the inoculated plants are planted impact the plants ability to access nitrogen? 

PLFA/NLFA analysis

The PLFA/NLFA analysis showed a wide range of values for the total living microbial biomass, which is a measure of all the organisms that could be counted in the sample, including both fungi, bacteria, and protozoa. This value ranged in the soil samples from 1868.78 ng/g to 11050.73 ng/g. Upon collaboration with our AMF experts at Valent Biosciences, it was determined that these values varied too widely to allow much analysis to occur from the test results. The soil samples analyzed were determined to be bacterially dominant. This was interesting, as a large portion of the sample was compost, and it would be expected that the compost might be fungally dominant. However, the compost purchased is turned regularly, and this encourages bacterial dominance. It would be interesting to see if over time this dominance switches to fungal as the soil is not tilled and AMF networks have time to establish without being disturbed. 

Impact of deep composted raised beds on tomato growth

Although it was not a part of our proposal to analyze the impact of the deep composted raised beds, it was a result that we were able to obtain from the research plot. The tomatoes within the study were stunted in growth and the yields were significantly less than in past years when plants were planted in tilled beds with no compost. However, they were planted late enough in the season, that this likely had significant impact on their growth and yields. The other tomatoes within the plot, but not included in the experiment showed significant growth difference. The plants were larger, there was more leaf biomass across the planting, and the harvests were more than there were in previous years. Harvestable tomato size was also significantly different than in previous years, specifically in the cherry tomatoes. The bing and sungold varieties can yield very small tomatoes when planted in beds that are not composted. The deep composted beds resulted in very large sungold and bing cherry tomatoes. There was no significant difference observed in disease onset. Although, our farm is located on a shared farm, where three other farms are also located. Although there was no difference in when disease became debilitating to the plants compared to our tomatoes in previous years, it was obvious that our plants lasted farther into the fall, continuing to produce fruit, long after each of the other three farms no longer had tomatoes to harvest, as their plants had succumbed to disease.

Participation Summary
6 Farmers participating in research

Educational & Outreach Activities

1 Other educational activities: The Prairie Farm Corps seasonal team of high school students.

Participation Summary:

5 Farmers participated
2 Ag professionals participated
Education/outreach description:

COVID impacted the education portion of this project in two main ways. In one way it pushed our planting and facilitation into a window where we didn't feel comfortable analyzing our results, publishing them, or sharing them with other farmers. Because of our late planting dates and our stunted tomato growth, it was determined that we would have had to run the experiment again to really have results we felt were worth sharing. Secondly, COVID prevented us from working with the high school science programs we would have worked with had it not happened. This meant that an additional portion of our outreach did not happen.

However, we did have a crew of 5 high school students that worked with us everyday on the farm, and they were our "outreach" activity for this project. They worked with the tomatoes, looked at roots under microscopes for root colonization analysis, they tracked disease prevalence, and recorded marketable yields. They were a regular part of the experiment and shared in our result findings on a regular basis. 

Additionally, although Valent Biosciences was not able to be present on the farm in the full capacity that they had hoped for, two of their scientists were in regular communication with us about the experiment acting as guidance. They also were able to think through the results, and it gave them both interesting avenues to consider for future projects with their AMF product and its application in organic systems.

Below you'll find the PowerPoint we used to initially discuss the soil health trial with the high school we were networking with. Although that project didn't come to fruition, we spent approximately 5 meetings planning with teachers and administrators to support the field trips and get students onto the farm. 

Soil health trial at Prairie Crossing Farm 11-23-2019

Learning Outcomes

2 Farmers reported changes in knowledge, attitudes, skills and/or awareness as a result of their participation
Lessons Learned:

In regards to the impact of the commercial fungal inoculant on tomato yield and disease resistance, we learned that it would seem that the inoculant did not have a significant impact. However, from our root colonization analysis, it was determined that in early stages of growth, the inoculant did not colonize the root structure of the plants. For the product to be impactful, it would need to demonstrate colonization of the roots. As mentioned in the results section, the colonization could have been limited in our system due to the deep composted raised beds. 

At this point, it is inconclusive as to whether the product would be helpful or not, and it deserves further study, especially in systems where tillage is occuring without high quantities of compost application. 

In regards to the deep composted raised beds, we were able to determine that they had a very positive impact on our tomato production, resulting in higher yields and more marketable tomatoes for the first year use. We will continue to use these and implement them throughout our farm, working towards no-till in many of our beds. 

The use of Marnero and Margold tomato varieties in field was determined to be a negative impact for us overall, as these two varieties resulted in fewer, marketable tomatoes and had a very high cost for the purchase of seed. Cherokee Purple and Striped German performed much better overall in our field trials, year after year, compared to these two varieties in this past growing season. 

Working with Valent Biosciences to execute this project was helpful and insightful. From working with two soil scientists to ask questions about our farm, learn research techniques and talk about production, it was very helpful. We are continuing our relationship with the scientist we first worked with and performing other trials on our farm. It is a benefit for the scientist, as he is allowed to explore some pet projects that he otherwise might not be able to work through on his own at Valent, and we are able to glean from his wealth of knowledge and a different way of viewing things. 

Additionally, they introduced us to an easy method of analyzing root colonization, with a method that we could complete in our farm kitchen. This analysis was priceless and interesting, and we would hope to be able to continue to examine the AMF colonization of the roots of many different plants on our farm utilizing this technique in the future. 

The basic soil testing we performed was helpful in understanding our phosphorus levels and the impact it might have on plants relationship with AMF. It would be helpful to see how this phosphorus changes over time with further compost application, or as the current compost intermingles with the soil, and if root colonization increases or decreases along with it. 

The rest of what we learned is well documented in the results section of this report. 


Project Outcomes

2 Farmers changed or adopted a practice
1 New working collaboration
Success stories:

Although our project did not impact any farm but our own, I was impacted as a farmer through this project. 

Working with Valent Biosciences was an incredible experience in many ways. The first way was having access to individuals that think about research on a daily basis and realizing the potential our farm holds as a research vehicle for moving agriculture forward. It was also refreshing and unique to work with individuals who operate in a very different sphere of agriculture, and ask questions that are very different from our organic point of view. The conversations we had with Valent were coming from the bioag technology sphere, and their different view point helped us think about our farm differently. 

Additionally, they were instrumental in teaching us new methods of doing research on our farm, which allowed us to see the potential for completing our own farm research on many topics in the future. 


Some areas for future study would be:

  • Does the weed pressure in our fields impact the AMF populations? 
  • What is the natural AMF population like across our farm and at different points in the season? 
  • Would the AMF have colonized more readily if the beds were not full of phosphorus rich compost? 
  • Does it impact colonization when you apply the AMF inoculant? 
  • Why did the AMF inoculated seedlings fair worse than the non-inoculated ones? 
  • What would the AMF inoculant impact be on other vegetables?


Thank you for your cooperation and kindness as we have adapted to COVID this past year. We are thankful for the support you were able to give us, and thankful for this research opportunity. Although our education portion fell through, we were able to be educated immensely through the project and know it will impact us and our high school students for many years to come. Thank you for your support. 

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.