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Meet the Soil Food Web

Updated: Apr 5

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.

A graphic showing the different organisms that live in soil, and their connection to each other
The Soil Food Web (Source: USDA NRCS) click to enlarge


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.

I graphic showing the different shapes bacteria can have
Bacteria morphology (source: WikiCommons)

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:

microscope image of bacteria at 400 times magnification
Bacteria and soil parent material 400X

The main functions in soil of aerobic Bacteria 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:

A microscope image of an actinobacteria filament, which looks like a hair
Actinobacteria at 400X


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

Saprophytic 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

Mycorrhizal 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):

Fungal strand that is brown, thick and has cross walls. This is a beneficial fungi.
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.

A microscopic image of clear fungi that is irregularly shaped
Probably pathogen: wilt, blight or mildew (©


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.

microscope image of a flagellate
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.

Stalked ciliates filter feeding bacteria
Stalked ciliates filter feeding bacteria
Ciliates feeding on a surface
Ciliates feeding on a surface


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

Naked amoeba carrying a spore
Naked amoeba carrying a spore, 400X
Testate amoeba
Testate amoeba, 400X


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:

a graphic showing nematode mouth parts
Nematode types (Credit: Ed Zaborski, University of Illinois)
A bacterial feeding nematode
Bacterial feeder
Predatory Nematode
Predatory Nematode
Root feeder nematode
Root feeder nematode


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

For more information about the soil food web, and how to get your soil or compost tested, contact us.


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