Holganix utilizes the microBIOMETER® test as a baseline for their customers to see the fungi and bacteria levels present in their soil. These results act as a starting point. Most of the soil initially tested is bacteria dominant. That is what the company is trying to change. The Holganix product used to amend the soil is fungal and protozoa dominant. By increasing these levels, they are increasing the soil health on their customer’s farms.
microBIOMETER® acts as a dashboard or gauge that shows where growers start, where they are during the course of the season and where they are at the end of the season. Holganix uses this information to build a database that records year over year results; with the goal of increasing the biology in the soil.
These two photos from the microBIOMETER® app show one of their check fields vs. the same field with their product. This is an accurate representation of how they like to package the information for their growers.
“microBIOMETER® is a simple to use test that opens the eyes of our growers all across the Midwest. When they see the real time results, they begin to understand how important living biology is for their soil.”
About Holganix: As the only true plant probiotics, Holganix Bio 800+ products contain an entire microbiome or community of organisms that is both abundant and diverse. In a single tote of Holganix Bio 800+ there are more than 800 species of active microbes, microbe food, and nutrient enhancers. Working together, the microbes in Holganix Bio 800+ unlock nutrients already present in the soil and optimize the uptake of nutrients you apply, maximizing nutrient efficiency and minimizing loss. Microbe food helps obtain the rapid establishment of beneficial microbes, while nutrient enhancers work with the microbes to promote strong root growth and healthier plants.
Holganix utilizes the microBIOMETER® test as a baseline for their customers to see the fungi and bacteria levels present in their soil. These results act as a starting point. Most of the soil initially tested is bacteria dominant. That is what the company is trying to change. The Holganix product used to amend the soil is fungal and protozoa dominant. By increasing these levels, they are increasing the soil health on their customer’s farms.
There are many soil tests on the market so it can be difficult for farmers to ascertain whether or not they’re choosing the right one. The truth is, there are pros and cons to every soil test. Therefore it boils down to finding which ones align best with your farming goals and which are easily and readily available to you without needing to stretch your resources too much.
Since microBIOMETER® is a relatively new soil test on the market, a lot of questions are raised on how this test is different from other commonly used soil indicators such as the Haney Soil Test and PLFA test. While all three are soil biological health tests, their methodologies are very different and the tests measure different parameters.
The microBIOMETER® is an on-site soil test that measures the microbial biomass and fungal to bacterial ratio of living and dormant bacteria and fungi. The test process works by measuring the color intensity of the microbial solution created and comparing the color to the test card comparator. This patented, colorimetric analysis process is generated through our microBIOMETER® Reader App and produces results within 25 minutes of starting the testing process. Test prices range from $13.50/sample to $6.75/sample. The low cost, rapid result detection, and on-site testing of living soil are what makes this test stand out against others. The microBIOMETER® has a slightly limited scope, however, as it’s only able to measure the overall biomass of fungi and bacteria. It does not differentiate between microbial species nor does it measure any other parameters.
The Haney Soil Test is a lab test that focuses on assessing a variety of soil parameters such as pH, microbial biomass, water extractable organic carbon and nitrogen, soil respiration, and inorganic plant available nutrients such as NPK. This test uses multiple methods in order to obtain results, including the Solvita CO2 Burst test to indicate soil microbial respiration and biomass, and the use of unique soil extracts to determine organic and inorganic nutrient availability. While this test offers a large array of soil parameters, there is controversy in the science community about using the Solvita CO2 Burst test methodology as a way of accurately predicting microbial biomass. This is because the soil is dried then rewetted to trigger a release of CO2 to measure microbial activity. Drying soil decreases microbial biomass, and while rewetting it will increase biomass again, it doesn’t necessarily repopulate back to the original microbial composition. The Haney Soil test is offered at several labs throughout the country and recommendations are included with results. Generally, this lab test costs about $50/sample and takes about 3-4 weeks to receive results.
The PLFA Soil Test is a lab-based technique that analyzes phospholipid fatty acids (PLFA), which are found in the cell membranes of living organisms, to determine an estimation of living microbial biomass, fungal to bacterial ratio, and to identify the general presence or absence of microbial functional groups in bacteria, fungi, and protozoa. For this test, labs first dry the soil overnight then use multiple solvents to extract fatty acids from the sample. Then, mass spectrometry is used to identify the sample’s microbial composition based on specific PLFA biomarkers. This testing process takes a few days to complete and generally costs about $60/sample depending on the lab. It is one of the most utilized testing methods since it gained popularity in the late 80’s. Since then, it was discovered that some of the PLFA biomarkers used for identification aren’t limited to one microbial group, therefore making it difficult to determine the accuracy of some results.
The value of each of these tests is to determine a baseline assessment of your soil health. The information obtained from any of these tests will help you gain a better and more rounded understanding of what’s happening in your soil.
We first had the pleasure of working with Briana Alfaro and Soul Fire Farm in 2021 when they began testing soil with farmers in their network as part of their SARE research project, Soil Carbon Capture for Diverse Farmers; Black, Latinx, Asian, Indigenous and other farmers and farm workers of color take the lead in testing soil carbon sequestration strategies and measurement protocols and disseminate those findings to the farming community in both English and Spanish.
Every two years the Soul Fire Farm team takes a closer look at the soil ecosystem and assesses how healthy their soil is. They do this by performing a series of in-field tests. Long before the western study of soil science, Indigenous communities practiced–and still practice–methods of evaluating soil health using characteristics such as color or the presence of specific plants or insects that tell us something about the system as a whole. On their soil testing days, they count the number of earthworms, perform a slake test to observe aggregate stability, look at soil color as an indicator of organic matter, and use the microBIOMETER® field kit to assess soil biology.
You can learn more in their Guide to In-Field Soil Health Measurement Protocols: How Alive is My Soil (English) & ¿Qué tan vivo está mi suelo? (Español), and by watching their Liberation on Land skill share videos: Soil Carbon part 1, Soil Carbon part 2 & Investigating Soil with an Auger.
BioHub Solutions, an Australian company that provides biological solutions to the agricultural industry, has incorporated microBIOMETER® into their business. BioHub Solutions believes measurements should be simple whenever possible to ensure their implementation and repeatability. microBIOMETER® has become an integral part of the BioPlan processes. Growers also like it because it provides instant feedback and accountability for Biohub’s biological strategies.
“Our trees continue to do well against the control in areas such as average plant height growth, trunk to height ratio, and fungi to bacteria ratio utilizing microBIOMETER®. This is pleasing so far and we will continue measurements.”
Green bean study in North Queensland.
Green bean trial in North Queensland (above). Initial samples taken 2 weeks before harvest. So far overall bean numbers are 36% improved over control. More importantly, marketable sized numbers are improved by 52%. This is where the margin is for the grower. Microbial biomass is also 28% higher than control which is pleasing. Looking forward to the full harvest figures if they reflect the initial samples taken.
Olive rootstock (below). The data has indicated on average, a 17% increase in stem diameter over the control. Root weight improvements of 47%, biology biomass improvements of 46% and fungal to bacterial ratio improvements of 56% over control. This illustrated that the BioHub solution achieved results in the manner the team had predicted. Photo depicts an example of the treated plug on the left and control on the right.
Olive rootstock – treated
Olive rootstock – control
Hypatia I is an interdisciplinary and multigenerational team of Catalan female scientists who journeyed to the Mars Desert Research Station (MDRS) in Utah in April 2023 for an analog mission to determine if there is life on Mars. At MDRS, they performed high-quality space-related research in a simulated environment, in which they also conducted outreach and science-based communication programs. Most importantly, their work aims to inspire the next generation of young girls interested in pursuing STEM-related careers.
For about 2 weeks, the Hypatia I crew conducted their research while contributing to the understanding of what living and working on Mars would be like. Throughout their time at MDRS, each crew member conducted experiments relating to their individual specialties. Some of the experiments included the development of an iron-based battery using materials in the environment surrounding MDRS, and a comparative seed experiment to study the potential effects of space travel on tomato seeds.
Additionally, the crew collected soil samples from the surrounding desert and, using the microBIOMETER®, tested the soil for evidence of life. The team found that the microBIOMETER® could detect life in 7 of the 11 different desert plots. While the microbial biomass levels were low, with a range of 50-120 ugC/g, the existence of any bacteria or fungi was exciting to see. Hypatia I’s analog mission shows promise for future studies relating to space biology.
Hypatia I is an interdisciplinary and multigenerational team of Catalan female scientists who journeyed to the Mars Desert Research Station (MDRS) in Utah in April 2023 for an analog mission to determine if there is life on Mars. At MDRS, they performed high-quality space-related research in a simulated environment, in which they also conducted outreach and science-based communication programs. Most importantly, their work aims to inspire the next generation of young girls interested in pursuing STEM-related careers.
The microBIOMETER® was developed with the need in mind to deliver a device that could be manufactured very reasonably so that it could service the whole world. For over 50 years scientists have known that microbes are the best indicator of soil health. One of the common methods used for determining soil microbial biomass is the Chloroform Fumigation Extraction (CFE) test. However, being a costly lab-based test makes it an unattainable option for many. Another method that’s often used to assess soil microbial communities is microscopy. While microscopy is one of the best ways to assess soil microbes, microscopes can be expensive, are often too large and heavy to bring into the field, and are not necessarily easy to use or easily accessible for growers around the world. In 2014, Dr. Fitzpatrick began developing the microBIOMETER® to address these shortcomings.
The microBIOMETER® was designed to detect bacteria and fungi by their pigmentation on a specially designed membrane. An extraction powder was developed that contains different salts, which, combined with precise whisking, separates the microbes from the soil particles. The addition of this extraction powder also helps to precipitate the soil so that the microbes stay suspended as the soil precipitates to the bottom of the test tube.
Once the microbes are separated from the soil, they can be detected by spectrophotometry. However, like a microscope, a spectrophotometer is both expensive and too large to use in the field. The solution, in keeping with the goal of manufacturing a very cost-effective device, was to make it a lateral flow membrane. Almost all medical devices do a vertical flow, but a vertical flow has many technical problems. In a vertical flow, different types of membranes are put together and then a clamshell type device is used to press it down, but this pressure then has to be regulated. And Dr. Fitzpatrick, having worked with many clamshell devices, knew this method caused a great deal of seepage around the outside. A lateral flow, on the other hand, is more rapid than a vertical flow which allows the sample to be put on more rapidly than you can when you’re using a vertical flow device. The flatness of the device is important as well. Most other devices that are vertical have a rim around the area where the membrane is which is called a sample well. If you look down the well you cannot see the bottom because the well walls are casting a shadow. But microBIOMETER® is flat, therefore, a shadow does not pose a problem.
To perform the test, three drops are applied to the membrane in the test card. The microBIOMETER® membrane was carefully chosen so that it would not bind any of the common pigments you might find floating in soil. It only collects microbes on the surface of this membrane. The membrane also whisks away the liquid and traps the microbes on the surface. The color that it gives to the membrane can be compared to a grayscale, which tells you that the intensity of the color, not the color itself. The intensity of the color correlates with the quantity of microbes you have. Just like with the colorimeter or spectrophotometer, the intensity of the color is linearly related to the concentration of microbes. Dr. Fitzpatrick came up with this grayscale idea while thinking about a quilting secret. Quilters want to make sure they not only have different colors but have different intensities of color as well. Therefore, we’re not just measuring color but also measuring the intensity of the color.
The next step in the development was to figure out how to read the test cards. In the early version of the microBIOMETER®, a red filter with a grayscale was used, turning it monochromatic. A piece of red cellophane was put over the grayscale in the sample window and the results were determined by how dark the center was. This earlier version of microBIOMETER® is still being used by customers who are non-tech users.
At this point, the test could be read visually but it lacked precision, and data storage and tracking capability. For this, it was decided a phone app was needed. One of the barriers to lab testing in developing countries is cost, but another is infrastructure. However, cell phones are ubiquitous. If an app to read the test cards and store the data was created, soil stewards all over the world would have the ability to track soil health over time and assess their management practices while making changes in real time.
The challenge to the cell phone is that cell phones have a camera and manufacturers utilize different software. Therefore, the image viewed isn’t raw and overcoming the differences between various phones becomes necessary. The microBIOMETER® does that with the monochromatic grayscale backing. This in essence “tricks” all phones to be in the same range in their software and white balance. The issue of different color temperatures was also encountered. When you’re out in the sun on a cloudy day or you’re in the shade on a sunny day that light is extremely blue. When you’re sitting in your living room and you have a 60-watt light bulb, that light is yellow/red. And if you’re at the office with a fluorescent light that light turns out to be white -where red, green, and blue are all equal. Therefore, accounting for differences not only in cell phones but in ambient lighting conditions became important as well.
This stage of test development consisted of vigorous testing and a good amount of trial and error. The process involved running around with a test card from light source to light source with five or six different phones making sure the readings were consistent. By utilizing the camera’s flash in conjunction with a monochromatic backing, the images between phones became uniform. Once the patented algorithm that compensated for differences in light color and intensity and phone software was finalized, in 2018, the microBIOMETER® was released to market.
A few years later, in 2020, Dr. Fitzpatrick and Dr. Trexler tossed around the idea of adding another soil test to the microBIOMETER® platform; the fungal to bacterial ratio. During one of these discussions, Dr. Trexler inquired if there was a way to use size to differentiate bacteria and fungi. As a microbiologist, Dr. Fitzpatrick knew that bacteria are much smaller than fungi and therefore could be differentiated based on size. Dr. Trexler then wrote software that could detect and pick out the bacteria and fungi. It was discovered that when looking at a fungal to bacterial ratio on the microscope, a slight change in the color was evident; fungi are a very, very slightly different color than bacteria. There was a correlation between the color of the sample and the fungal to bacterial ratio that was detected microscopically, which turned out to be a groundbreaking discovery. After trying various methods for determining the fungal to bacterial ratio by color, it turned out cell phone cameras had the ability to pick up the difference. This discovery led to the fungal to bacterial ratio data being added to the microBIOMETER® app.
The following year, another exciting feature was added to the platform; Project Management (PM). A big advantage of reading results with a cell phone is that the data can be stored on the cloud. When the app was first written, there were a few different data fields for each sample. There was crop quality, crop type, soil class, and a couple other generic fields. It was soon realized that people using the test were likely more knowledgeable about what data and metrics assisted with farming. So, the app was updated to allow users to create their own fields based on their needs. This development was the release of Project Management (PM). Now, users can have as many fields of data as they want and it’s completely adjustable. Another benefit of PM is it lets users create a project and anyone on the team can upload their test results to the project. Before PM, everyone’s samples were on their own phone and in their cloud account. Now all the samples, regardless of who performed the test, are in one place and can be easily downloaded for analysis. Users can create as many projects as they want to keep trials separate from each other, but with all the data aggregated. There is one microBIOMETER® customer who currently has 20 different projects that match up with each of the properties they manage.
microBIOMETER® allows users to quickly determine if they are achieving the improvements they are looking for; track soil microbial activity over time and see how it varies with practice in order to assess what is working and what is not. With an innovative, yet inexpensive soil test like microBIOMETER®, $7 to $14 compared to much more expensive tests, growers can sample more per acre, allowing them to acquire a better understanding of their crops. With the ease of multiple sampling combined with data storage, users can view year over year and season over season results to see if their microbiology is increasing and if their soil health is increasing as a result.
It is important that the microbiology increases because there’s an incredibly high correlation between soil biology and soil health. We know that as microbial activity increases, so does the water holding capacity of the soil. It also makes crops more resistant to excess water – which can lead to erosion. Soil microbes build soil structure, which mitigates drought as well as flooding risk because it improves the texture of the soil. Microbes make a glue-like substance which enables them to stick to the soil. This stickiness remains after the microbes die and causes the soil to become clumpy. These clumps allow the soil to hold more oxygen, as it provides more aeration. Growers can improve the amount of carbon in their soil since the stored carbon in your soil is the bodies of dead microbes. When a microBIOMETER® soil test is performed, you’re looking at a snapshot of the microbes. They’re constantly turning over and they are food for other predators in the ecosystem. But that turnover demonstrates that you have a large number of microbes and that the entire ecosystem is being fed.
When you feed the soil ecosystem – from microbes to earthworms to mammals – that’s when you achieve the healthiest soil. Many creative and innovative practices are being developed that understand that healthy soil is part of a healthy system. The start is a healthy microbial ecosystem and microBIOMETER® gives you a glimpse into that very, very quickly. There’s nothing else like it.
This article is based on the video The History and Science behind microBIOMETER®
Bio-Extractor
Over the past decades, scientific awareness and appreciation of soil microbiology in agricultural systems has dramatically expanded. Flourishing microbial communities interacting with plant root networks play a direct role in plant growth, crop nutrition, disease and pest resistance, and soil aggregate structure, leading to increased soil oxygen flow and water holding capacity. Unfortunately, many agricultural soils have depleted functioning microbial ecosystems through decades of physical and chemical disturbance. Regenerating these microbial ecosystems is crucial to refocusing agricultural production on soil, human, and environmental health.
One extremely promising method of regenerating soil biology is through the production and application of liquid compost extract. Microbially-rich compost can be produced on-farm from locally-sourced and inexpensive organic materials, through systems such as the Johnson-Su bioreactor process and / or vermicomposting. Vermicompost also includes many naturally-produced bio-stimulants, such as humic and fulvic acids. These compost products, while valuable in solid form, can be extracted into a powerful liquid biological amendment to increase their efficiency and soil infiltration, inoculating beneficial microbes directly into root zones or onto the surfaces of leaves.
In addition to being both biologically beneficial and cost-effective to produce, liquid compost extract is also extremely versatile. Microbial foods, such as blackstrap molasses, kelp, and fish hydrolysate can be added for additional stimulation. Injecting oxygen into the liquid prior to application will activate the microbes and multiply the population (this is often referred to as “compost tea”). Application systems can be tailored to desired effects, including fertigation, soil drenches, soil injections, seed soaking, and foliar sprays. Improving soil biology not only benefits crop production, but also pastures, lawns, and turf, including athletic fields. Here’s a sample operation in New York’s Hudson Valley that uses compost extract for all of the above.
At Hiwassee Products, the goal is to help make this potentially transformative process both scalable and adaptable to a wide array of situations by designing and manufacturing innovative equipment solutions. The Bio-Extractor, released for production in 2022, is the only commercially available continuous-flow compost extractor to date, able to extract at 700 gallons per hour to meet any target volume, large or small. The company will continue to release equipment in the upcoming year, focusing on continuous-flow-through (CFT) vermicomposting systems and biologically-friendly spray systems, which differ from high-pressure chemical applicators. These equipment items can be combined into one closed-loop system (potentially including a pre-composting system to make vermicomposting more efficient), or be used as components of other soil biological management systems.
Created and performed by microBIOMETER® intern, Leanna Ramus, environmental science student at Siena College, this sample experiment is appropriate for high school and advanced middle schoolers.
The research project is designed to help students study soil health and understand the impact of soil biology on soil health and plant growth. Supplies are minimal cost and nothing recommended is dangerous or controlled. We expect students to use this as a guide to develop their own experiment.
We love supporting young minds with a passion for soil science. They are the future of soil health! If you are an educator that would like to bring microBIOMETER® soil testing into the classroom, we have three Academia Kits available for purchase. We are also happy to cater supplies to your specific needs. Please contact us for more information!
