Soil Life

Soil Life: Microbiology on the farm

Getting to know the members of your soil community.

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.