Soil Life: Microbiology on the farm

By Mary Edmonds and Natalia Pinzón
Rodale Institute Seasonal Research Technicians

The diverse ecosystems that are found in soil determine the productivity of our land. Without the billions of bacteria, millions of fungi and protozoa, and the thousands of other critters living under our feet, we would be hungry indeed. This micro-community, or soil food web, transfers nutrients through the soil, makes other nutrients into forms plants can use, and helps protect crops from soil-born pathogens.

The very structure and health of your land is directly influenced by this complex set of biological and chemical interactions which decompose, retain, and recycle nutrients within the soil. And all of the food web organisms have their roles and functions.

Who is part of the ideal soil community?

Different groups of critters do different things in the soil. For example, bacteria and fungi take nutrients from the soil which are “non-available” (meaning plants can’t use them) and retain the nutrients as they grow. Their waste products (from the decomposition of plant material or residues) also retain those nutrients in non-leachable forms. The bacteria and fungi are then consumed by predators, releasing soluble, or plant-available, nutrients, making them usable for your crops.

Bacteria also build microaggregates, the smallest units of soil structure. If we think of the soil as a city being built, microaggregates act as the bricks. Fungi are the mortar that binds the individual bricks together, forming walls, ceilings and floors. The larger organisms like protozoa, nematodes and microarthropods construct the buildings. They re-arrange the bricks to build the condominiums in the city that we call soil structure. All these organisms congregate around plant roots acting as a castle wall, and protecting the roots from disease organisms and/or pests.

When analyzing your soil, there are a few specific beneficial microorganisms you’re looking for:

Bacteria are vital for recycling nutrients. Bacteria can be recognized by their shape and motion. Bacteria are mostly round or rod shape. Some filamentous bacteria are required for the growth of some plants while they are quite detrimental to the growth of other plants.

Fungi. A fungal hyphae can be distinguished by its strand-like appearance with straight cross walls. A hyphae should be uniform in diameter, and not less than 2 micrometers thick. The best hyphae in our soil are those that are wide in diameter and dark in color. (Generally, when speaking of soil health, dark is always good.) These wonderful networks of the soil food web help to hold and transfer nutrients directly to plants through symbiotic relationships. They also promote healthy soil aggregation.


Fungi-Bacteria (F:B) Ratio. What we are specifically looking for in good soil is not merely the presence of different species of beneficial fungi and bacteria, but the ratio of the overall biomass of the two organism groups. This is crucial because different plant communities require different F:B ratios. For example, weeds require a soil with lots of bacteria whereas forests require much more fungi.

Predators. There are far fewer predators in the soil than there are bacteria and fungi. The predators prey upon the bacteria and fungi, and their predator-prey interactions are crucial to the processes of decomposition and the cycling of nutrients.

Protozoa. We recognize these organisms primarily by their motion. They are defined more particularly as flagellates, ciliates, and amoebas. Soil protozoa feed on bacteria. This keeps the bacteria communities healthy and growing by preventing overpopulation and overuse of nutrients which would be detrimental to everyone in the soil community. As they digest bacteria, protozoa release excess nitrogen from the bacteria in plant available forms around roots.

Nematodes (shown above) hold and recycle the nutrients present in the organisms that they feed upon. These fellows are shaped like tiny worms with pointed ends. They are fun to watch wiggling around in the soil aggregates, and hard to keep up with in the scope. A trained observer can identify both beneficial and detrimental nematodes, which are distinguishable by their mouth parts.


Microarthropods. Micro- meaning “very small” and -arthropod meaning “having jointed legs.” Simply put, these are very tiny insects. They are at the top of the soil food web that is visible through the microscope. These creatures are food for larger predators that we are more familiar with like earthworms and bigger bugs. Predator-prey relationships between microarthropods and other soil fauna are necessary to foster a complete food chain within, and beyond, the soil.


Since different agricultural practices affect these complex communities in different ways, the microbiology of your soil can give you a peek into how your farming practices are affecting your long-term productivity, for better or for worse. For example, when we find bacteria that thrive in low oxygen conditions, we know that soil is becoming anaerobic. To remedy this problem, we can immediately aerate the soil. Being able to identify each of these organisms and certain indicator species can help you make informed, real-time decisions about your soils.

At the Institute

Some of the questions we’re trying to answer with our research here at the Rodale Institute are: How detrimental are tillage and soil disturbances to fungal networks? Do cover crops enhance the diversity of microbial communities by keeping soil productive year round? How does soil compaction by tractors affect these communities? We are also interested in the potential for healthy microbial communities to control weed-crop competition dynamics.

In the end, our main goal is to create the ideal conditions in which these beneficial organisms can thrive. Our team of researchers has begun working more in depth with our composting process to create the conditions for the ideal microbial community.

Compost is an incredibly important and dynamic source of nutrient inputs and micro-biodiversity. We are analyzing how different starting materials affect both the relative sizes of the microbiological communities and the amount of time it takes to make healthy compost. We have also begun looking at pre-made compost products and what sort of microbiology they could potentially contribute through application.

Though controlled inputs and monitoring techniques, we want to reliably produce and reproduce compost with the correct ratios of fungal to bacterial biomass that will support healthy crop communities. And we are beginning to use microbial research in conjunction with our other ongoing research projects to enhance our understanding of all of the systems and how microbiology affects each experiment.

Do-it-yourself guidance

Nature has spent billions of years evolving and refining the essential set of functions we call sustainable farming. By encouraging the diversity and balance of appropriate soil ecosystems, farmers are able to enhance the productivity of their land, reduce or eliminate the need for pesticides and herbicides, improve water retention, reduce erosion, and create healthy soils that provide for future generations.

Applying techniques that bring about specific microbial communities requires education and understanding about the function of our soil life. This way we can work with the natural processes of our soil ecosystem– selecting those microbial communities that most fit our agricultural needs

If you are interested in analyzing the micro-community in your soils, as farmers around the country have begun to do, a compound light microscope is a good place to start. A quality microscope can be purchased for approximately $300-500. Analyzing your own soil biology can be as simple as taking a daily or weekly sample and checking it under the microscope in order to immediately make decisions based on the living contents of your soils.

7 Responses to “Soil Life: Microbiology on the farm”

  1. Mike Eason

    I am most interested in learning how to analyze my soil.

    What is the fee for this until I can get up and going

    also what specific kind of Microscope do I need for this?

  2. David Karp

    You mentioned that one can tell a beneficial nematode from a detrimental one by the mouth parts. How so?

    I love your site. We plan on using it in our AP Bio class.

  3. Carl Spence

    I purchased a microscope, understand how to use it, make slides etc.
    looking for reference pictures in order to be able to identify the various organisms.
    Also salts or minerals

  4. Adrian Lawrie

    Is there reviewed research or similar reports regarding work completed and published on varying Ratio’s of Fungi : Bacteria that might influence different crops and weeds ?

    Great work Rodale ! – you are helping the world make choices with confidence of expected outcomes on how they might approach food production. When we have secure knowledge about soil life, and how we can enhance their function, we are empowered with choice. Some of us will choose not to genetically or otherwise modify our food production. Having choice in food production is all we need.

  5. Rose Thom

    I am trying to figure out if soil containing more predators than prey in terms of organisms found using a belese funnel and a pitfall trap can be classified as a poor man’s rainforest??


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