History and Science Behind microBIOMETER®

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®