Microscopy for Monitoring Soil Health

The soil microbe biome works to cycle nutrients, breakdown and incorporate organic matter applied to fields, and aggregate soil particles.  The 7 types of life interact, as a complete ecosystem, with each other and plants to maintaining and improving soil health, and by extension, soil tilth and fertility.  Biological farmers have many tools to choose from for monitoring their soil microbe biome to evaluate the effectiveness of soil management practices.  One such tool is the light microscope – an instrument that can magnify an object hundreds of times to making even the small bacteria and fungi spores visible. 

This post describes how looking at components of the soil food web up close can inform next steps for soil management.

Microscopy 101

Microscope for soil biology

The use of a microscope to assess soil health is called “microscopy”, “direct microscopy”, or sometimes “direct counts”.  The lenses of a microscope create a magnified image of an illuminated sample.  For soil samples, this magnification is usually around 40-400 times, allowing us to see even single celled creatures.   

Microscopy can be used to measure the relative levels and diversity of microbes and animals from multiple trophic levels in soil: fungi, bacteria, and their ratio (F:B); protozoa like amoeba, flagellates, and ciliates; types of nematodes.

To make a measurement, microorganisms are extracted intact and alive from the soil.  A known amount of extraction solution is added to a specific amount of soil.  Then, drops of the extract are applied to a microscope slide, and the number of each organism in the field of view is counted: bacteria, fungi, protozoa, or nematodes.  Sometimes special dyes are used to distinguish active bacteria or fungi by coloring only the organisms that take up the dye. The analyst can also determine what type(s) of protozoa and nematodes are present based on unique physical characteristics.

The analyst uses the information about how much extract they applied to the slide, how much total extract they created, and how much soil they used to estimate how many of each organism is present in the original soil sample. Knowing the number and average size of bacteria and fungi present in a soil sample also allows the analyst to calculate the total mass of these organisms using conversion factors that relate size to mass.

Interpreting the Results

Presence of sufficient bacteria and fungi indicate the potential of the soil to immobilize nutrients to prevent leaching or volatilization from the soil.  The F:B measurement can be used to choose soil management practices that better tailor this ratio to the desired crop if necessary, since different crops have different optimal ratios

Testate Amoeba, a type of Protozoa

Levels of beneficial nematodes and protozoa, organisms that feed on bacteria and fungi, indicate the potential of your soil to release the nutrients collected in fungal and bacterial biomass and make them available to plants.  Evaluating the relative levels of different types of protozoa – flagellates, amoebae, ciliates – can give clues about whether soil aeration might be needed.  Looking at the types of nematodes present – bacterial feeding, fungal feeding, predatory, root feeding – allows the analyst to determine whether root feeders (the only type harmful to plants) are present.

Ciliate and Beneficial Nematode interacting

DIY Microscopy

Quantifying and identifying components of the soil microbe biome by direct microscopy requires expertise and training.  That said, for biological farmers interested in learning more about their soil there is “value [in] qualitative analysis as well…having a microscope on site to check your soil and observe what’s in there without counting the organisms,” says Katharine Hinson, President of Science at SymSoil.  It can be worth learning how to recognize some of the biological components in your soil to become familiar with them while also working with a lab to gather the quantitative data.  

Basic microscopes can be purchased for a modest investment.  There are also handheld scopes that can be used for initial observation.  There are many resources online for learning more.  Check out this video from Elaine Ingham for an introduction to microscopes. Microscopy is central to the teaching by the Soil Food Web Institute, founded by Dr. Ingham. For those who want to go deeper, the 4th Foundational Course in the Soil Food Web program is devoted to microscopy, which is essential to their approach to Soil Health.  There is also a 30 minute introduction video by Meredith Leigh, of Living Web Farms, that shows some of the organisms you’ll see under the scope.

Lab Testing from SymSoil

SymSoil team members routinely perform microscopy to gain insight into our own work product.  We offer testing and soil management recommendations based on the results as well.  Check out our Soil Lab Tests options including soil assessment and consultation packages.

This it the 1st in a series of articles on testing for soil health. Visit us here:

About SymSoil® Inc.

SymSoil is a leader in development of biological soil amendments for agriculture that restores the microbes that provide the right food to the plant roots, improving plant health, and making food more nutrient dense and flavorful, the way nature intended. SymSoil has products and services for growers using regenerative agriculture methodologies which improve profitability. Its flagship product, SymSoil® RC (Robust Compost) is a complex community of soil microbes, which includes in excess of 1,000 species, covering broad biodiversity of bacteria, fungi, amoebae, and other protozoa, beneficial nematodes and microarthropods. SymSoil was named one of 2019’s AgTech Companies to Watch. Accredited Investors can learn more about SymSoil as an impact investment here.

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