Measuring the Number of Microbes in Soil – The Microbial Biomass

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Robert Pavlis

Gardeners have come to understand that the microbe population in soil is critical for healthy soil and healthy plants. There is also tremendous chatter on blogs and in social media about “doing the right thing” to increase microbe populations. Companies have packaged microbes to produce garden “probiotics”. Just sprinkle a bit on your soil and watch the magic happen. So I think we can agree that gardeners should take care of their existing microbes and work on increasing their numbers.

More microbes = healthier soil = happier plants

But ….. there is a catch. How does the gardener measure the current microbe population? If you can’t measure it today, how do you know that you have increased the population over time? How do you know which method of soil improvement worked the best?

Do purchased probiotics work the best? How about compost tea, or weed tea? Does compost alone work?

Without a method for measuring microbes, you are flying blind. In this post I will discuss some lab methods, some DIY methods and some new technology that is just coming on the market.

Measuring the Number of Microbes in Soil - The Microbial Biomass
Measuring the Number of Microbes in Soil – The Microbial Biomass, source: Alice Dohnalkova

Can Scientists Measure the Amount of Microbes?

With all the talk about the importance of microbes you would expect the answer to be yes, but it turns out it is very difficult to count microbes.

You have probably seen microbiologists grow microbes in petri dishes and then count colonies. That does work but only for species that grow on the food in petri dish. The majority of soil organisms won’t grow this way.

Dr. Elaine Ingham from the Soil Food Web Organization promotes  the use of a microscope for counting organisms in soil, but as I have discussed before this really does not work, especially if done by trained gardeners. Even when done in a lab it has limited value for determining total biomass.

One teaspoon of topsoil contains around 1 billion individual microscopic cells and around 10,000 different species.”

There are many different types of microbes and their numbers are huge. They are mostly very small and like to hide inside soil channels. Measuring their number is difficult.

From a soil health point of view it is more important to measure the mass (weight) of microbes rather than the number because mass accounts for the vast difference in size between organisms.

YouTube video

Scientists have developed several indirect ways for measuring the microbial biomass and you can order these tests from various soil testing laboratories.

The Fumigation-Incubation Method (FI)

Two soil samples are collected. One is untreated and the other is fumigated to kill all living organisms. Living microbes are added to the samples and they start digesting any dead organisms which releases CO2 as part of respiration. The measured amount of CO2 is uses to calculate the mass of dead organisms due to the fumigation. This is an accurate method for some types of soil.

Microbe Science for Gardeners Book, by Robert Pavlis

The Fumigation-Extraction Method (FE)

Two samples are collected and one is fumigated. The amount of carbon (FE-C), nitrogen (FE-N) or phosphorus (FE-P) resulting from the dead organisms is used to determine a biomass value. This method works for a large number of soils including wet soils and acidic soils. When chloroform is used for fumigation the method is called CFE.

The Substrate-Induced Respiration Method (SIR)

Two samples are collected and one is fumigated. Sugar is added to the samples and CO2 is measured. The amount of CO2 produced is relative to the amount of microbial respiration caused by the added sugar and is therefore an indirect way of measuring the mass of microbes. The method is simple, fast, and allows for the estimation of the fungal to bacterial ratio (F:B). One problem with the test is that it only measures microbes that are able to consume sugar.

The ATP Activity Method (ATP)

The microbial cells are destroyed in one of two samples, which releases ATP. This is extracted and measured. The amount of ATP is proportional to the mass of microbes killed in the sample.

Measuring Microbes with Earthworms

Earthworms consume microbes that are found on organic matter. An increase in microbes results in an increase in earthworms and therefore counting earthworms is an indirect way of measuring microbial mass. The following is taken from the book Soil Science for Gardeners, by Robert Pavlis.

“Measure out a square foot of soil. Dig down 12 “and remove all of the soil. Spread it out on cardboard or newspaper. Break up the soil and count all of the worms you find. If your soil is healthy, you’ll find at least 10 earthworms per cubic foot (0.092 cubic meters).”

The method does not provide an actual count of microbes or a mass, but the method is easy to do and will show improvements in microbe populations over time.

Measuring Microbes with Earthworms
Measuring microbes with earthworms, source: Earthworm watch

The Tighty Whitie Soil Test

Microbes consume organic matter and so you can add some cotton to the soil and see how quickly the microbes digest it, a method known as Tighty Whitie.

It is fully described in Tighty Whitie Soil Test – A Brief Review.

The method does not provide accurate numbers but it does give you an approximation of soil health and can be done by any gardener.

Tighty Whitie Soil Test – measures the microbe population in your soil
Tighty Whitie Soil Test – measures the microbe population in your soil


The microBIOMETER is a new home/field test that was developed specifically for measuring microbial biomass and the fungal:bacterial ratio. I will be reviewing and testing this product shortly, so I won’t say too much now. The kit comes with an extraction powder that you mix with water. When this is mixed with soil, it extracts the microbes from the soil. You then take the extracted liquid and place it on a test card where it reacts with a dye. Wait 2 minutes for the dye to react and then take a picture of the sample using their cell phone app which converts the image to mass and ratio values.

The app counts stained microbes. It is not clear how it converts these counts to mass? The ratio can be estimated because bacteria and fungi stain different colors. There is no mention of other types of microbes or how these affect either of the results.

Three drops of extracted sample are added to the microBIOMETER card
Three drops of extracted sample are added to the microBIOMETER card, source: microBIOMETER

Does the microBIOMETER work? The company certainly thinks it does and they do have internal testing to show it does, but they have no third party testing to support their claims. There is a masters thesis research project that uses the kit and it found inconsistent results. I have not been able to find any other research that used the technique and the company acknowledged that their only testing has been done by their personnel.

If we start with an average sample of say a billion microbes per teaspoon, work through the procedure and dilution process, and assume all microbes are extracted, you will put 50,000 microbes on the card in a 1/4″ diameter circle (area = 0.005 inch squared). It is hard to believe a cell phone can be accurate enough to count such a large number in such a small space? It is possible that the extraction is not 100% effective and that the app corrects for this.

Can Gardeners Measure Microbial Biomass?

You can certainly order such a test from a soil lab but they are not cheap. The two above mentioned DIY tests give a very rough idea of soil health but they don’t provide microbial mass values. The microBIOMETER costs about $15 US per test for the initial kit and drops to $9, or $7 if you buy refill kits. This price is reasonable for a home gardener. The key question with this kit is about reliability? It just has not been tested enough to know how well it works.

I do plan on some testing and will report back here when I have the results.

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Robert Pavlis

I have been gardening my whole life and have a science background. Besides writing and speaking about gardening, I own and operate a 6 acre private garden called Aspen Grove Gardens which now has over 3,000 perennials, grasses, shrubs and trees. Yes--I am a plantaholic!

23 thoughts on “Measuring the Number of Microbes in Soil – The Microbial Biomass”

  1. I use the microbiometer professionally with my consulting clients and have found it to be a very useful tool to give a rough sense of what is happening with the biology in a given soil, therefore informing management, amendment and ferilization practices appropriate for the context. Is it a perfect tool? I doubt it, but for the cost and ease of use in the field it has been very valuable and helped me tremendously. I’ve used lab microbial tests as well, but they are cost prohibitive for most situations outside of high value crop production where the limiting factor can be deduced to a microbial imbalance. I also dabble with microscopy, but I don’t think it has much practical application for most contexts outside of satisfying curiosities.

    I find you hyper analytical articles helpful, if not a little excessively reductionist. To think we can grasp every last thing about what is happening at the microscopic level is foolish. I harken to the roots of science where a dose of mysticism and wonder keeps us humble. As robert anton wilson was keen to say, a measurement is only as accurate as the tool measuring it. We aren’t perfect beings, therefore science is an ongoing process where in the end, we may be wrong because we can’t understand everything in it’s entriety. Thats my belief, much to the chagrin of materialsist reductionists. To each their own.

  2. Thank you for your work in sharing useful information. A couple of years ago I found a company that has a new method of microbial analysis (in terms of quantity and species, but also funcionality). The company is called Biome Makers and the tool for analysis is Becrop. I am a consultant in viticulture and I use Becrop on some clients who are willing to pay for these analyses as they are not cheap (200$ each).

  3. I agree with Mike Sterland and use the principle “build it and they will come”. No need to count ’em – just observe how your garden is growing.

  4. I would need to read the original post about why you think that using shadowing microscopy doesn’t achieve anything, to make an informed comment, is that post available?

      • “Dr. Elaine Ingham from the Soil Food Web Organization promotes the use of a microscope for counting organisms in soil, but as I have discussed before this really does not work, especially if done by trained gardeners. Even when done in a lab it has limited value for determining total biomass”.
        .You said it doesn’t work, doesn’t achieve anything is pretty much the same statement, shadowing microscopy is the technique used

        • No they are not the same thing. What I said was it does not work for determining microbial biomass. That is specific – not “anything”.

          • The microscope anal is about determining what ratio of different biology is in the sample, which includes total numbers, fungi is total area, thus providing a level of functionality. it is not limited in value, it then allows an ongoing anal to after compost applications to then further see if the applications are increasing biomass of beneficials

  5. Excellent info, as always. Eagerly waiting to see your final opinion on packaged micro organisms for soil and their effectiveness and usefulness for gardeners.

  6. IMO many people tend to overthink the management of their soil’s health.
    Unless there’s an evident imbalance or deficiency, adding around an inch of good compost every year appears to keep my soils microbiological & fungal health where it needs to be.
    How do I know?
    Because I can harvest more than 400lbs from a 40×10′ plot year after year with the only change being a steady increase.


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