Closing the Mushroom Production Loop: Evaluating Soil Microbe Changes Following Field Application of Compost Inoculated with Spent Mushroom Substrate

Progress report for ONE22-422

Project Type: Partnership
Funds awarded in 2022: $24,712.00
Projected End Date: 12/31/2023
Grant Recipient: NOFA/Mass
Region: Northeast
State: Massachusetts
Project Leader:
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Project Information

Project Objectives:

This project seeks to accomplish the following objectives:

  • Evaluate which ratio of compost:spent mushroom substrate (SMS) best increases the microbiological activity of finished compost over the duration of a 14d period, and
  • Determine whether the application of compost inoculated with SMS improves soil health characteristics including soil microbial activity, active carbon, bulk density, and soil hardness when applied to vegetable production systems.

Positive findings from these objectives will provide the following benefits to farmers:

  • Provide mushroom farmers with a use for a production byproduct, sustainably closing the production loop
  • Offer vegetable farmers an opportunity to increase soil fungal activity and soil health characteristics, likely leading to improved crop growth and production without requiring much additional time or a change in management

If this project is successful, we envision developing partnerships between specialty mushroom and vegetable farms in the Northeast to create a continual cycle of SMS utilization in compost. The compost inoculation method is a straightforward and time-efficient way to increase microbial communities in an amendment vegetable farmers are already using, making it easy for this to be widely adopted and successful within the farming community.


Nationally, the mushroom industry was responsible for over $1.09 billion in sales in 2019-20. Specialty mushrooms, or all mushrooms except the ubiquitous Agaricus mushrooms (which include the button, portobello, and crimini varieties), make up just a fraction of total mushroom sales nationally. However, their consumption has been growing since the introduction of shiitakes to supermarkets in the 1980’s and is predicted to continue to increase as consumers find more uses for them and consume them as meat alternatives.

Over recent years, specialty mushroom producers have been falling short of demand in the Northeastern United States. While the Agaricus production industry is dominated by larger-scale farms primarily in Pennsylvania, California, and Florida, specialty mushrooms are typically produced by geographically-scattered small-scale farms producing for local markets. In 2014 there were 57 specialty mushroom growers in the Northeast, and there has been a recent push to increase the number of growers to meet increasing consumer demand.

Mushrooms are considered to be one of the most environmentally-friendly foods to produce, yet their proliferating production has required increased secondary outlets for the substrate that results after mushrooms are harvested. Specialty mushrooms are grown on mushroom substrates: grain, sawdust, or plug spawn that is typically used for 1-3 production cycles, or flushes. Following the final flush, the mushroom substrate is considered “spent” and is then discarded, creating waste as a byproduct. Despite being unusable for further mushroom production, spent mushroom substrate (SMS) is nutritionally rich and abundant in fungal spores. While it can be used as a soil amendment, as compost, and for animal feedstock, among other uses, the mushroom industry’s growth has created more SMS than can be consumed, leading to a surplus of SMS that threatens the sustainability of mushroom production. Developing new outlets for SMS that pair the mushroom industry with vegetable farming can create a closed-loop synergy that benefits both the environment and farmers.

Despite known soil health benefits derived from SMS application to farm fields, SMS produced in the Northeastern U.S. is underused by farmers and many small-scale mushroom producers do not have an outlet for their SMS. Particularly in organic agriculture, compost is a popular soil amendment that offers nutrient and soil-building benefits, similar to SMS. However, it is frequently devoid of beneficial fungi that can help improve both soil health and vegetable growth. As a fungus-rich substrate, combining SMS with finished compost offers a method of inoculating compost with fungi to improve the microbial diversity of the compost farmers are presently using. Simultaneously, it can increase the utilization of SMS by vegetable farmers who are already familiar with applying compost as a part of their production while gaining additional benefits as conferred by the SMS and creating a demand for the waste product that hampers mushroom production.

Proposed Work
In an effort to close the production cycle of specialty mushroom farmers in Massachusetts, this project will evaluate the ability of fungal populations in SMS to inoculate finished compost and measure the effects of applying combined compost and SMS on vegetable production systems and soil health. Fat Moon Farm, a certified organic mushroom farm, will provide SMS to a total of five farms and community gardens throughout Massachusetts for this use.

The goals of this project are to evaluate whether finished compost can be inoculated by SMS over the duration of a 14d period, and whether the resultant amendment induces any changes in soil physical and biological properties following application in a manner typically used by small-scale vegetable growers. It is expected that the findings from this project will reveal the capacity for SMS to inoculate compost, increasing its overall fungal communities to enrich the microbial biodiversity of compost and benefit soil biological and physical properties. Our preliminary trials have shown SMS to effectively increase fungal communities within compost, yet we have not yet evaluated its impacts when applied to a vegetable production system. Positive results from this study can demonstrate a use for the SMS waste produced by specialty mushroom farmers, helping to alleviate the disposal issues created by this burgeoning industry while offering vegetable farmers an abundant, locally-produced source of soil-benefitting microbes and carbon. Farmers will be able to use these findings to create a consumption cycle of SMS, offering an outlet for the mushroom production byproduct that benefits vegetable production soils.

To address these goals, this project will be divided into two phases. Phase 1 will evaluate the effects of SMS on finished compost by evaluating the change in microbial communities following a 14d incubation period. Phase 2 is a field trial, wherein farmers will apply the amendments resulting from Phase 1 onto their production fields to evaluate physical and biological changes.

NOFA/Mass acknowledges the historic marginalization of Black, Indigenous, and People of Color (BIPOC) farmers both in Massachusetts and throughout the U.S., and deliberately strives to address these issues in all of our work and outreach. The outcomes of this project will be relevant to all individuals regardless of color, but BIPOC individuals will be directly involved throughout this project, including with essential NOFA/Mass staff and three of the five farmer participants. Furthermore, the community garden partner, Home City Housing (HCH) in Springfield, MA, gives us the unique opportunity to work directly with BIPOC youth. HCH youth volunteers are integral to the HCH production staff and will be directly involved in this project’s farmer responsibilities. This project will provide youth volunteers with the opportunity to implement and oversee the proposed experimental design, rendering an immersive learning opportunity while also potentially benefiting their soils and vegetable production. Finally, BIPOC staff from NOFA/Mass will be closely involved in several aspects of this project at HCH, giving the youth an opportunity to see them as role models for potential knowledge and personal growth.

This project will contribute to Northeast SARE’s outcome statement by increasing mushroom production sustainability, diversifying value-added compost products, and improving the health of soils essential to environmentally low-impact and regenerative farming while providing healthful products to consumers.  


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Materials and methods:

The project will be divided into two phases, aligning with an evaluation of fungal populations in compost inoculated with spent mushroom substrate (SMS) (Phase 1) and an assessment of the inoculated compost on soil health (Phase 2). Five farmers will be participating in the trials using the SMS provided by Fat Moon Farm.

Phase 1: Evaluation of Compost + Spent Mushroom Substrate Mixture Fungal Development
Setup – To evaluate the effects of inoculating compost with SMS, compost and SMS will be mixed at Compost:SMS (C+SMS) rates of 10% SMS, 25% SMS, and 50% SMS. The evaluation will include controls of compost without SMS and SMS without compost. All piles will have a total volume of 0.5 cubic yards. Five piles will be created: two controls (compost, no SMS; SMS, no compost), and three piles with the different C+SMS ratios.

Designated volumes of compost and fresh SMS will be evenly mixed by hand using a pitchfork or similar farming tool. All amendments will be watered to 50% moisture capacity, as evaluated using a soil moisture meter, and covered with a tarp to maintain moisture content. Control piles will be watered and covered with a tarp using the same procedure as for the C+SMS amendment piles. Tarps will be anchored at each corner to keep in place. Piles will be watered with tap water. Water-derived chlorine may have a potentially deleterious effect on fungal populations, yet the study is deliberately not controlling for chlorine in water to make procedures easier for farmers to replicate independently.

A quart-size volume of representative sample will be collected from all treatment and control piles to be used for baseline electrical conductivity (EC), pH, and fungal activity measurements. Samples will be preserved in quart-size plastic zipper bags and analyzed for all three parameters within 24 hours of collection.

EC and pH will be measured using a hand-held Hanna Portable pH/EC/TDS/Temperature meter. The probe will be calibrated prior to use at each farm per manufacturer recommendations. For both EC and pH measurements, a soil slurry will be made by thoroughly mixing soil in deionized water at a 1:2 ratio. The slurry will rest for 15 minutes before sampling per meter instructions. The probe will be rinsed with deionized water when switching between amendment types to minimize any potential contamination.

Microbial activity will be evaluated using the Microscope Assessment Procedure established by Dr. Elaine Ingham as a part of the Soil Food Web evaluation practice. These techniques are based upon peer-reviewed soil microscopy methods and are effective means for identifying soil microbial activity. Microscopy will be performed using a biological compound microscope with 40X-400X total magnification to identify microorganisms by morphological groups and obtain a biomass count. Fungal counts are evaluated by length, width, and a description of melanin. Fungi and bacteria will be reported in µg/g of soil.

Monitoring – During setup, NOFA/Mass staff will train farmers on evaluation protocols for assessing the piles and adding water. Farmers will monitor the piles every other day for two weeks for moisture, temperature, and physical changes to the piles, including changes in color, odor, and mycelial growth. Moisture will be measured using a pre-calibrated soil moisture meter; tap water will be added using a 5-gallon bucket demarcated in 2.5-gallon increments to maintain 50% moisture on all piles. Temperature will be evaluated using a soil thermometer. Farmers will be trained on evaluating physical changes to the piles during pile setup. Farmers will record all observations and water additions throughout the two-week period.

Final Evaluation – After two weeks, the fungal inoculation process will terminate. A final microbiological, EC, and pH sample will be collected from each pile and will be evaluated using the same procedure described in the pile setup.

Phase 2: Field Trial Evaluating Compost + Spent Mushroom Substrate Impacts on Soil Criteria
Amendment Application – The effects of the C+SMS mixture on soil chemical and physical composition will be observed following field application. Farmers will apply each amendment in a completely randomized design in a field plot of their choosing. Farmers will apply the amendment using the same method and rate of application as they would use for a standard compost application to best simulate their typical management practice. Once the amendment has been applied, farmers will be instructed to manage the test plots as they would if the trial was not occurring, including future plantings and soil management based upon standard practices to continue to replicate their actual management practices. Farmers will provide NOFA/Mass with details regarding how the plots were managed, including any tillage, cover cropping, or cash cropping that occurred following the addition of the amendments. If cash crops are planted in these locations we will advise farmers on taking weight-based yield measurements from within each plot. All amendments developed during Phase 1 will be applied to the soil within 1 week of Phase 1 completion.

Field Testing – Test plot soils will receive baseline testing for soil microbial activity, soil type, earthworm count, soil aggregation, water infiltration rate, and active carbon, slake, and hardness (penetrometer). EC and pH will also be using representative soil samples collected from each plot using the same procedure as in Phase 1. Composite soil samples will be taken for baseline Standard Soil Test chemical analysis by Logan Labs to assess for pH, organic matter, total exchange capacity, sulfur, phosphorus, calcium, magnesium, potassium, sodium, boron, iron, manganese, copper, zinc, aluminum, and percent base saturation of Ca, Mg, K, and Na. One sample will be taken per farm with the assumption that field plots will have received the same prior management and will not significantly differ. Plot locations will be identified and recorded using GPS and/or permanent physical geolocators. Field testing will be repeated every 6 months over the duration of the project to evaluate any changes due to the amendments.

Replication over Time & Data Analysis
Initial Phase 1 and 2 trials will occur in fall 2022 and will be repeated in spring 2023 to determine any seasonality impacts. Field testing will be repeated every 6 months for the project duration, with a testing schedule as follows:

  1. Fall 2022: Baseline field testing of Fall 2022 Amendment Trial Plots
  2. Spring 2023:
    • 6 month testing of Fall 2022 Amendment Trial Plots
    • Baseline field testing of Spring 2023 Amendment Trial Plots
  3. Fall 2023:
    • 12 month testing of Fall 2022 Amendment Trial Plots
    • 6 month testing of Spring 2023 Amendment Trial Plots

Procedures will be replicated at each of the 5 participating farms. Data will be analyzed using a repeated measures analysis of variance (ANOVA) to analyze the statistical differences in changes in soil health parameters, yield, and microbial diversity. With supplemental funding from another organization, Phases 1 and 2 will be repeated in the following year to strengthen the statistical power of these findings. Pending the additional funding, findings will be written up and disseminated in a peer-reviewed scientific journal, such as HortScience.

Research results and discussion:

Four rural farms and one urban farm performed tests of inoculated finished compost. Compost was either purchased commercially or done in-house. All compost was inoculated with spent mushroom substrate with the goal of increasing fungal activity, these were applied at the following rates: 10%, 25% and 50%. The piles were then allowed to incubate for a minimum of two weeks.  All piles were evaluated via direct microscopy using a compound microscope in brightfield mode. In addition to this test, background microscopy testing was also performed on the fields where the inoculated compost would be applied to. Following this incubation period pH and electrical conductivity were also performed on the compost to ensure that these values were within the recommended range for field application. Lastly background testing was also performed in the field for soil hardness, bulk density, infiltration rate, visual structure, and aggregate assessment, slake and active carbon. These background tests will be repeated following inoculated compost field applications to track any potential changes.

Finding from soil testing will be shared with farmers following full analysis of data during winter 2023. Preliminary findings show the following:

  • Initial microscopy results indicate that all background/baseline soil testing showed an imbalance of fungi and bacteria, with the fungal activity being the most suppressed i.e., low fungal biomass was observed in all background soils. The samples of compost also appeared to have lower fungal values that are expected of biological diverse compost.
  • Protozoan values were consistent with the classic predator prey interactions meaning that high bacterial counts were typically associated with high protozoan values as bacteria are the primary food source to these microorganisms. However, this was not consistent within all fields tested as some soil background/baseline samples were completely void of protozoan populations.   
  • Nematodes were also evaluated as part of the microscope assessment and were not present in significant values in the soil background/baseline samples. No trend was observed when looking at soil samples; however, one significant outcome was the increased values of nematodes present post compost inoculum.
  • In addition to the microorganisms mentioned above other microarthropods were noted if present to indicate higher trophic levels and diversity. These organisms are also used a proxy for nutrient cycling.  These organisms were not found in all samples background or compost and only represented a minor value in the overall biomass of the samples.
  •  Another visual note during the microscope assessment was the overall “density” of the samples, in other words density is referred to the amount of mineral and aggregates present during the assessment. These data will be used to compare any potential changes over time after the inoculated compost is applied to the field.
  • Initial results for pH seem to indicate that with increasing spent substrate inoculum a decreasing pH value was observed. This would be consistent with increases in fungal activity and their respective enzymes, as these enzymes tend to fall on the lower pH scale. Whereas in with electrical conductivity values a specific trend could not be determined.  
  • Initial background/baseline sampling for soil hardness, bulk density, infiltration rate, visual structure, and aggregate assessment, slake and active carbon in the field plots indicate that these soils are not highly compacted and that the soil can support life provided proper and continued management. This portion of the testing will be monitored throughout the period of this grant and hopefully beyond.
Participation Summary

Education & Outreach Activities and Participation Summary

Participation Summary:

Education/outreach description:

NOFA/Mass’ focused commitment to research and education on soil health, and the underlying sustainability of food production, has positioned us as a leader in agricultural education and outreach. In 2021, NOFA/Mass led 125 education workshops and events, reaching nearly 5,000 attendees to in-person and virtual events. Events are recorded and published on the NOFA/Mass YouTube channel following each event and typically attract between 200-2,000 views within a few months of an event. Our webinars, podcasts, and newsletters attract approximately 150 live and asynchronous participants, 700 subscribers, and 3700 subscribers, respectively. To disseminate the findings from this project, NOFA/Mass will perform outreach and education through two on-farm events, a written summary and report, one podcast, and a winter conference workshop.

On-farm events will occur at partner farms during spring and summer 2023. Fat Moon Farm will host one event to help educate farmers and growers about mushroom production and SMS, including its development and availability, and use as a soil amendment. The second on-farm event will be with one specialty crop farmer to discuss the project, the compost+SMS development process, uses, and project findings. When not limited by Covid restrictions, NOFA/Mass on-farm events each typically attract over 50 participants. The on-farm events proposed here will be recorded and made available on the NOFA/Mass YouTube channel to further expand their audience. All participating project farmers are women, and 5 of the 13 NOFA/Mass staff and farmers participating in this project identify as a part of historically marginalized or oppressed communities. Through deliberate event promotion, NOFA/Mass will extend its outreach and education to marginalized or oppressed communities to ensure the findings of this project are shared with predominantly BIPOC communities to the same extent they are shared with predominantly white communities.

The podcast will be recorded and made publicly available at any point following the completion of fall phase 2. It will provide an opportunity for two farmers participating in this project to share their management practices and how they effectively incorporated SMS into their compost use and field-based application. They will also discuss the nature of the SMS, including practical tips for its acquisition and use in vegetable cropping systems. The winter conference workshop will occur in January 2023 and feature a farmer or other mushroom expert discussing SMS and its potential uses in vegetable production systems.

Findings will be reported in the NOFA/Mass Be a Better Grower e-newsletter and the NOFA regional The Natural Farmer printed publication. The Be a Better Grower e-newsletter has a monthly email subscriber audience of nearly 14,000 subscribers, primarily in Massachusetts, and The Natural Farmer is distributed to 5,000 subscribers quarterly throughout the Northeast. We will also explore sharing written deliverables with other local newspapers, including in predominantly BIPOC communities, to further inform growers about the project beyond the circulation base of the NOFA/Mass e-newsletter and The Natural Farmer.

2022 Update

During late summer and fall 2022, project activities were focused on purchasing and distributing equipment for the project, setting up the amendment trials, and analyzing amendment and soil samples. All educational activities will be performed during 2023; we are currently planning an education event discussing mushroom production in February or March 2023, a NOFA/Mass Summer Conference workshop in August 2023, and an on-farm event in summer or early fall 2023. We elected to shift the planned 2023 Winter Conference workshop to the 2023 Summer Conference to incorporate additional data and findings into the workshop, allowing participants to have a greater understanding of the microbial development of the SMS-compost amendments and the impacts they may have on soil health. The podcast will occur late spring or early summer 2023 to summarize some of the findings from the first in-person event with Fat Moon Farm and share the knowledge and promote the forthcoming conference workshop and on-farm event.

Learning Outcomes

9 Farmers reported changes in knowledge, attitudes, skills and/or awareness as a result of their participation
Key areas in which farmers reported changes in knowledge, attitude, skills and/or awareness:

Farmer gained knowledge, skills, and awareness through the increased exposure to a new potential soil amendment, and the process of inoculating finished compost with Spent Mushroom Substrate (SMS). Through the inoculation process, farmers were directly observing and recording changes in the inoculated compost piles, giving them the opportunity to visually evaluate and understand the fungal growth and compositional changes that were occurring on a macro-scale. In addition, the participating produce farmers have been connected with a mushroom farmer, creating new connections for consumption of a mushroom production byproduct and use of a soil amendment. These skills were also taught to four youth participants at the Tapley Court community garden site who assisted in all parts of the measuring, mixing, and amendment evaluation and application process.

Project Outcomes

5 Farmers changed or adopted a practice
4 New working collaborations
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.