Soil Food Web – What’s All The Fuss About?

The soil food web refers to an army of tireless workers in the soil – 20,000 to 30,000 different species of soil organisms in a teaspoon of healthy soil.

We call it a web to focus on not only the soil life, but more importantly on how they relate to each other, how they interact. There are 6 kingdoms of life: bacteria, archaea, fungi, protists, animals and plants. My focus tends to be as much on what they do as on what they look like.

You may wonder why it’s so important to learn about all of this soil biology when you’re learning about organic gardening. It turns out they’re as important to the garden as the soil, fertilizer, water and everything else.

Soil Food Web Diagram

Soil Food Web Drawing

I hope this soil food web drawing helps explain in more detail what the food web is all about.

Why Is The Soil Food Web So Important?

Basically, these soil organisms the soil and maintain it. They build themselves villages, and they delegate tasks based on their individual strengths.

Many are extremely small soil microbes, but despite their size they rule the world and they rule our organic gardens. They transform the minerals and organic matter in the soil into something that can support an abundance of life.

Many nutrients won’t be taken up by plants until soil microorganisms have converted them to the right form. Some of them pull nitrogen out of the air and change it into a form that they, and plants, can use. Some bring nutrients directly to plants in exchange for food from those same plants.

Without a vast array of soil biology players, we wouldn’t have soil. They also work to protect plants from plant-feeding predators, both in the soil and above ground. Some of them eat dead things and some of them eat living things and eventually they die themselves.

All of this contributes to the organic matter and mineral content of our world. Yes, a few of these soil food web organisms also eat plants, but the vast majority are friends of plants just like the vast majority of bacteria in our body are friends of ours.

What Hurts Them?

If we use toxic chemical fertilizers or pesticides, or withhold water from the landscape (such as by using drip irrigation), or do a lot of deep rototilling or other soil disturbance, many of these soil food web organisms probably won’t be around for very long.

Even if we do something seemingly benign, like use any of the horticultural soap products, we destroy many of them. We really, really want them to be around. Without them, our organic garden becomes a desert.

What Helps Them?

Ultimately, that’s what this website is all about. Rather than thinking about taking care of our plants, it might be more appropriate to think about taking care of our soil biology, including our bacteria, fungi and protists – our soil microbes.

Getting familiar with the soil food web is the first step towards creating a healthy garden. Some of our most important organic gardening tasks involve making sure we have enough soil microbes.

Most of our other tasks involve making sure they have what they need, and those tasks are what I cover often on this site.

The Microorganisms

When people talk about soil food webs, they’re referring to the (mostly tiny) inhabitants of the soil, and more specifically, the complex relationships between them (hence the word “web”).

Here, I’m writing about the tiny soil organisms – the microorganisms. It turns out they have some very important jobs. They basically make the soil and maintain it. They transform the minerals and organic matter in the soil into something that can support an abundance of life. They rearrange soil particles to create good soil structure.

What Do They Need?

Some microbes breathe air, just like us. They’re called aerobic microbes. Other microbes die in the presence of gaseous oxygen, so they live in places where there is none, such as deeper in the soil. They’re called anaerobic microbes, or anaerobes. Others switch between oxygen and other methods.

Microbes need water, some more than others. Some microbes need light. In fact, some of them photosynthesize like plants. They all function best in their own specific temperature range. So, just like our plants, they need air, water, certain temperatures and sometimes even light. Let’s look at the 3 groups, or “kingdoms”:


Bacteria are the tiniest members of the soil food web. They are single-celled organisms – they each have just one cell. There are hundreds of millions of them in a gram of healthy compost, even a billion. Bacteria occupy the majority of the leaf and root surfaces of a plant. They break down simple substances and toxins and aggregate the basic building blocks of the soil.


Fungi are another vital life form in the soil food web. They may be single-celled (such as the yeast that makes your bread, yogurt, wine and beer), or they may have billions of cells (like in a mushroom). A mushroom is the fruit of certain types of fungi, but the majority of those fungi’s biomass is actually underground, winding through the soil kind of like a microscopic root.
They eat complex organic materials that most other living things can’t easily digest (such as lignin), and they harvest minerals from rocks that are virtually inaccessible to other organisms until released by the fungi (such as phosphorus). Like bacteria, fungi get food in the form of carbohydrates from the plants in exchange for their services.


Protists are the outcasts in the soil food web, whose main distinguishing feature seems to be what they aren’t – they’re neither bacteria nor fungi nor animals nor plants. A protozoan can eat 10,000 bacteria in a day. During this process, nitrogen is converted to ammonium, upon which many of your plants will happily dine.
We say that bacteria and fungi immobilize nutrients by storing them in their bodies, and then protists (along with other microbes, plants and animals) mineralize these nutrients – meaning they make them available again.

Plants And Animals

Of course, many plants and animals are part of this food web, too. Here, I just want to make sure we’re all on the same page with the knowledge that it’s very important to take care of our soil food webs.
Here are a few more articles about the soil food web.

How To Make Effective Microorganisms – Step By Step

How To Make Effective Microorganisms (EM)Last night, when deciding what to write about for today, I looked around my apartment, saw my probiotic fermenting away on the shelf, immediately took this photo, and proceeded to write this step by step process for making effective microorganisms.

In gardening, there’s a lot of talk about chemistry – the fertilizer, NPK, carbon, etc.

All important stuff, but I like to spend just as much time on the biology – the microorganisms, insects, animals (and of course plants).

It’s especially the microorganisms that really rule our world, our bodies (we contain 10 times as many microbes as we do human cells), and our gardens.

Today I’m pumped to get right into teaching you about these good microbes and how to make effective microorganisms.

These efficient microbes improve the soil, increase plant health and yield, help keep pests away, and are some of the most important beneficial bacteria and yeasts that make up our world. Read More

Soil Inoculant For Plant Nutrition (And Fewer Pests)

Using a soil inoculant may seem kind of unnatural, so let’s start with why it might be a good idea.

The most important life forms in your garden are too small to see.

Microbes cover every soil surface and even inhabit the insides of all larger organisms.

They have a dramatic effect on plant health and nutrition, as well as our own.

In most gardens, the microbiome has been thrown out of balance by things like tilling, chemical fertilizers and pesticides.

And also the generally toxic environment we live in with pollution, antibiotics and other pharmaceuticals in our air and fresh water. Read More

Amazon Jungle Lesson 3 Of 3 – The Soil Food Web

Click for video transcription

Phil: In the first two videos, I talked about how to balance our soil fertility, so that we can grow the kind of plants that we want to grow and then also how to learn from nature to bring organic matter in to our gardens. The third video is about the soil food web and that’s really about the organisms living in the soil, whereas organic matter was more about that when they’re dead, when plants and animals and organisms are dead.

This is more about when they’re living. So it’s bacteria and fungi and earth worms and insects and animals and even the plants are part of the soil food web too. If you had x-ray, microscopic vision and could look down in to the soil here, you would see a web of fungi that are going between all of these different trees and attaching the trees together, what the fungi do, is they effectively extend the root system of the trees and they go deep into the soil and far in to the soil. They bring water and nutrients to the trees. They also wrap right around the roots, that’s where the connection occurs and they protect the roots from plant feeding organisms.

And then the trees in return, they manufacture carbohydrates during photosynthesis and they send that carbohydrate down to the fungi as food. So it’s a real borrowing system. Even if you don’t have microscopic visions, although I can’t see any right now, you can sometimes see the fruits of these fungi, which are mushrooms. So the mushrooms come up and that’s kind of the fruits and that’s one way that the fungi spread themselves.

Even more interesting to me than that border, although that’s really cool, is that the trees can actually share probably water, certainly nutrition, and probably even knowledge with each other through this fungal network, so they things through the fungi to each other to help each other out.

And then there are bacteria in the soil, there are proteas in the soil, they will have slightly different roles, but they’re all… they all do important things for the community and they’re very inter-dependent. They all consume each other and relate to each other and sometimes help each other. Some of the things they do are they… as I said, they feed plants, they protect plants, they breakdown organic matter, so they take that mulch that falls from the trees or the animals or everything that’s dead. They turn it into a kind of a mulch and then eventually in to a humus.

It takes some of them, taking nitrogen from the air and convert in to a form that plants can use. Some of them take toxins in the soil and make them non-toxic anymore.

Any kind of role that we need in our human communities happens in the plant communities. Taking up the cabbage and being the doctors and all things like that, all… — there is all different roles, the organisms have to play in the soil. In the forest, the conditions are pretty nice for these microorganisms, for these fungi and bacteria and all these little guys is pretty good.

In our gardens, often not so much. We’ve had a lot of maybe construction work in our gardens, maybe we have a lot of compaction from equipment, lawn mores, kids running around and playing soccer. We have a monocultures that, the lack of diversity causes issues, may be we have… some one is used chemical fertilizers or pesticides in the past, which really decimates that soil food web. And so in our gardens, we may not has as abundant of a soil food web as healthy as diverse of the soil food web as naturally occurs here in the forest.

So in our gardens, we may to do something to introduce this, microbial diversity back in to our soil. The first way and arguably definitely one of the best ways to do it is compose, which I talked about in the organic matter section. A lot of people know composed is organic matter, which is good, its nutrients, which are good. But it’s also just important… it’s a way of growing and multiplying beneficial aerobic microorganisms, bacteria and fungi. If you have good composed that smells good, that was made properly and you have a good beneficial organisms you can bring in to your garden and immaculate your garden with those organisms.

So that’s the one thing to do, but we don’t usually have as much composed around, especially good composed as we would like. And so in that case, there are other things you can do, either to supplement the composed or even if you don’t have composed to bring is like microbes in to your garden. I started off this post talking about micorize a fungi that are in the forest here.

You may very well not have them in all that… in abundance in your garden. And so there are ways that you can propagate them from healthy tree roots, but you have to know a lot of about how to do that properly, it takes some time. For me, the best thing to do is just to go and buy a small amount of them, you can buy them as an inoculants. And then every time you are seeding or planting anything, you put a little bit of fungi on the roots around the seeds and you’re going to get them in to your soil that way. Otherwise, you can culture a lactic acid bacteria, which is something it’s very, very useful bacteria for your soil.

But again, to me, and I like doing the homemade stuff, but sometimes it makes sense, there is a mosquito in front of the lens makes sense to buy a product. So there is a product called the effective microorganisms, you can buy from usually $15 to $30 depending on what kind you get. Bring that in to your soil, it’s going to bring a bunch of different fermenting microbes, including, but not limited to lactic acid bacteria. And they’re going to provide many benefits to your garden, to your soil, to your composed pile and to your plants.

Another one is composed tea. It’s a little more work to make a good composed tea, but if you can do it, what you’re doing there is your bringing in a huge ray of… tens and thousand of different species of microorganisms in to your soil, whereas the EM is just a few really important microbes, composed tea has many different microbes.

And the cool thing about the EM, which is effective microorganisms and the composed tea is, you can also spray them on to your plants and inoculate the leaves, where they can feed the leaves, the plant right through the leaves and protect the plants from diseases like that leafs seems to have. So there composed is the best, but there are other ways that we can bring in these inoculants in the garden.

Of course, we also need to stop the killing of our soil, which is hard on microorganisms the compacting, the chemical use, the pesticide use and we also have to make sure we provide them with a good home. So that means we need to water the whole soil, not just drip irrigation to the plants, we need to give water to all of these microorganisms.

We need to give them mulch, a nice leaf layer and organic matter in the soil, so we need to do what I talked about in the first video, which is balance out the nutrients just to make sure they have the proper nutrient ratios in the soil. So we need … all the things I’ve been talking about, we need to do, not just for the plants, but for all of these organisms in the soil.

Okay. We’ve made it back to our cabin, alive although we do have some lights on our legs. But I hope you’ve enjoyed these three videos in these Smiling Gardner Academy, I get in to a lot of these inoculants on how to activate your own EM, so that it really brings the cost down to like $1 to $2 per litter, how to make a special kind of compose called Bokashi with EM, how to brew your own composed tea, how to get your own indigenous lactic acid bacteria. So all kinds of cool inoculants to improve the soil food web and of course composed in too, the price as I said goes up Monday night.

So if you’re thinking about that, may be have a look at it, other than that I hope you’ve enjoyed it.

In the first two posts I covered how important it is to balance the mineralization in the soil in order to be able to grow the kinds of plants we want to grow, and then how to increase organic matter in soil the way nature does it.

Now I want to get into the third part of this soil health triangle, the soil food web.

This refers to the life in the soil, especially the bacteria, fungi and other microorganisms, and the insects and other small animals.

The plants are part of this too since they have a tremendous impact on the soil. Read More

Compost Tea Recipe – Inoculate Your Garden With Microbes

Compost Tea Recipe

Update: Nearly 2 years after writing this, I decided to start selling the same compost tea brewer that I use. You can check it out (and learn more about compost tea) here.

A compost tea recipe doesn’t have to be complicated in order to be effective.

In fact, the simplest compost tea recipes are often the best because they’re easier to experiment with.

In case you don’t know, compost tea doesn’t look like my literal interpretation in the picture here.

Read More

Effective Microorganisms® (EM®) – Best Inoculant For You

Effective Microorganisms (EM)

I’ve been referring to Effective Microorganisms® (EM®) a fair amount on this blog, so I figure it’s time to get into more detail as to why it’s so incredible to use in organic gardening.

What is EM?

“Effective microorganisms” is a liquid culture of specific “facultative anaerobic” microbes that can provide amazing benefits for your organic garden when combined together in specific proportions.

Read More

In An Organic Vegetable Garden, Insects Are Our Friends

Organic Vegetable Garden Sheet Mulch
Here’s the beginning of my sheet mulch – newspaper and manure

This week, I started laying the groundwork for an organic vegetable garden.

I’ve been digging out some grass for the beds (6-8 inches below soil level in some spots to put in a good, deep path) and sheet mulching other areas right on top of the grass.

I’ll post a video tomorrow to show where I’m at.

Read More