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!
Seasonal dynamics are a major driver of soil microbial communities. Much like you and I, microbes are more active during some seasons, and more dormant during others. This can be attributed to the different responses microbes have to nutrient inputs, climatic conditions, and other soil properties. As there are a lot of factors that affect microbial activity, it can be difficult for farmers or researchers to make definitive statements regarding the relationship between their soil microbial communities and seasonal changes. Specifically, temperature, moisture content, and the existence of plant life are considered the most important factors affecting microbial growth and activity within a season.
The presence of plants on the soil has a large impact on microbial life. As plants form, they begin to cultivate microbes surrounding their roots by producing nutrients for the microbes to essentially feed on. As the microbial community grows, they undergo a series of processes allowing them to obtain nitrogen and mineral nutrients from the soil and then provide the nutrients back to the plant to stimulate growth. This is part of the symbiotic relationship between plants and microbes– they support each other through the mining of nutrients from the soil and sun.
Just like plant presence, temperature greatly influences soil microbial properties. During cold seasons, temperature is considered a major limiting factor of microbial activity, whereas water availability could be a limiting factor during the summer season. Soil temperature can affect organic matter decomposition and mineralization rates, thereby impacting microbial biomass and activity levels. Bare soil, or soil without any plants growing, will have lower microbial activity occurring, regardless of season. This is why researchers and land stewards have emphasized the planting of cover crops between growing seasons in regenerative agriculture– as cover crops can alter soil properties and increase the biomass and diversity of microbial communities. In the warmer or hotter seasons, the addition of cover crops can also help to mitigate how much heat the soil is absorbing.
Studies show that microbial activity in agricultural soils increases in the fall when compared to other growing seasons–likely due to an increased level of nutrients and soil organic matter from crop and plant residue post harvest. Throughout the wintertime, or non growing season, microbial activity and composition is thought to be stagnant, but stable. An increase in microbial activity is said to occur after the thawing of frozen soils and can be linked to the freeze-thaw cycle (FTC) that colder climates experience. As snow freezes over soil, it inhibits air diffusion from occurring, creating anaerobic conditions for the microbial communities and therefore altering the soil community structure. In turn, this causes an increase in denitrification, respiration, and production of greenhouse gases, which are being trapped under the frozen layer. Once temperatures begin to rise, the soil begins to thaw, allowing oxygen into the soil. This provides labile carbon and other nutrients to the soil, which increases microbial activity and biomass. However, once thawing occurs, those greenhouse gases that were once trapped, are released into the air. This exact dynamic between microbial activity and the FTC is still being debated due to different soil properties greatly affecting freeze/thaw rates and as researchers use different methodologies, making it difficult to compare results between studies.
But despite the controversy surrounding the exact relationship between microbes and seasonal temperature changes, researchers do agree that microbial biomass and activity are related to seasonal temperature fluctuations. They’ve found that generally, microbial biomass decreases once the temperature increases past a certain point. As temperature increases, there is also an increase in CO2 being released from the soil, which we refer to as respiration. So when more respiration occurs, more carbon is being put into the air. This respiration process is sensitive to temperature change, which is why it’s imperative to have a better understanding of the seasonal dynamics of microbial communities.
As soil microbial life varies naturally by season, it might be hard to differentiate the natural seasonal changes from the changes related to your regenerative growing practices. Understanding the short term seasonal dynamics of microbial communities in various soil conditions is key in furthering our understanding of soil biology. Documenting and analyzing periodic readings with microBIOMETER® can assist you in differentiating between natural and seasonal changes in your soil.
References:
Bates, Todd B. (2018, Oct 10). How Plants Harness Microbes to Get Nutrients. Rutgers.edu.
https://www.rutgers.edu/news/how-plants-harness-microbes-get-nutrients
Bizzell, E. (2018, April 16). Plants and the bacteria at the root of it all. ASM.org.
https://asm.org/Articles/2018/April/plants-and-the-bacteria-at-the-root-of-it-all
Gao H, Tian G, Khashi u Rahman M and Wu F (2022) Cover Crop Species Composition Alters the
Soil Bacterial Community in a Continuous Pepper Cropping System. Frontier Microbiology. 12:789034.
Jensen G, Krogstad K, Rezanezhad F and Hug LA (2022) Microbial Community Compositional
Stability in Agricultural Soils During Freeze-Thaw and Fertilizer Stress. Frontier Environmental Science. 10:908568.
McDaniel, M. D. and Grandy, A. S.: Soil microbial biomass and function are altered by 12 years of
crop rotation, SOIL, 2, 583–599, (2016).
onwuka B, Mang B. (2018) Effects of soil temperature on some soil properties and plant growth.
Adv Plants Agric Res. 8(1):34-37
Pietikäinen, J., Pettersson, M., & Bååth, E. (2005). Comparison of temperature effects on soil
respiration and bacterial and fungal growth rates. FEMS Microbiology Ecology, 52(1), 49–58.
Simon, E., Canarini, A., Martin, V. et al. Microbial growth and carbon use efficiency show seasonal
responses in a multifactorial climate change experiment. Communicati
An interview with the San Antonio Food Bank who is using microBIOMETER® in their Farm and Garden Program.
How are you using microBIOMETER®?
We are using microBIOMETER to track the soil health on our farms, gardens and compost. This test allows us to understand if we are providing an environment for our crops to thrive. Because we grow fruit trees, herbs and annual edible crops the fungal to bacterial ratio helps us identify the current soil health and help us understand what strategies we can look to implement to improve that environment over time.
How does microBIOMETER® help people understand the importance of soil biology as opposed to the historical focus on soil chemistry?
Traditional soil tests give you a window into what nutrients are or are not available within your soil. It can give you insight into how much organic matter might be present in your soil, but not how you might work to track progress on soil health, diversity or improving your soil food web on an affordable level. While knowing the nutrient breakdown is helpful information it does not help you understand if you are providing an ideal environment for those micro and macro organisms to thrive and ultimately aid your crops or plants in receiving those nutrients and so much more. The microBIOMETER® test kit has helped us better understand our complex food web and what strategies we can do to create a more balanced environment for our crops and our soil.
How did the microBIOMETER® information assist you with your project?
This test helps us to educate not only our staff on soil health strategies, but also our volunteers and anyone who attends are Teaching Garden classes. The data we collect helps us to showcase how the strategies we are employing to improve our soil health are making a difference from season to season as opposed to every two years from a traditional soil test. That enables us to make better recommendations to our community of growers about ways they can improve their soil, too.
About the San Antonio Food Bank
The San Antonio Food Bank takes pride in fighting hunger, feeding hope in our 29-county service area. We believe that no child should go to bed hungry, adults should not have to choose between a hot meal and utilities, nor a senior sacrifice medical care for the sake of a meal.
Founded in 1980, The San Antonio Food Bank has quickly grown to serve 90,000 individuals a week in one of the largest service areas in Texas. Our focus is for clients to have food for today but to also have the resources to be self-sufficient in the future.
Fighting hunger is our number one priority but we also serve to educate and provide assistance in many other ways. We achieve this through our variety of programs and resources available to families, individuals, seniors, children, and military members in need.
Our Farm and Garden Program consists of two locations and six growing spaces, including two farms and the garden at the New Braunfels Food Bank. Together these areas total more than 100 acres and provide 300,000 pounds of fresh local produce annually to our 29-county service area. We utilize 5,000 volunteers annually to assist with our operation and to provide local produce to the community.
Our Farm and Garden Program strives to provide quality, local produce to the community and to provide resources to teach those in our community how to grow food for today and in the future. In order to meet those goals, we start with our soil. By understanding our soil biology and health we get a window into what is happening at the root level and better understand the environment where our crops live and how to make improvements so we are growing healthy plants and nutritious crops. We believe everyone deserves access to nutritious fruits and vegetables.
Our Teaching Garden classes provide information about the importance of soil and composting as a foundation for building soil diversity and health. We utilize cover cropping on the farms and in our gardens to reduce erosion, build soil fertility, reduce weed pressure and increase organic matter. We create and utilize composting to increase the diversity of our soil, divert valuable resources from the landfill and introduce the community to the benefits of composting at home or in the community.
Informal science education is a key for community engagement and healthy gardening. Community gardening brings numerous benefits such as fresh produce, therapy, physical exercise, reduction in grocery bills, improvement of mood among many others.
“Last weekend I had the privilege to teach community gardeners on the importance of soil testing side by side with my very first student at NYBG Adult Education program (class 2015). Dr. Joan Basile is a clinical psychologist who has developed her own horticulture therapy program incorporating soil knowledge brining therapy & soil science & gardening together.” – Dr. Anna Paltseva, soil_expert.
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“While the microBIOMETER® results showed there is room for improvement, the result from last year’s beds also proved that composting and mulching practices are paying off in increased soil life. This means that sandy soil will gradually be able to hold nutrients better and better!” – Dr. Basile
The Biospheres, working through the CDA*, accompanies and trains farmers/agricultural companies in the agroecological transition based on a soil conservation approach. The group is also working on applied research projects and therefore on trials under real farming conditions in which they evaluate the impact of certain changes in practices on different indicators (biological, chemical, physical, economic).
“One of our primary objectives is that farmers succeed in putting biology back into their soils to ensure their natural fertility. We are therefore very interested in everything that lives in the soil, from earthworms and microarthropods to microorganisms (bacteria, fungi, nematodes). For us, microbial biomass is one of the most important indicators that help us understand soil biology. Fungal to bacterial ratio, which is a less documented indicator for the moment, remains interesting to observe in certain situations and is the object of real research by our R&D team to understand how best to interpret it.
We have been using microBIOMETER® for 8 months now to test the soil in different projects in our panel of biological indicators. microBIOMETER® provides us with quick and easy results on microbial biomass and F:B ratio which is a real plus for us. We can perform tests directly in the field and present the results to the farmers. Moreover, the affordable price of the analysis allows us to perform soil biology tests in projects where we had no affordable way to do so before.”
*CDA, Centre de Développement de l’Agroécologie, are affiliates dedicated to R&D and advisory.
Ariel White; Post-Wildfire Forest Reboot Kit
Ariel White, a ninth grader at Pretty River Academy in Ontario, Canada, utilized microBIOMETER® in their science fair project titled Post Wildfire Forest Reboot Kit.
The project was awarded first place at their high school and chosen to compete at the Simcoe County Regional Science Fair. At the regional fair, Ariel was awarded a gold medal, Best of Earth and Environmental Sciences, Best of Fair, The Dufferin Simcoe Land Stewardship Network Award, and was one of seven students selected to represent their county in the Canada Wide Science Fair where they won a silver medal!
About the project: Forest fires have increased due to climate change, causing forests to burn down at an unbelievable rate. Now we need forests more than ever, yet they have been taking years if at all to regrow. This project explores the question “how can we boost the speed of forest regrowth after forest fires?”. For phase one of this experiment, each plant was graded for performance using tests such as success-rate, growth-rate, compost-value, and self-propagation. For the second phase, it was seen what effect this plant had on the soil microbiome; which is key to healthy, speedy plant growth and isn’t evident after fires. It was concluded that the morning glory substantially increased the microbiome health from inevident to healthy, and had an almost perfect performance score. These results are very important to our world’s future as they could help to deter climate change and repair our forests and their diverse ecosystems.
Soil testing
Modern agriculture practices have led to the systematic degradation of the world’s soil and release of carbon into the environment. The effects are increased need for expensive and environmentally dangerous inputs (fertilizers, pesticides, and herbicides), the loss of fertile top soil, decrease in water holding capacity of soil and dangerously high levels of atmospheric carbon.
Farmers, industry, and environmentalists are looking for cost-effective and reliable ways to measure soil health, to assess impacts of progressive changes on soil and harvest management, and to measure carbon in soil. Before microBIOMETER®, growers have traditionally relied on expensive lab testing of soil. Many current methods are technique and individual lab dependent. Therefore, run-to-run and lab-to-lab variation can greatly affect consistency leading to increased variability. Current methods are performed in labs and the soil is aged and changed from the time of collection. Furthermore, lab tests are difficult to use in developing countries as they can cost upwards of $500 per sample. This makes the test prohibitive to some markets and limits the number of times a grower can test their soil.
Our mission at Prolific Earth Sciences is to enable soil stewards all over the world to use mobile technology and our low-cost soil test to assess regenerative soil practices, to improve soil health, and work towards increased soil carbon sequestration. microBIOMETER® equips growers with the data necessary to make decisions on which practices are the most cost-effective. Inputs such as fertilizers are expensive and changes to practice are risky. Monitoring soil microbial biomass inexpensively, in real time, can help a soil steward quickly assess if an input and practice is improving soil health and worth the investment. In other words, assess before you invest! We also envision microBIOMETER® one day being a powerful tool in the measurement and audit of carbon sequestration programs.
microBIOMETER® has been on the market for over 3 years with direct and distributor sales and currently has customers in over 20 countries.
