The Soil Food Web: How to Build Healthy Soil

By Monica Mansfield
Published: December 8, 2017 | Last updated: June 14, 2022 05:42:40
Key Takeaways

Mother Nature doesn’t have to think twice when she creates perfect soil, but we do. It is a lengthy, intricate process but once accomplished creates healthy, vibrant plants. Here are some pointers on developing the soil food web in your garden.

There is soil and then there is dirt. They look alike to the untrained eye, however, there is a huge difference between the two. Dirt is made of silt, sand, and clay. It contains the minerals that we want our plants to eat, but dirt alone will not feed a plant or help it grow.


Soil will. Soil is dirt that is teeming with life. Bacteria, fungi, nematodes, protozoa, arthropods, and earthworms are the tiny critters that convert those minerals into forms that plants can use.

The Soil Food Web

The soil food web is an ingenious nutrient cycling system designed by nature. Everything is connected in the soil food web. Nothing goes to waste and everything has multiple functions. Look at the forest. No one fertilizes or waters there, yet it is lush and green. This is the soil food web at work.


This intelligent system works perfectly when it is supported by the soil’s environment, starting with the root system. All of the action happens in the rhizosphere. This is why nature does not like bare soil. No roots, no soil life. The root exudates are made up of sugars, carbohydrates, and protein, much like a sweet dessert in the microbial world. Bacteria and fungi can’t get enough of them.

Then the nematodes, protozoa, and arthropods come along and eat up the bacteria and fungi, turning them into waste that is chelated and readily available for plants.

Even better, this waste contains all the essential macro and micronutrients that the plant needs, instead of the select few they might receive from a bottle. These microorganisms act as storage units for nutrients. Without them, these valuable vitamins and minerals would wash out of the soil into our groundwater.


The bacteria and fungi also create the soil structure and tilth you find in healthy soil. The bacteria create a kind of glue that holds all the silt, sand, clay, rocks, and pebbles together. The fungi grow filaments that bind these soil aggregates together. This creates a structure that holds space for oxygen, water, and root systems.

Earthworms, protozoa, nematodes, arthropods, and even mammals can now tunnel through the soil and create more of these pockets because the soil is not compacted.


Aerobic, oxygenated soil is essential for a healthy soil environment. In fact, once the soil starts to compact and go anaerobic, you will start to see pathogenic bacteria and fungi move in and create problems. However, these pathogens simply cannot survive in well oxygenated soil.

In modern agriculture, we till the soil to break up the compaction, bring in oxygen, and release nutrients. Unfortunately, when we do this, we are also harming members of the food web and breaking up the soil structure that the biology has worked so hard to build.

The ratios of microorganisms in the soil also play a role in its pH. The biology creates the chemistry. Too many bacteria will create an alkaline environment, but mycorrhizal fungi will release acids and balance the soil, keeping it in a range between 5.5 and 7.0.

Healthy, balanced soil needs both mycorrhizal fungi and beneficial strains of bacteria like Actinomycetes to thrive. Additionally, different plants need different ratios of fungi to bacteria. For example, grasslands do well with bacteria-dominant soil, whereas old growth forests need fungi-dominant soil.

In current agricultural practices, we tend to create unhealthy soil environments where pathogens flourish, then try to clean up the mess, which ultimately makes the situation worse.

In fact, the very products we go to for help contain salts that harm the soil biology. We use these products because our soil is already unhealthy and we are dependent on them to do the jobs that the soil life would normally do.

When the soil environment is aerobic and full of life, pathogens cannot survive. When the soil biology grows, so do your plants. You will not get pests and disease because they cannot survive in your soil, and your plants will be too healthy for them to eat anyway.

Believe it or not, garden pests and diseases have a very important job. They are nature’s cleanup crew. They get unhealthy plants out of the way so the healthy plants can grow. They don’t attack healthy plants.

How to Build Healthy Soil

If our goal is to build rich, healthy soil full of beneficial microorganisms, there are certain practices we should and should not do. Let’s start with the should-nots. Keep in mind that not doing these things doesn’t create healthy soil, but it will stop us from destroying our soil further.

We should not till our soil. Although it may initially unleash a burst of nutrients from all of the microorganisms dying, you are killing the very microorganisms that create the nutrient cycling system.

Over time, tilling will deplete your soil instead of building it. Historically, this is why we have rotated fields to plant, or have even had to move farms once the soil, or more accurately the soil biology, dies. If you manage your soil properly, the biology in your soil will do the tilling for you. There is no need for you to break your back tilling in amendments every spring.

Consider using organic fertilizers, pesticides, and herbicides. Some chemicals can be full of salts which kill the biology in the soil. If your soil doesn’t have the microorganisms storing the nutrients in their bodies, about 80 per cent of the fertilizers will wash through the soil to the ground water anyway.

This being said, you may need to use additional fertilizers or pest control methods for a few years while you build up your soil. Fish emulsion and bone meal will add to the soil instead of depleting it. Pure, cold-pressed neem oil is a completely natural pesticide and fungicide that is very effective without harming beneficial insects or soil life.

Also, overwatering and excessive soil compaction will both lead to an anaerobic environment in your soil which is ideal for pathogens, so best to avoid those.

Now, for the things we should do. These are the practices that create a healthy soil food web.

Compost Tea

We should use compost tea. It is one of the fastest, most effective ways to add life to your soil. Compost tea is full of beneficial bacteria and mycorrhizal fungi that will attach to your plants’ root systems and start eating their exudates. Once your microbial colony grows, it is sure to attract nematodes, protozoa, arthropods, and earthworms.

Organic Matter

We should also add organic matter to our soil as much as possible. Add layers of compost and mulch. When you prune, drop the leaves on top of the soil. Leave weeds on top of the soil, as long as they don’t have seeds. Organic matter is food for microorganisms, and when they are done digesting it, you are left with nutrient-rich humus.


Mulch has additional benefits. It will prevent soil from compacting, hold moisture to be released in times of drought, and prevent erosion. Ideal mulches include shredded leaves, straw (not hay unless you want the seeds that come with it), and even wood chips. If you use wood chips, be sure not to till them into the soil or else they can tie up nitrogen as they decompose.


We should plant an understory in our garden. The understory should be made up of short, perennial plants with large root systems, such as creeping thyme or sedum.

This way they never overpower the other plants in your garden, yet their root systems will encourage soil biology and prevent the soil from compacting. If you plant a variety of seeds for this purpose, one will always pop up, regardless of differences in weather from year to year.

When you want to sow seeds or plant a start, just remove the understory plants in that area and dig a hole. The soil in that spot is already bursting with life and has plenty of oxygen, so your seedling will quickly grow taller than the understory.

We have been taught that these plants would steal nutrients from our crops, but when you are building your soil food web, these plants and their root systems are actually providing the biology that will feed your plants without the use of fertilizers.

Be Patient

It will take a few years to build your soil, even if you follow these practices to the letter. All good things take time, and building soil biology is no exception. It may take three to 10 years to create a thriving ecosystem in your garden, but you will start seeing progress even in the first year.

Your job now as a gardener is to manage your soil. Check on it. Make sure the conditions are right for the soil biology you want to attract, and then let the soil food web do your work for you.


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Written by Monica Mansfield | Homesteader, Owner & Writer of The Nature Life Project

Profile Picture of Monica Mansfield

Monica Mansfield is passionate about gardening, sustainable living, and holistic health. After owning an indoor garden store for 5 1/2 years, Monica sold the business and started a 6.5-acre homestead with her husband, Owen. She writes about gardening and health, as well as her homestead adventures on her blog at

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