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

Soil research in Kenya with microBIOMETER®

Janet Atandi, a nematology PhD student in Kenya, is currently working on an assessment of banana fiber paper on soil health as part of a Wrap and Plant technology study. In brief, she is testing the long-term effect of using modified banana fiber paper to manage plant-parasitic nematodes and its impact on the beneficial soil microbial communities.

The banana fiber paper is used as an organic carrier for either ultra-low dosages of nematicides (abamectin and fluopyram) or microbial antagonists (Trichoderma spp.) and is to be compared to unmodified paper.

This study is being conducted using potatoes and green peas as the test crops over five consecutive seasons. With the aid of a microBIOMETER® test kit, Janet will be able to assess the impact of the paper on the soil microbial biomass and thus will be able to determine whether the banana paper is effective or detrimental to soil health.

Wrap and Plant technology sources:
NC State explores promising pest-control strategy with high-impact potential for sub-Saharan Africa
Banana’s Waste, potatoes gain
Potato farmers conquer a devastating worm—with paper made from bananas]

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.

microBIOMETER® assists grower in selecting best fertilization regimens

Austin Arrington of the Plant Group

Austin Arrington of Plant Group NYC performed a research study on hemp’s capacity to sequester carbon. Austin utilized microBIOMETER® in this research. We originally had the pleasure of meeting Austin through Indigo Ag’s Terraton Challenge. Plant Group is a fellow semi-finalist and alumni.

Hemp has the promise of being a twofer: a financially successful crop as well as a carbon crop that increases soil carbon for carbon credits and increased fertility. Austin used microBIOMETER® to evaluate two organic fertilizer regimens for a hemp crop; an early fertilization during the vegetative phase and a month later during the flowering phase.

Honeysuckle Hemp 2021: Research Notes

One hectare of industrial hemp can absorb up to 22 tonnes of CO2 per hectare. The fact that industrial hemp has been proven to absorb more CO2 per hectare than any forest or commercial crop makes it an ideal tool for carbon farming (Vosper, 2011). 

Two acres were hand seeded with Maya hemp grain on 05/23/21 in a silt clay loam soil in Council Bluffs, IA. Prior to tilling (with a rear tine tiller) and seeding with hemp the area was covered with white clover. The area was split into two zones that each received organic fertilizer at different times. The Early Fertilizer Zone was fertilized on 07/25/21. The Late Fertilizer Zone was fertilized on 08/08/21. Mega Green (2-3-2), the organic fertilizer applied for the study is derived from squid waste and was diluted with water for application across the field.

The microBIOMETER® spectroscopic tool was used to estimate microbial biomass carbon and fungal to bacterial ratio. Microbial biomass carbon is a measure of the carbon ( C ) contained within the living component of soil organic matter (i.e. bacteria and fungi). Microbes decompose soil organic matter (SOM) releasing carbon dioxide and plant available nutrients. The measurement unit of the device is ug C / g (micrograms microbial biomass carbon). Click here to read full study.


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,



microBIOMETER® testing for soil health and yield stability

Nature article reports that microbial biomass estimates by microBIOMETER® correlates with soil health and yield stability.

The microBIOMETER® soil test was used to report microbial biomass in a recent Nature publication*. Scientists Dr. Judith Fitzpatrick and Dr. Brady Trexler of microBIOMETER® collaborated with a University of Tennessee team headed by Dr. Amin Nouri. The team evaluated the effects on soil health and yield stability of 39 different methods of raising cotton over 29 years. The conditions tested included till, no-till, various cover crops and different levels of nitrogen fertilization.

The study found that the major impacts on yield were very dry or wet conditions, and low or high temperatures. The deleterious effects of these weather extremes on yield were mitigated by regenerative agricultural practices which resulted in adequate soil, C, N, soil structure and microbial biomass.

Conservation agriculture increases the soil resilience and cotton yield stability in climate extremes of the southeast US

*Nouri, A., Yoder, D.C., Raji, M., Ceylan, S., Jagadamma, S., Lee, J., Walker, F.R., Yin, X., Fitzpatrick, J., Trexler, B. and Arelli, P., 2021. Conservation agriculture increases the soil resilience and cotton yield stability in climate extremes of the southeast US. Communications Earth & Environment, 2(1), pp.1-12.

Soil testing at a hemp farm in Iowa

soil testing
Austin testing soil testing at a hemp farm with microBIOMETER®

PLANT Group is a team of designers, engineers, and ecologists. The company is building systems to connect humans and nature. In the process, they are soil testing at a hemp farm in Iowa, Honeysuckle Hops & Hemp.

First, through their partnership with Blue Forest Farms, the team at PLANT Group is using microBIOMETER®. They are utilizing the tool to research soil health and carbon sequestration implications of growing hemp.

Furthermore, Austin has an interest in publishing research on their alternate organic hemp production methods.  microBIOMETER® is assisting them in collecting some “pretty cool data on microbial biomass and fungal ratios in the soil in response to these strategies.”

Meanwhile, the company recently launched a new line of hemp food products, Hemp Hearts. They grow each plant regeneratively. This includes a focus on soil carbon, biodiversity, and ecosystem health.

Did you know one hectare of hemp can absorb 15 tons of CO2 per hectare? Hemp’s rapid growth makes it one of the fastest CO2-to-biomass conversion tools available. Therefore, let’s stop cutting down our forests. Plant some hemp instead!

Lastly, please visit the PLANT Group website to meet the rest of the team and learn more about their business. And follow them on Instagram to keep up to date on their progress!

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