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Measuring Microbes a Step Toward Soil Health

Measuring the microbes present in your soil is a step toward understanding how to achieve fertility.


Hidden in just one teaspoon of healthy soil are more micro-organisms than the Earth’s entire human population.

These microbes break down organic matter in the soil and make essential nutrients like carbon, nitrogen, phosphorus, sulfur and others available to plants. According to a 2020 study published in Nutrient Cycling, microbes contribute about 60 percent of the bioavailable soil carbon in farms and grasslands. A recent study published in the ISME Journal of Microbiology correlates soil microbial biomass with ecological biodiversity. A healthy microbiome improves water retention, helps ward off plant diseases and makes a farmer’s job a heck of a lot easier.

The regenerative farming movement has long drawn upon both the cultural traditions and scientific literature supporting the supreme importance of microbial health for cultivating plants. Gardeners and farmers can observe different “tells” indicating different mineral deficiencies or depleted microbes. Lower leaves turning yellow and falling off the stem might indicate low nitrogen levels, while poor nodulation in legumes hint at a lack of sulfur.

But how can growers know if their soil is on the verge of a deficiency before the leaves turn yellow and their crops are negatively impacted? How might a grower learn precisely how effectively a plot is reacting to their cover crop?

Until recently, testing soils for microbial contents has been too expensive and time-consuming for many farmers. Plus, many microbes do not survive the trip to a lab, which leads to inaccurate test results.

Dr. Judith Fitzpatrick and her product, microBIOMETER, are changing the world of soil testing, making healthy soil a goal that any farmer can accurately measure and work toward achieving. “MicroBIOMETER will allow growers to see the positive impacts of their changes in practice in real time,” says Laura Deck, the president of Prolific Earth Science, which makes the tool. “They can both assess which practices are more effective and also prove out the efficacy of biologics as they go — making compliance and uptake faster and more thorough.”

Creating an Accessible Tool

Earlier in her career as a microbiologist and medical test developer, Dr. Fitzpatrick founded and ran the company Serex, through which she created over 15 medical diagnostic tests and produced 3 million FDA approved tests a year. After the National Science Foundation awarded a $600,000 grant, Fitzpartrick began teaching at Bergen Community College and developing quality assurance control training.

The inception of microBIOMETER occurred when Fitzpatrick saw a gap in traditional soil quality testing, which typically analyzes soil content and chemical volumes without giving special attention to microbes and their impact. Her goal was to build a tool that was low cost to manufacture, user friendly and highly accurate.

In 2015, Fitzpatrick collaborated with regenerative landscaping designer James Sotillo. Sotillo felt his work was hampered by having to test his soils the old fashioned way: collecting a sample, sending it to a lab and waiting weeks for a result that cost over $100 per test.

Working with neurophysicist Dr. Brady Trexler, Fitzpatrick developed an app that processes and analyzes the data collected from soil samples.

Interestingly, the most difficult part of developing the test was coming up with affordable tools to replicate in the field the careful mixing and analysis done in the lab. “Fitzpatrick actually had a custom mixer made that’s similar design to a milk frother,” Decker says.

After three years of development and testing, microBIOMETER was released to the public in 2018.

In the Field

The test itself works with a comparatively minimal number of steps. Users collect a soil sample and follow instructions to mix it with water and the company’s proprietary extracting compounds. “Soil microbes secrete a substance that binds non-living soil particles to each other and to themselves,” the microBIOMETER instructions explain. “Our patented method extracts the microbes from the bound soil particles which then settle to the bottom.” After 20 minutes, and after all the particles have settled in the extraction tube, users take a sample of the tube with a pipet and place several droplets onto a card which gets scanned into the app with the phone’s camera, similar to a QR code. The app measures the test’s results in micrograms, or µg, of microbial carbon per gram of soil and shows a fungal to bacterial ratio as F:B.

Decker says users typically have little trouble applying the test with the instructional video and step-by-step directions in their kit, but when problems arise it has often been from agronomists. “One time we had an agronomist call us very frustrated saying, ‘Your test didn’t work,’ but it turned out they had swapped their own tubes and applied their own mixing tools, which the test is not designed for.” Decker says each element of the kit is carefully calibrated and those who follow the instructions typically don’t run into problems.

Fitzpatrick and her team designed microBIOMETER with a global mindset. Once downloaded, the app is able to read tests without internet access. “Additionally,” Decker adds, “it was designed with no dangerous or controlled ingredients, making it easy and safe to ship around the world.” While other tests range in the $100+, microBIOMETER costs $13.50 per test and $7 per refill. “The ease of using the test is especially helpful in developing countries where lab test are impractical and prohibitively expensive, but where cell phones are ubiquitous,” Decker says.

Measuring Success

Shortly following its release, microBIOMETER attracted attention. In January 2019, FuzeHub awarded Prolific Earth Science a grant in their Innovation Incentive Prize Program. Then, in November, microBIOMETER was selected as the Innovator for Soil Carbon by the Global Terraton Challenge. Several recent studies have used microBIOMETER in their research, including one paper published in Applied Soil Science documenting the impacts of Roundup and microplastics on soil health.

Decker explains that because the results delivered by the test is data only, it’s useful to users who want information rather than prescriptions. “We would love to be able to tell you exactly what you need to do once you get your results, but at this point the app can’t do that.” She postulates that this is why researchers and independent farmers tend to be more interested in the test than most agribusinesses the company has pursued. “We’d be happy to work with agribusinesses,” she says, “this kind of information can make a positive impact.” But so far, a focus on soil microbial biomass has remained largely outside the scope of these players.

But all of that isn’t to say that microBIOMETER’s following isn’t loyal — and growing. “Our tool tends to attract the grower who is curious and creative, Decker says.

Author of “Teaming with Microbes,” Jeff Lowenfels calls microBIOMETER “an advancement in measuring soil food web activity that finally lets us know if our inputs are working. Finally, there is a way to measure if soil or related products actually team with microbes!”

Another user and now microBIOMETER distributor in Kuwait, Dr. Jassem Bastaki, shares on the Prolific Earth Science blog that he’s worked long and hard to educate his community about soil microbiology in an attempt to reverse practices that kill off microbes. “It’s common to see people in our region praising the life in the soil (finally),” Bastaki writes, “but then professing solarization at the end of or the beginning of a growing season. This is an obvious clash in concepts that we hope are not deeply understood. We believe with popularizing the use of the microBIOMETER, we can help clear the fog!”

Microbes are the Future

As the climate imperatives increase, data will play an important role in promoting regenerative solutions. For Decker, Fitzpatrick and the team at Prolific Earth Sciences, microBIOMETER and the ability to easily and affordably measure microbial biomass and track soil health over time couldn’t arrive a moment too soon.

Several states already have programs to incentivize climate-sensitive agricultural practices, and Decker says microBIOMETER could play a role in demonstrating the efficacy of regenerative practices over time. “We definitely see ourselves as part of the carbon markets,” she says.

For so long microbes have done their crucial work underground invisible to the human eye, and often squelched by poor practices. “Tests are a window to what’s going on,” Decker says.