Introduction to the Soil Food Web

What is the Soil Food Web?

The Soil Food Web is the very beginning of the food chain.

It’s a living, breathing “superorganism” filled with microscopic and macroscopic beings, all working to turn death’s remains back into life.

These same organisms are what populate worm bins and work in cooperation with worms to break down food scraps and other organic debris. You may not be able to see them, but there are multitudes of microorganisms feasting on all of that material, far outnumbering the worms in your bin.

This article will discuss the first few levels of the soil food web, the very beginning of the food chain. 

Soil Food Web Characters

The soil food web is made up of tiny, mostly one-celled individuals that decompose organic matter, create soil structure, and work to cycle nutrients within the soil.

In soil food web parlance, we call these individuals “characters.”

Just like the worms in our bins, all of these microorganisms rely on air and moisture to survive and continue the work of decomposition.

Food preservation is a good analogy.

Humans dehydrate certain foods to preserve them or keep leftovers in airtight containers. By removing the water or access to air, we are making it difficult for microorganisms to start the decomposition process.

First Trophic Level – Photosynthesizers

It all starts with sunlight, carbon dioxide, water, and plants. Through photosynthesis, plants convert sunlight into chemical energy which is stored as carbohydrates within the plant. Some of those carbohydrates are used by the plant for future growth and other activities, but many of them are sent out through the roots to attract soil microorganisms. 

Mycelium - critical components of the Soil Food Web
Root-zone mycelium

Carbohydrates, proteins, and sugars are released as exudates through the plant’s roots to lure and provide food for bacteria and fungi. These microbes feed off of the root exudates as well as dead tissue that the plants slough off as they grow further into the soil. They also consume other dead and decaying organic matter. Excess nutrients are stored within these tiny beings, and as they die or are eaten by predators, those nutrients are released into the rhizosphere (root zone) in a plant-available form. 

Plants have a mutualistic relationship with bacteria and fungi. The plants provide food for soil bacteria and fungi through the exudation process. In exchange, bacteria and fungi are then in place so that when they expire, they can provide nutrients the plant can readily take up. 

Second Trophic Level – Plant Decomposers


Bacteria are second trophic level decomposers in the soil food web
Bacteria are tiny microorganisms and can be categorized as decomposers, mutualists, pathogens, and lithotrophs

Bacteria are tiny, single-celled prokaryotes that are one of the most abundant organisms on planet Earth. In fact, if added together, their total biomass is only surpassed by plants. They are responsible for converting all kinds of nutrients from the air and soil into their more basic elements.

Soil bacteria can be divided into four groups: decomposers, mutualists, pathogens, and lithotroths. This article will focus on the decomposers and mutualists.


Decomposing bacteria consume plant litter with low carbon to nitrogen ratios as well as root exudates. These bacteria prefer green, chlorophyll containing foliage like grass, fresh leaves, shoots, and plants that break down more quickly. Some of these bacteria will even break down pesticides and other pollutants.

The importance of decomposing bacteria is that they retain nutrients in their cells that otherwise may leach into the water table, ending up in rivers, lakes, and oceans. These nutrients are mineralized by bacteria into a form that is readily taken up by the plant, thus cycling nutrients within the soil. When the correct biology is present in the soil, plants are able to manage their own nutritional needs.


Mutualists form direct relationships with plants.

Nitrogen-fixing bacteria are one of the most important mutualistic bacteria that aid in plant health. They make associations with certain plants, depending on the species, and convert atmospheric nitrogen into fixed nitrogen in the plant.

Nitrogen-fixing bacteria enter the root hairs of host plants where they form root nodules by growing and enlarging alongside root cells. Inside these nodules they transform free-living nitrogen into ammonia that is readily available to the plant. 

Inoculums of nitrogen-fixing bacteria can be purchased and used to coat the seeds of their associative plants.


Most all fungi are multi-celled and generally filamentous microorganisms. 

They grow in threads called hyphae. When hyphae overlap and grow in a mass, it is referred to as mycelium. Soil fungi can be separated into three groups: saprophytes, mycorrhizae, and pathogens. We will focus on saprophytic and mycorrhizal fungi in this article.


Saphrophytic fungi

Saprophytic fungi consume dead and decaying organic matter. 

They prefer material higher in carbon, lignon, and cellulose. Things like sticks, stalks, dead leaves, paper, and cardboard. You may have noticed the mycelium of a saprophyte in the forest. If you flip over some leaves or sticks, there are usually white threads of fungal mycelium that have come up through the soil to consume and break down the forest debris. 

Almost any edible mushroom found for purchase at a market will be a saprophyte. Growers take advantage of their nature of consuming carbonaceous substrate to cultivate a variety of edible mushrooms. Shiitake, lion’s mane, and oyster mushrooms are all saprophytic fungi that feed off of logs (shiitake) and straw (lion’s mane/oyster) among other things.

If it weren’t for saprophytes especially, there would be woody debris littering large tracts of the environment. They turn trees, branches, stalks, sticks, and all kinds of wood matter into rich, earthy soil.


Mycorrhiza create underground networks between roots in the soil food web
Mycorrhizal fungi form associations between plant roots

Mycorrhizae have become more well-known in the past few years, especially with the release of the 2019 documentary “Fantastic Fungi”.

These fungi develop relationships with about 95% of terrestrial plants, colonizing the root zone and extending far out into the soil. Plants exchange carbon and in return gain nutrients and minerals from their fungal friends. 

Mycorrhizae are able to reach much farther into the soil and grow into tiny pores in stone, places that plant roots cannot access. This means the host plants can get more water, nutrients, and minerals. Mycorrhizal colonization on a plant also means added protection from pathogens and diseases, resulting in healthier foliage and fruit aboveground.

Mycorrhizae connect plants with each other through a network of fungal hyphae.

As you walk through a forest, you are walking amongst a group of connected species, sharing resources and sending signals to each other. This underground mycorrhizal network is much like the world wide web. Older trees will send extra nutrients to younger saplings to help them to survive. Sometimes resources will be cut off to a tree’s diseased sections.

There are two main types of mycorrhizal fungi: ectomycorrhizal and endomycorrhizal


Ectomycorrhizal spores colonizing a root blade
Ectomycorrhizal spores colonizing a root blade

Ectomycorrhizal fungi grow around the outer cortical cells of plant roots and around the surfaces of roots, but do not penetrate the root cell.

Ectomycorrhizae are mainly associated with trees. Ectomycorrhizal fungi often appear as a covering of visible, interwoven fungal hyphae on the surfaces of roots.

Ectomycorrhizal fungi form fruiting bodies, or mushrooms, in order to make spores and complete reproduction. Morels are a popular edible mushroom that is the benefit of mycorrhizal associations.


Endomycorrhizal fungi form associations with a much larger array of plants. Grasses, vegetables, trees, vines, and shrubs all benefit from endomycorrhizae. These fungi actually penetrate the cells of plant roots, but do not form thick masses on the exterior of the roots. They reproduce by forming spores within the soil rather than forming a fruiting body above ground.

There are multiple types of endomycorrhizal fungi but the most common group is the arbuscular mycorrhizae fungi (AMF). Arbuscular mycorrhizae get their name due to the fact that their structures resemble tree shapes inside the plant’s roots. AMF associate with the greatest number of species in the plant kingdom.

Science has identified 200 species of AMF, with many undiscovered species, that form associations with more than 300,000 plant species.

There are other, less prevalant types of endomycorrhizae that are more specialized to certain types of plants like blueberries, cranberries, rhododendrons, azaleas, and orchids.

Wanna Learn More about Mycorrhizae?

Watch a livestream where Troy expounds upon the identification and importance of mycorrhizae in our soil!

Third Trophic Level – Shredders, Predators, and Grazers


soil protozoa with vivid blue and orange colors

Single-celled protozoa feed primarily on bacteria and help to release excess nutrients, especially nitrogen, for use by plants and other soil organisms. Depending on shape and means of movement, protozoa fall into one of 3 categories. The smallest being flagellates, next are amoebae, and the largest are ciliates. All three work to mineralize nutrients into a plant-available form through their consumption of bacteria.

Protozoa are the main organisms that most earthworms prey upon to gain nutrition.



Flagellates bring samples to life under the microscope. They swim and move around, searching for a buffet of bacteria amongst organic matter, sand, silt, and clay.

One or more whip-like tails, called a flagellum, propels them through films of water in the soil. Their movements are of a bumbling motion, resembling a bee slowly moving about in search of nectar or pollen.


Amoebae are generally larger than flagellates and fall into two groups: testate amoebae and naked amoebae. They transport themselves by means of a pseudopod which is a temporary projection from the body. Their pseudopod reaches out, grabs hold of a surface, and pulls the rest of their body along.

Testate amoebae have a test, or shell-like enclosure, connected to their main body that they may pull themselves into for protection. They often appear as olive or balloon-shaped beings under the microscope (see photo above).

Naked amoebae are formless, like The Blob in the 1950’s movie. It can be difficult to identify them on a microscope slide since there is no apparent shape to look for. Both naked and testate amoebae move slowly through their environment, searching for bacteria to ingest. 

One group of amoebae, called vampyrellids, use enzymes to bore holes in fungal hyphae and consume the contents of the fungal cell. We haven’t yet learned if they die when stabbed with a stake or are repelled by garlic and crosses! 😉


Ciliates are the largest of the three groups of protozoa. They consume bacteria as well as flagellates and amoebae. Ciliates move about with the motion of their cilia, or hair-like protrusions on the perimeter of their body. Their movements tend to be quick and fast, zooming from here to there, although they may stop to browse on some bacteria attached to an aggragate.  

Ciliates are an indication of low-oxygen or anaerobic conditions.


Nematodes are non-segmented worms and are the most abundant animal on planet Earth. They wriggle and twist, looking like a fast-moving worm or snake. Select species may even be visible with the naked eye. Nematodes are mainly identified by their mouth parts.

Many people have heard of nematodes in a negative manner due to root-knot nematodes. These root-feeding nematodes parasitize certain cash crops, and an outbreak can mean losing a large amount of the harvest. There are actually many types of nematodes in the world. The soil dwellers that we will focus on are bacterial-feeders, predatory nematodes, fungal-feeders, and root-feeders. All of these depend on soil with adequate moisture levels to survive.

Bacterial-Feeding Nematodes

Bacterial-feeding nematodes squirm through micro-films of water in the soil, looking for bacteria to feed on. In my analysis of soils sent in from clients, the most nematodes I see are bacterial-feeders. These nematodes are normally smaller in size than their counterparts. Bacterial-feeders have simple mouth interiors, but sometimes have ornate lips.

Duck-faced social media influencers have nothing on bacterial-feeding nematodes.

Predatory Nematodes

Predatory nematode eating another nematode
Predatory nematode consuming another nematode

Predatory nematodes feed on all other nematodes within the soil.

Certain species of predatory nematodes even show a preference for root-feeding nematodes. They keep the populations of bacterial, fungal, and root-feeders in check.

So they naturally thrive in soils with high numbers of nematodes, which are normally undisturbed grasslands and forests. When viewed under a microscope, predatory nematodes have a wide, open mouth with a large tooth, or multiple small teeth, near the opening.

Predatory nematodes are larger than other nematodes within the soil.

Fungal-Feeding Nematodes

Fungal-feeding nematodes are distinguishable by the spear-like stylet that comes to a point at the open end of their mouth. This stylet stabs out into fungal cells to pierce the walls and slurp up the contents.

They literally drink the milkshake of fungi.


Fungal-feeders are more prolific in forest soils than in grasslands and crop soils, as there is more fungal food for them in a forest system.

Root-Feeders & Parasitic Nematodes

Root-feeding nematodes also have an observable stylet, like the fungal feeders, except they also have two knobs at the bottom of the stylet, opposite of the mouth end.

These knobs are large muscle attachments that help to generate enough force to push the stylet through thick plant cell walls in order to gain nutrients.

Higher Trophic Levels – The Big Fellas


Moving up in trophic levels, arthropods are one of the most observed macroorganisms in the soil food web. 

Microarthropods like mites are excellent decomposers

Arthropods are all invertebrates that are covered with an exoskeleton. They range in size from microscopic to several inches in length. Arthropods include insects (springtails and beetles), arachnids (mites and spiders), crustaceans (isopods), myriapods (millipedes and centipedes), and scorpions.

Most soil arthropods are shredders. Others are grouped as predators, fungal-feeders, or herbivores. These shredders eat through organic matter to consume bacteria and fungi on the surface, decreasing particle size and increasing the surface area.

This quickens decomposition and creates humus at a faster pace.

Some herbivores can turn into pests as their populations increase and cause crop damage by feeding on roots or foliage of plants.


hands holding soil

After arthropods, worms are the next most prolific character in the soil food web.

Earthworms outnumber all soil invertebrates in both number and biomass, including the arthropods mentioned in the previous section.

There are more than 7000 species which range in length from an inch to as long as nine feet(!).

(We’re worm peeps, but dang, that’s the stuff of nightmares.)

Earthworms are decomposers, chewing through soil and organic matter to gain nutrients from bacteria, fungi, and protozoa. As they eat, they break things down into smaller particle sizes, increasing the surface area, and making it more accessible to smaller organisms. 

Their castings are inoculated with beneficial bacteria and growth hormones. 

Types of Earthworms: Anecic, Endogeic, and Epigeic

Burrowing and feeding habits determine an earthworm’s category.

Anecic worms like nightcrawlers move and burrow vertically within the soil. They feed on organic matter from the surface that they pull into their burrows. Most endogeic worms live in the upper layers of the soil and burrow horizontally. They dwell in impermanent tunnels that fill up with castings as they eat and travel along.

Epigeic worms live in the litter layer and near the soil surface. Composting worms, like red wigglers, are epigeic. They live in the thin layer of organic matter and are especially good at breaking down organic matter, making them ideal composters.

Wanna Learn More about Vermicomposting?

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Check out the Ultimate Guide to Vermicomposting and read the web’s most comprehensive guide to recycling organic matter with earthworms!

Decomposition, Cycling, Building, Filtering: Soil Food Web Functions

Every organism has its function in the soil.

Through their activities, microorganisms decompose organic matter, cycle nutrients, filter water and toxins,  as well as form soil structure and aggregation. Macroscopic organisms also help to make tunnels in the soil, adding porosity for increased aeration and water-holding capabilities. 


Large heap of rotten fruits and vegetables at compost sorting and recycling station. Separate organic waste collection and compost
Large heap of rotten fruits and vegetables at compost sorting and recycling station. Separate organic waste collection and compost

Decomposition of the world’s organic matter is a big feat. 

If all of the food scraps, landscape debris, dead vegetation and other organic waste never broke down, our world would start to look like that of Sarah Cynthia Sylvia Stout’s from Shel Silverstein’s “Where The Sidewalk Ends”, with waste piling up all around.

Soil microorganisms are like the digestive system of nature.

They turn foods (organic waste) into consuamble nutrients, much like the bacteria and fungi in the human digestive system help us to access and absorb nutrients.

Nutrient Cycling

Plants manage nutrient needs through their symbiotic interactions with microbes.

Once a healthy soil food web is established and growers focus on feeding the soil rather than feeding the plants, you’ll rarely need additional nutrient inputs. Getting the proper biology in place and keeping it there by always having living roots in the ground means reduced labor and input costs.

A healthy soil food web also leads to disease resistance, hardening the defenses of the soil and then the plant against pathogens.

Beneficial microorganisms outcompete pathogens and other disease-causing organisms, preventing them from getting a foothold.

Soil Building

Bacteria and fungi do not have mouths like you and I.

They secrete enzymes that allow them to break down organic matter and absorb nutrients.

These enzymes are sticky and glue-like. They work to hold tiny soil particles together, creating aggregates.

As various arthropods and worms move through the soil, they leave tiny channels and tunnels everywhere they go. This permeability allows for greater water holding capacity, allowing the soil to act as a sponge, soaking up rain and holding it in for future use.

It also means greater airflow in the soil which benefits both soil life and plants.

Nature’s Filters

Microbes also work to break down pollutants that remain in the soil.

Bacteria and fungi work away at things like chemical pesticides and other toxins. Based on the species, fungi have the ability to break down select heavy metals. Microorganisms also filter water as it flows down through the layers of earth, creating clean water that life relies on.

Conventional Ag’s Negative Impacts On the Soil Food Web

The conventional approach to gardening and farming does not take the health of the soil microbiome into consideration.

Tilling, chemicals, and compaction all have a negative effect on microorganisms in the soil. As a result, this has an impact on the rest of the soil food web organisms up the line, as there are considerably less foods for them.


Tillage destroys fungal hyphae leading to a more bacterial soil subject to increased weeds.

Fungi grow in long threads (hyphae) amongst the soil.

Tilling or plowing breaks those threads, disrupting the fungal network.

Tilling leaves a bacterial soil, setting the stage for more weed growth. By tilling to remove weeds, growers set themselves up to make the situation worse by creating bacterial dominant soils.

Bacterial-dominant soils lead to pulses of nitrate which promote pioneer weeds and early successional species.


Agriculture tractor spraying fertilizer on green tea fields, Technology smart farm concept

Chemical fertilizers are high in salts which harm beneficial soil biology.

Using chemicals to provide plants with the nutrients they require sets them up to become chemically dependent. They take up nitrogen and other nutrients with ease, no longer needing biology to cycle nutrients.

Chemical herbicides can have similar effects as tilling on soil biology harming the life in the soil, especially the predators and fungi. 


Compaction is usually caused by large equipment (tractors), over-grazing of herd animals, and heavy foot traffic.

Compaction results in hard pans within the soil.

These hard pans can act like concrete, collecting water, and creating anaerobic conditions.

Plant roots grow happily to a certain depth and then run into this anaerobic zone which can be creating plant-killing alcohols and phenols.

How Does Vermicompost Help the Soil Food Web?

composting worms in vermicompost

This is where vermicompost, compost, and liquid compost amendments come into play.

They help to get the life that was just described back into the soil where it may have been disrupted due to conventional practices. The black gold you dig out of your worm bin is loaded with all kinds of organisms that are itching to find a home near a plant in your garden to help it live a long and fruitful life. 

Bacteria and fungi ready to feed off of a plant’s root exudates.

Protozoa and nematodes eager to eat those bacteria and fungi, cycling excess nutrients.

Arthropods and earthworms munching away and breaking down organic matter.

Nature’s recyclers, each and every one.

Do Your Part To Help The Earth

Reducing your waste stream by composting food scraps, paper, and other organic debris helps to lower your carbon footprint.

Not only that, adding vermicompost to your garden soils helps to sequester more carbon in the soil by incorporating this carbon-based material.

Increasing soil fungi through the addition of vermicompost also helps by continuously sequestering carbon underground as fungi grow and multiply.

You can do it!

And we can help.

Reach out to us if you have any questions or concerns regarding vermicomposting. And if you are not currently vermicomposting, we’d love to get you started!

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If you want to know if your soil is appropriate for your crop, or if you need help our help with anything else, engage our services today!

One thought on “Introduction to the Soil Food Web

  1. What an extremely good article, and written so a non-scientific reader can easily understand it. As a fairly recently retired peasant scale farmer for over 60 years and a continuing vermicomposter I refer to the UWC site from time to time, but I have missed this article previously.

    Whilst it did not directly deal with my search for info and others’ experiences of feeding straw based spent mushroom compost to my wormeries (I need far more vermicompost than I can possibly produce so do not want to put it direct into raised beds I am making) I found it most interesting.

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