A Comparison of the Microbiome Population Induced by Different Microbial Foods for the Production of a Safe and Effective Aerated Compost Tea

View the project final report

Commodities

• Vegetables: tomatoes

Practices

• Crop Production: nutrient management, compost tea
• Soil Management: composting, soil microbiology, soil quality/health

Introduction

Brewing aerated compost tea (ACT) is an increasingly popular practice among farmers and gardeners seeking to improve soil fertility using biologically active inputs.

However, a persistent concern is the potential proliferation of human or plant pathogens, such as Enterobacter, Citrobacter, and Klebsiella, especially when ACT is fed with high-sugar microbial foods like molasses.

Balancing the need for a microbially rich and effective compost tea with safety is critical.

Objective

This study aimed to identify microbial food sources that support the growth of beneficial microorganisms, particularly plant growth-promoting bacteria (PGPB), while minimizing the proliferation of potentially pathogenic microbes in aerated compost tea.

A second objective was to test whether the safest and most effective tea improved yield, disease resistance, and nutrient density in field-grown tomatoes.

Background and Preliminary Research

The image above is data from a study conducted by a biological amendments company in Switzerland called EdaPro.

Appendix2_2019-032_Bioinfo

Recent data from a Swiss biological amendments company, EdaPro, indicate that microbial foods significantly influence compost tea's bacterial profile. Their 2019 study ("Appendix2_2019-032_Bioinfo") examined three ACT brews:

• Molasses-fed tea showed a spike in both beneficial and pathogenic bacteria, including Enterobacter species.
• An alfalfa and kelp blend promoted beneficial microbes with minimal pathogenic bacteria presence.

In a separate DNA analysis of my own vermicompost tea, fed with a blend of fish hydrolysate, humic acids, and kelp, I observed a similar dual outcome: elevated levels of both beneficial PGPBs and potentially harmful Enterobacter.

These findings emphasized the need to isolate the effects of specific microbial foods to determine which additives offer a favorable risk-benefit profile for ACT brewers and farmers.

Methodology

Using the EdaPro study as a starting point, we determined the biological richness and identification of the microbiome of 16 compost tea treatments fed with the following microbial foods and their pairwise combinations: alfalfa meal, kelp meal, fish hydrolysate, humic acids, and molasses, plus an unfed control. All brews used the same base vermicompost and brewing conditions (aeration, water source, brew time, temperature, and equipment) to isolate the variable of microbial feed. Each treatment was sampled at 12 and 24 hours, plus one sample of the unbrewed vermicompost, for a total of 33 samples analyzed by 16S rRNA gene sequencing for:

• Presence and relative abundance of PGPBs
• Presence and relative abundance of potentially pathogenic genera (Enterobacter, Citrobacter, Klebsiella)
• Overall microbial richness and evenness

Humic acid-fed ACT, chosen for keeping the community that had many different beneficial bacteria and among the lowest Enterobacteriaceae, was then applied to tomatoes in two field seasons.  

In 2025 it was compared against an unfed control and a nitrogen treatment, with leaf sap analyzed by Apical Ag.

In 2026 it was compared against a water-only control and an organic fertilizer (Espoma Tomato-tone, 3-4-6) in nine randomized beds, with every fruit weighed at harvest and fruit analyzed for nutrient density by Apical Ag's Crop Nutrient Analysis (CNA).

Expected Outcomes

This study set out to:

• Identify microbial inputs that enhance compost tea efficacy while maintaining safety
• Provide actionable guidance to growers on microbial food selection
• Contribute to the ongoing development of standards for compost tea use in sustainable agriculture
• See if ACT can be used to grow tomatoes with higher yields and higher nutrient densities

Conclusion

1. Compost Tea Microbiome Conclusions:

Through DNA-based microbial profiling, this project found that feed choice shapes the compost tea microbiome more than brew time within the 12 to 24 hour window.

Because no plate counts were run, we rated each tea with DNA-based definitions reviewed by our technical advisor, Dr. Zack Jones of AggregoData.

A safe tea is one that is non-pathogen-promoting, meaning the family Enterobacteriaceae (which includes E. coli and Salmonella) stays at or below 0.1% of reads, and effective when plant growth promoting bacteria make up 30% or more.

Molasses alone and molasses with humic acid were the only feeds rated non-pathogen-promoting and effective at both 12 and 24 hours, driven by a bloom of Fictibacillus.

Humic acid alone stayed closest to the starting vermicompost with among the lowest Enterobacteriaceae, but added few beneficial bacteria.

Every kelp tea was pathogen-promoting by 24 hours,
and molasses plus fish hydrolysate was the least safe tea in the study.

2. Tomato Trials Conclusions:

In the tomato trials, humic-fed ACT did not produce a statistically significant difference in yield.

In 2026, ACT plots produced 103 lb 12.5 oz against 90 lb 14 oz for the water-only control and 118 lb 11.5 oz for the fertilized plots (ANOVA p = 0.597).

ACT-treated fruit scored highest on our Nutrient Adequacy Score and was highest in calcium, potassium, magnesium, iron, zinc, sulfur and boron, but with one pooled sample per treatment this is descriptive only.

Recommendations:

Our recommendation to growers is to:

1. Avoid kelp and fish hydrolysate blends
2. Keep brews short
3. Choose molasses or humic acid depending on whether the goal is more beneficial bacteria or a tea closest to the original compost,
4. And treat compost tea as one part of a system that also includes polyculture, mulch, fertilization and soil cover.

Defining Terminology

The proposal defined safety using E. coli and enterococci plate counts (CFU/100ml). No plate counts were run, so the definitions below were rebuilt on the 16S DNA sequencing results and reviewed by our technical advisor, Dr. Zack Jones of AggregoData. Because no study has yet linked 16S results to plate counts, "safe," as used in this project's title and proposal, means non-pathogen-promoting as defined below, not a plate-count result. Each definition uses the unfed compost tea (vermicompost, water and air only) as the reference point.

Potential pathogens - bacteria in the family Enterobacteriaceae. This family contains the organisms typically tested for in organic certification (Salmonella and fecal coliforms such as E. coli), along with Enterobacter, Klebsiella, Citrobacter and Shigella. Salmonella was not detected in any sample. Enterococcus was also searched for as the DNA counterpart of the enterococci test and was not detected.

PGPBs (Plant Growth Promoting Bacteria) - genera widely documented as plant growth promoters that were present in our samples: Pseudomonas, Bacillus, Paenibacillus, Lysinibacillus, Fictibacillus, Azotobacter, Azospirillum, Rhizobium group, Ensifer, Mesorhizobium, Bradyrhizobium, Acinetobacter, Flavobacterium, Streptomyces, Microbacterium, Arthrobacter, Sphingomonas, and Burkholderia-Paraburkholderia.

Acinetobacter is included because it is only an opportunistic pathogen, is not part of agricultural pathogen testing, and long-read sequencing of one of our samples found beneficial species such as A. johnsonii (unpublished data, AggregoData). 

Fictibacillus is included based on recent work identifying it as a potential plant growth promoter (El Chater, 2025).

Aeromonas and all Enterobacteriaceae were left out.

Non-Pathogen-Promoting Tea - Compost tea that is brewed with an additive and found to have Enterobacteriaceae making up 0.1% of DNA reads or less (no more than 1 in 1,000). The starting vermicompost had none, and the unfed tea measured 0.06% at 12 hours and 0.08% at 24 hours, so this limit allows only what brewing in water contributes on its own.

Pathogen-Promoting Tea - Compost tea that is brewed with an additive and found to have Enterobacteriaceae making up more than 0.1% of DNA reads.

Non-Pathogen-Promoting & Effective Tea - Compost tea that meets the Non-Pathogen-Promoting limit and in which PGPBs make up 30% or more of DNA reads. For comparison, PGPBs made up 3.9 to 4.5% of the unfed tea.

These are relative (percent of reads) measures, not live cell counts, and 16S sequencing cannot always tell a harmful strain from a harmless one in the same genus. A plate count on at least one tea would be needed before calling a tea "safe" in the regulatory sense.

Compost extract = no aeration, no feed.

Aerated compost tea (ACT) = aerated, with or without feed.

Research Question and Objectives

In this study, I aimed to first and foremost answer the question, "Can we brew a safe and effective compost tea from vermicompost with the addition of microbial food?"

Through the course of the research I also aimed to answer several sub-questions:

1. What is the safest and most effective microbial starter to use for brewing compost tea?
2. What is the optimal brewing time to produce the safest and most effective compost tea?
3. If Enterobacters (to which pathogenic bacteria such as E. coli and Salmonella belong) are present in my vermicompost, can proper brewing methods decrease their populations? What methods would those be?
4. Do the safest and most effective ACT treatments increase yields, disease resistance, and nutrient density in tomatoes?

In this study, the presence, absence, and relative abundance of bacteria, including potentially pathogenic genera were measured, in 15 fed compost tea treatments from vermicompost and one unfed control (16 treatments in total), brewed for 12 and 24 hours.

Relative abundance and identification were determined using DNA sequencing and microbial analysis from AggregoData.

The compost tea treatments were fed five different microbial starters separately and combined in pairs:

The control was not fed a microbial additive. Results were returned as Krona graphs, barplots, and microbiome reports, biological richness which revealed bacteria quantities and classifications.

The analysis of these reports was used to rate each tea for safety and effectiveness.

The study then tested the effects of regular applications of the safest and most effective compost tea on tomato:

• Yield
• Disease resistance
• Nutrient density

Research Hypothesis

I hypothesized that it is possible to consistently brew a safe and effective batch of aerated compost tea using specific microbial foods.

Current research suggested that molasses would prove to be the most unsafe additive to use as a compost tea feed, and that humic acids, alfalfa, and kelp, or a combination of these, may prove to be potentially safe and effective additives to use in brewing ACT.

A secondary hypothesis was that regular application of the safest and most effective ACT treatment would deter disease and improve yields and nutrient density in tomatoes.

Data Collection & Measurements

Findings of compost tea treatments' microbiome identification and relative abundance for 33 samples (16 treatments at 12 and 24 hours, plus the unbrewed vermicompost) can be found here.

Variables: relative abundance of Enterobacters, relative abundance of PGPBs, and alpha differentiators (Observed and Shannon).

Findings of the effects of the safest and most effective ACT treatment were logged in a second tracking workbook (Tomato Trial Tracker).

Variables: yield, disease and pest pressure, and nutrient density.

• Yield: every fruit harvested was weighed individually, or in labeled bulk batches for very small fruit, and logged by date, plot and treatment across 18 harvest dates from August 16 to September 25, 2026. Fruit set was counted per plant on August 11, 2026.
• Disease and pest pressure: onset of disease and pest damage (hornworm, stink bug, blossom end rot, leaf curl) was noted by plot and date in a plot observation log.
• Nutrient density: samples were sent to Apical Ag (Apical Crop Science LLC) for Leaf Extract Analysis (new and old leaf, September 2, 2025) and Crop Nutrient Analysis of fruit (August 24, 2026).
• Weather: daily high and low temperature and precipitation from NWS weather reports for Dulles Airport (KIAD) were overlaid on harvest and application dates.

Water testing

All teas in this project were brewed with water from the farm well, which was tested twice.
A Culligan Micro Special analysis (June 7, 2023) found E. coli not detected and total coliform detected.
A Virginia Household Water Quality Program analysis (sample #36885, March 25, 2026) found E. coli absent (non-detect) and total coliform present at 26.2 MPN/100ml, with nitrate at 3.4 mg/L, pH 6.4, and all health-based metals within limits except first-draw copper (1.3 mg/L; 0.7 mg/L after flushing).

The water met the E. coli standard both times. The coliform result means the well is not sterile, and coliform bacteria from the water may contribute to the low levels of Enterobacteriaceae DNA seen in the unfed tea.

Water test results can be found here.

Measuring Nutrient Density in Crops

The original plan was to send tomato samples to the Bionutrient Institute (Bionutrient Food Association) for nutrient-density analysis. When the Bionutrient Institute could not accept our tomato samples, they referred us to Apical Crop Science as a comparable lab. Apical extracts sap from the tissue, dilutes it, and measures each analyte on an automated spectrophotometer against calibration curves.

Their CNA  (crop nutrient analysis) report compares each value against a crop-specific "value desired" built from USDA FoodData Central, the UK CoFID database, and Apical's own internal data.

Location and Choice and Map Plotting

The research was conducted in the production garden on our farm, Bethany Farm, 41558 Stumptown Rd., Leesburg, VA 20176, using nine 6 x 4 ft beds (24 sq ft each).

In 2026 the nine beds were arranged in a 3 x 3 grid (row A at the bottom near the entrance and lowest elevation, row B in the middle, row C at the top), with each of three treatments assigned to one bed in every row:

• Compost Tea (ACT): humic acid-fed ACT, 10 gallons per application from a watering can as a combined foliar spray and root drench.
• Fertilized: Espoma Tomato-tone (3-4-6, organic), 3 tbsp per bed plus 10 gallons of water, applied on the same dates as ACT.
• Control: 10 gallons of plain well water on the same dates.

Variables: crop yield, pest and disease incidence, nutrient density.