Meet the Soil Food Web

posted in: Regenerative Ag, Video | 1

By Josh Weybright, Bright Way Agriculture, LLC

The Soil Food Web (Source: USDA NRCS)

The soil food web is the network of organisms living in soil ecosystems that include plants, bacteria, fungi and protozoa, plus a host of larger predatory species and shredders. In healthy soils these organisms work to break down organic matter, maintain friable (fluffy, crumbly texture) with spaces for water and air, and make nutrients available to plants. Healthy soil food web systems are naturally self adjusting, resistant to disease and pests, and do not require synthetic inputs from growers.

I. Bacteria

Bacteria come in many shapes and forms. Healthy soils are aerobic (oxygen rich) and support beneficial bacteria. These single celled organisms are too small (1µm in size) to be seen without a high-power microscope. While identifying them to a species level requires DNA analysis, we can group them by their morphology (defining characteristic, e.g. shape), and use this information to tell if a soil sample has become anaerobic (oxygen limited) or if disease organisms exist. For example, the spirilla (corkscrew), spirochetes (snake like) and the vibrio (comma shaped) bacteria indicate anaerobic conditions. The graphic below shows the main bacteria forms.

Bacteria morphology

Because they are uniform in size (typically 1 micrometer in diameter), you can use the bacteria to measure and evaluate other organisms such as fungi and actinobacteria. Under the microscope, at 400X total magnification bacteria look like this:

Bacteria and soil parent material 400X

The main functions of aerobic bacteria in soil are:

  • Make alkaline glues that hold soil parent material (sand, silts and clay) together into micro-aggregates, allowing for good soil structure.
  • Make enzymes to extract nutrients from decomposing organic matter or directly from the parent material.
  • Some enzymes bind (make inactive) or break down toxic chemicals.

Actinobacteria are a filamentous (strand forming) bacteria that are between 1µm and 1.5µm in diameter and up to 50µm long. When in focus, they look like hairs at 400X magnification:

Actinobacteria at 400X

II. Fungi

Fungi are best known for the large fruiting bodies (mushrooms) that grow above the soil, but most of their biomass is the form of hyphae (branching filaments). When analyzing soil and compost samples, we look to the morphological characteristics such as diameter, color and structure to determine the functional groups of fungi.

Saprophytic (decomposition) fungi excel at breaking down more complex (higher carbon) food sources, such as lignin (wood materials). These types of fungi release their stored nutrients when they are eaten by nematodes, arthropods and earthworms.

Mycorrhizal (root zone) fungi form an association with a plant’s roots, either as endomycorrhizal (growing inside the roots) or ectomycorrhizal (living outside the roots). Most crops depend on mycorrhizal fungi to deliver water and nutrients from beyond where the roots can reach.

Beneficial fungi will have a diameter of 2.5µm, have some color, and septa (cross walls):

Beneficial Fungi at 400X

Pathogenic Fungi is typically less than 2.5µm in diameter, is clear, and has few or no septa. Growth patterns are also an indicator of a detrimental type of fungi, such as a forming a weft (a tangled mat) or irregular thickness along the hyphae. This group consists of wilt, blight and mildew species. This type of fungi are harmful to plants and prefer anaerobic conditions. In a healthy soil food web with good soil structure, these organisms will be outcompeted by beneficial aerobic fungi.

Probably pathogen: wilt, blight or mildew (©

III. Protozoa

These single celled microbes eat bacteria and release excess soluble nutrients into the soil for plants to take up.

Flagellates have one or more flagella (whip-like appendage) that are used for locomotion and to help funnel food into their mouths. These protozoa can be differentiated from ciliates by their bumbling motion. Flagellates are typically aerobic organisms, their presence in your soil or compost is a good sign of a healthy soil food web.

Flagellate 400X (©

Ciliates have small hair like cilia that they use for locomotion and to filter feed bacteria. They are typically very fast, zooming around in search of food. They are typically seen as stalked ciliates (anchored by a long tether) or free roaming. These protozoa are generally anaerobic, so too many of these in your soil or compost is not a good sign.

Click to enlarge images

Amoeba in the soil generally come in one of two forms, testate amoeba that have a hard shell, and naked amoeba which ooze about unrestrained. Like other protozoa, they are predators that help release stored nutrients in bacteria.

Click to enlarge images

IV. Nematodes

Nematodes can be categorized by what they eat: bacteria, fungi, roots, predatory (other nematodes) and omnivores (eat whatever fits). While root feeding nematodes can be very detrimental to crops, nematodes in a healthy soil food web are highly beneficial predators. Nematodes can be identified by their mouth parts and digestive structures:

Nematode types

Click to enlarge images

V. Micro-arthropods

Micro-arthropods are larger, multicellular critters that either shred organic matter or are predatory species who consume smaller organisms.

Click to enlarge images

We hope you enjoyed meeting these members of the Soil Food Web! For more detail, watch this video:

Josh Weybright is a certified lab technician who helps gardeners and farmers grow more nutrient rich food, using less water and chemical inputs. He practices regenerative agricultural principles himself, using the Soil Food Web and Permaculture techniques. Learn more at

All images by Josh Weybright unless otherwise mentioned.

  1. Jan-Willem Jansens

    Super cool. Thank you!

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