Fungal testing Johnson-Su Bioreactor compost with microBIOMETER®

This article was provided to us by Scott Hortop, a retired volunteer and now student of soil, located in the Ottawa Valley, Ontario, Canada.  Scott wants to use his retirement to do one important thing for the climate.

At ONfungi we own two microBIOMETER® soil testing kits which we use to determine the fungal to bacterial ratio (F:B) of the Johnson-Su fungal dominant compost (FDC). The ONfungi group makes FDC from tree leaves.

We are excited by the potential of leaf mold to:

• Reduce agricultural dependence on external inputs• Divert leaf organics from landfills• Replenish the inventory of carbon in the soil by drawing down the carbon in the atmosphere• Grow knowledge about working with mother nature to address climate change

Our first FDC bioreactor batch was started in Spring 2018. Since then, we have put up a total of 15 batches; 8 of them in fall 2021.“It took us 3 batches before we faced the fact that we needed to know whether what we were producing was actually what we hoped it was. Our enthusiasm needed to be grounded. What is the fungal bacteria (F:B) ratio in our FDC?,” says Scott Hortop, wizard of compost for the ONfungi group. “This is why we have found the microBIOMETER® to be our most useful tool.”“Dr. David Johnson’s talks have shown us eloquently how the F:B ratio is the most meaningful indicator for soil health”, Hortop explains. “As we share our fungal dominant compost (FDC) with other users, we owe them a solid measure of what they are getting. When we and others share our FDC experiments with each other at the Chico State University Registry of Johnson-Su Bioreactors, the majority of us have been unable to report F:B ratios. This has now changed. With the microBIOMETER® we can confirm that we have the right ratio of ingredients by taking a real measure of the F:B ratio.”Its All Relative – Isn’t it the change and the direction of changes that we really need to know? Of course, it might be nice to think every microbe was identified and counted under a microscope, but that precision comes at a HUGE cost and most likely doesn’t alter the conclusion. The next thing we need to do to strengthen the microbial community.
Immediacy – When you are checking in on living microbes in soil, some of whom are reproducing and dying in a matter of minutes and others taking years, the best timing for a test is here and now. In a world rich with distraction and delay, its awesome to get a result from your testing efforts immediately.
True Cost Per Data Point – For the purpose of our bioreactors, give it a think: the modest variable costs per test, the modest labour to execute a test which is just minutes beyond the time required for sample collection, the VERY efficient and effective recording of results, and the $0 sample shipping cost.

In an ONfungi citizen science trial last summer by one of our volunteers in White Lake, Ontario, 2 sunflower seeds were planted in late June into moderately degraded farmland (microBIOMETER® F:B 0.7:1; 464 µg C/g).The control seed (left) received no soil amendments. The 2nd seed (right) was planted with 50 grams (a small handful) of Johnson-Su fungal dominant compost (microBIOMETER® F:B 1.7:1; 700 µg C/g) surrounding the seed. For 8 weeks both plants received identical, adequate watering. The 8-week photo below shows the control sunflower on the left suffering from an invasion of cucumber beetles with less than ½ the height and 1/3 the stalk width compared to the sunflower on the right with FDC at its root zone. Although beetles were observed on the FDC sunflower, some disease resistance was evident.One of ONfungi’s targets this year is to do monthly tests on completed FDC material to chart the staying power and degradation curve of finished FDC, not yet put to use and in several storage modes. We are also using the microBIOMETER® to look at carbon sequestration in lawn soils.About ONfungi; ONfungi is a happy conglomeration of active volunteer folks. Their goal is to explore, through citizen science, the use of Johnson-Su fungal dominant compost (FDC) in improving soil, storing carbon, and enhancing plant health and nutrition. Learn more at

Are you increasing the nutrient value and disease resistance of your crop?

microBIOMETER® can tell you if you are increasing the nutrient value and disease resistance of your crop.

A Rodale study showed greatly increased levels of the vitamins and minerals in sustainably farmed soils as opposed to mineral fertilized crops. And at Rodale, the sustainable practice yields are the same as the paired fields farmed with mineral fertilizers – and in bad weather, and disease years significantly better. Rodale is only one of many studies showing the increased nutrient value of organically and sustainably grown food.

Now Dr. Montgomery of the University of Washington’s team in a similar study has shown that if you are increasing your microbial biomass you are increasing the nutrient level of your crop: “soil health is a more pertinent metric for assessing the impact of farming practices on the nutrient composition of crops”.

Biklé, A. and Montgomery, D.R., 2021. Soil health and nutrient density: beyond organic vs. conventional farming. Frontiers in Sustainable Food Systems.

Hepperly, P.R., Omondi, E. and Seidel, R., 2018. Soil regeneration increases crop nutrients, antioxidants and adaptive responses. MOJ Food Process Technol, 6(2), pp.196-203.

Nitrogen fertilizer study at Ursinus College

University study demonstrates legumes are more efficient at improving soil MBC than grasses

Under the direction of Assistant Professor Denise Finney, Kylie Cherneskie, biology student at Ursinus College, conducted an experiment on the impacts of nitrogen fertilizer addition on soil microbial communities. Kylie measured microbial responses using microBIOMETER®.

Click here to view the finished poster presentation. If you would like to incorporate microBIOMETER® into your classroom studies/academic research, we offer a selection of Academia Classroom Kits.

Study shows microBIOMETER® correlates with Chloroform Fumigation Extraction

Calibration of microBIOMETER® to units of µg microbial carbon / gram soil

The gold standard of laboratory soil microbial biomass testing is Chloroform Fumigation and Extraction (CFE). The multiple steps, time, and labor involved with CFE require pricing at up to $500 per sample. CFE works by comparing the difference of chemically extractable carbon between two portions of a soil sample: One that has been treated to break open microbial cell membranes and expose the carbon-containing biological molecules to extraction, and one that has not. The difference in carbon for the two portions is reported as microbial biomass carbon (MBC), in units of µg C / g soil.

microBIOMETER® is calibrated to the same units by a different method. Estimates of bacterial dry mass converge at around one trillionth (1×10-12) of a gram (1 pg) for a 1 µm bacterium. We measured the area of microbes in known volumes of microBIOMETER® extract (both by manual counting on a hemocytometer and by digital analysis of micrographs) and calculated total microbial mass, which was then converted to µg / g for the whole 0.5 ml sample of soil in the extract. We found that on average, 0.5 ml of soil weighs 0.6 g when fully dried, independent of starting moisture content. The 1 pg dry mass per bacterium is 50% carbon, so we also had to account for that in our calibration.

Here’s an example of the conversion.

Let’s say that in 1×10-8 liter (10 nl) of microBIOMETER® extract we measured 240 µm2 of microbes. 240 µm2 = 240 bacteria equivalents (BE). 240 BE x 1×10-12 g per BE = 240×10-12 g of dry microbes. The volume of original extract is 10 ml (1 x 10-2 liter), and 10 nl of microscopically examined extract represents 1×10-8/1×10-2 = 1×10-6 of the total mass of the microbes in the extract. So 240×10-12 g microbes / 1×10-6 = 240 x 10-6 g microbes in the whole extract. 50% of the 240 x 10-6 g of microbes is carbon, so we have 120 x 10-6 g microbial carbon. We started with 0.5 ml = 0.6 grams of dried soil in the extraction process, therefore 120 x 10-6 g microbial carbon / 0.6 g soil = 200 x 10-6 g microbial carbon / gram soil, or 200 µg microbial carbon / gram soil.

While we arrived at µg microbial carbon / gram soil through a different method than CFE, it turns out our methods are on par with the CFE test. We compared measurements of µg carbon / gram soil via CFE and microBIOMETER® from 28 soils from across the U.S.

The slope of ~1 of the regression line indicates our units are on par with CFE, and the 94% correlation indicates that users can be confident that the $10 or less microBIOMETER® test gives results as accurate and informative as one priced $500.

Things you need to know about the Fungal to Bacterial Ratio (F:B)

    • microBIOMETER® is the only non-laboratory test for F:B.
    • The methods of measuring F:B ratio give very different values 1-11. The Gold Standard for estimating fungal biomass is microscopy, which calculates fungal biovolume.  Note that microBIOMETER® detects the same range as microscopy- not surprising as it was validated by correlation with microscopy.  For review of these measures see Appendix 1.  For measuring progress, stick with one method.
  • Different methods measure different fungal and bacterial populations.  The chart below, adapted from Wang et al review of 192 different F:B ratios, illustrates how three different methods came up with three different F:B ratios for Forest, Farmland and Grassland.  Note that microBIOMETER® correlates well with the gold standard, microscopy. By plate culture, forest F:B is about 1/3 that of farmland, whereas PLFA forest F:B is slightly higher, and microscopy and microBIOMETER® forest F:B are 10 times higher than farmland.
  • In addition, F:B ratios are strongly affected by the following variables:
    • Crop type – forest is typically higher than agricultural,
    • AMF – soil of crops that are colonized by AMF have higher F:B
    • pH – fungi tend to increase at lower pH
    • Sampling site – the rhizosphere of AMF colonized plants has higher F:B
    • fertilizer and litter composition – high nitrogen lowers F:B, organic fertilizer regimens increase F:B as well as MBC.
  • microBIOMETER® cloud data demonstrates an F:B range of 0-13.5. Note that as the literature predicts, generally the F:B correlates well with MBC.  The cloud data portrayed is not identified by user and so we do not have information on the type of soil or crop.  From conversations with users, we believe that about 2000 ug MBC/gm soil is the highest seen in agricultural soil, while engineered soils can read higher.



    1. Anderson, J.P. and Domsch, K.H., 1978. A physiological method for the quantitative measurement of microbial biomass in soils. Soil biology and biochemistry10(3), pp.215-221.
    2. Bååth, E. and Anderson, T.H., 2003. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biology and Biochemistry35(7), pp.955-963.
    3. Bailey, V.L., Smith, J.L. and Bolton Jr, H., 2002. Fungal-to-bacterial ratios in soils investigated for enhanced C sequestration. Soil Biology and Biochemistry34(7), pp.997-1007.
    4. Bardgett, R.D. and McAlister, E., 1999. The measurement of soil fungal: bacterial biomass ratios as an indicator of ecosystem self-regulation in temperate meadow grasslands. Biology and Fertility of Soils29(3), pp.282-290.
    5. De Vries, F.T., Hoffland, E., van Eekeren, N., Brussaard, L. and Bloem, J., 2006. Fungal/bacterial ratios in grasslands with contrasting nitrogen management. Soil Biology and Biochemistry38(8), pp.2092-2103.
    6. Johnson, D.C., 2017. The influence of soil microbial community structure on carbon and nitrogen partitioning in plant/soil ecosystems(No. e2841v1). PeerJ Preprints.
    7. Khan, K.S., Mack, R., Castillo, X., Kaiser, M. and Joergensen, R.G., 2016. Microbial biomass, fungal and bacterial residues, and their relationships to the soil organic matter C/N/P/S ratios. Geoderma, 271, pp.115-123.
    8. Malik, A.A., Chowdhury, S., Schlager, V., Oliver, A., Puissant, J., Vazquez, P.G., Jehmlich, N., von Bergen, M., Griffiths, R.I. and Gleixner, G., 2016. Soil fungal: bacterial ratios are linked to altered carbon cycling. Frontiers in Microbiology7, p.1247
    9. Soares, M. and Rousk, J., 2019. Microbial growth and carbon use efficiency in soil: links to fungal-bacterial dominance, SOC-quality and stoichiometry. Soil Biology and Biochemistry, 131, pp.195-205.
    10. Wallenstein, M.D., McNulty, S., Fernandez, I.J., Boggs, J. and Schlesinger, W.H., 2006. Nitrogen fertilization decreases forest soil fungal and bacterial biomass in three long-term experiments. Forest Ecology and Management222(1-3), pp.459-468.
    11. Wang, X., Zhang, W., Shao, Y., Zhao, J., Zhou, L., Zou, X. and Fu, S., 2019. Fungi to bacteria ratio: Historical misinterpretations and potential implications. Acta Oecologica, 95,



Community gardening with microBIOMETER®

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.

“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

microBIOMETER® Soil Testing in France

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.



microBIOMETER® featured in award-winning science fair project.

soil microbe testing
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.

microBIOMETER® educating farmers in the Gulf Region on the importance of life in the soil.

Sustainable Organic Q8 was launched in mid-2018, educating people on recycling their organic waste, being environmentally aware and teaching people how to grow whatever and wherever they can. As far as gardening/farming styles, Sustainable Organic focuses on the value of the living soil and the soil food web and teaching home gardeners and farmers to slowly shift the general culture from MONOCULTURE, “Babysitting plants” and providing all their needs from nutrients to medicine to DIVERSITY, Building and regenerating an ecosystem that will take care of itself or at least be a bit less exhaustive and much more sustainable.

Sustainable Organic has helped bring diversity above grounds back to the region in the past couple years. However, many people are still very new to the life underground and living soil. Their gardening/farming practices rely heavily on providing nutrients and immunity/medicine to plants. To them it is cheap, it works, and they’re so set in their ways that the idea of change is becomes a source of anxiety.

Although more and more gardeners are praising the life in the soil, they also practice routine solarization and refuse to refrain from it, reflecting their hazy understanding of soil biology and the soil food web and what it really takes to construct. Testing the soil to most growers means checking nutrient availability, water content and pH.

For the sake of adding some objectivity to soil biomass and increasing the value of soil biomass testing, Sustainable Organic sent microBIOMETER® test kits to popular gardeners in Kuwait, Saudi and Dubai to experiment with by testing their soils and compost. These gardeners have a large number of followers and they educate via social media, gardening courses, and workshops. By starting to broadcast microBIOMETER® as a means of testing the biomass in the soil and amending it based on the readings received, Sustainable Organic intends to create a trend in the region shifting the focus more on the life in the soil than the mineral content.

“microBIOMETER® is an innovation that has made it possible to quantify the life in the soil. This economic tool, I believe, not only helps us improve our soil at the gardening/farming level, but it can also help us deepen our understanding and comprehension of the soil food web and the LIFE underground. This will ultimately lead to a tremendous positive change at the psychological and behavioral level.  It’s common to see people in our region praising the life in the soil (finally), but then professing solarization at the end of or the beginning of a grow 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!

It’s beautiful to see people go out in the middle of the desert and start digging holes to “build” soil, plant trees and mulch around them; then announce seeing mushrooms and biologic diversity; start talking about soil biology, arbuscular fungi and carbon sequestration and tell farmers near them to try out the living soil method learned from Sustainable Organic. They say think globally and act locally. We intend to revive the desert in the Arabian Peninsula with Mother Earth and her fever at heart!”

About Dr. Jassem Bastaki. Originally from Kuwait, Jassem acquired his education in Head and Neck Endocrine Pathology in Pittsburgh, PA. In 2012, he left Pittsburgh to practice diagnostics and oncology in Kuwait and in doing so transitioned from fertile land to urban settings in some of the harshest climates in the world. The stress from his line of work led him back to gardening; indoors and hydroponic initially until he learned how to garden outdoors no matter the climate or conditions. Every second he spent with his plants taught him more and more about life and the reality we are unaware of. “We are guests on this earth with everything else that lives on it and in it.” The more he realized what was missing and where to find it, he wanted to help everyone find their way back to earth.

Jassem is a microBIOMETER® distributor in the Gulf Region as well as Iraq, Jordan and Egypt.

Microbial Biomass vs. Microbial Respiration

What is the difference between microbial biomass (MB) and microbial respiration rate (RR) ?

Both parameters are used to assess soil microbial health. The respiration assay measures the amount of carbon dioxide produced by the microbes in a given weight of soil. The soil is dried and then rewetted and put in an airtight jar that allows measurement of the amount of CO2 produced over 24 hours. The CO2 is produced by the activity of the microbes in the rewetted soil. Between 20% and 70% of the microbes die during drying but their dead bodies often provide nutrition for the survivors to use and regrow the population to its original level.

Respiration reflects the regrowing work that is being done. The respiration level is often mistakenly believed to predict microbial biomass (MB), but it does not. Microbes in a low pH or toxic soil have to work harder, therefore, their respiration rate is higher, just as your respiration rate in the gym is higher than when you are watching TV. Outside of the U.S. the respiration rate (RR) is only considered in relation to MB and this q-value RR/MB is used to determine the level of stress in a soil. If RR is high for the MB, the soil is in trouble.

MB, as measured by microBIOMETER®, correlates with chloroform fumigation—always and microscopic evaluation of soil. It is an excellent predictor of soil health because the size of the microbial population correlates with the nutrition available in the soil. If the soil is deficient in carbon, nitrogen, phosphorus or any other mineral, or contains toxins, MB will be low. In fact, MB is low in any soil that is compacted, has a low pH or is overly dry, because microbes need oxygen and moisture and the correct pH for enzymatic activity.

In nature, the plant uses 30% of its food production to feed a microbial population that will mine the soil for the N, P, K, S etc. that it needs. Interestingly MB is low in soil treated with high levels of mineral fertilizers; researchers have shown that the stimulus for the plant to grow a microbial population is its need for nitrogen and phosphorus. If these are artificially supplied the plant is not stimulated to feed the microbes that usually provide these nutrients to the plant. And since the microbes are at least half of the immune system of the plant, you now need lots of pesticides to protect the plant.