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Health of soil: A comprehensive guide for the garden nerd

For many, we teach us from a young age to stay as far away from soil as possible. Getting dirty is a bad thing and therefore soil is a bad thing. But soil is an important part of our lives and history and we wouldn’t be here without it. It is the birthplace of the vast array of plants we see covering the earth, including the ones in our gardens. It provides structure, nutrients, and water, among other things, for everything we plant to begin and carry out their lives. Hence why health of soil is so important.

So how is the soil formed? And how to keep it healthy? Here’s everything you need to know.

How is the soil formed: the beginning

Around 3.8 billion years ago (about 1 billion years after the formation of earth), the constant barrage of meteorites slowed, letting the earth cool enough so that liquid water could form. The new lakes and seas eroded the rocky surface of earth, creating the first step of permanent soil.

When some of the first living organisms, cyanobacteria, colonized and began to break down rock, they added oxygen and organic matter into the mix. True soil began to form. However, this new level still was not fit for any other forms of life, as the simple structure drained too quickly and was nutrient-poor.

Then came a relationship that changed the soil and our planet forever. Lichen, an organism made up of both algae and fungi (and sometimes bacteria) was able to colonize the lacking soils. Fungi are extremely good at collecting water and taking up nitrogen, and the algae was able to photosynthesize, providing energy. Using any available water and nutrients, they colonized bare rock, breaking it down and paving the way for plants to move out of the oceans and onto land.

As soon as plants started colonizing land, they changed the soil drastically by adding more and more organic matter and creating structure in the soil.

The soil we grow our plants in today has this rocky past (pun intended) and took billions of years to develop. It should be looked upon with awe and in recent years this has begun to happen. Soil has been studied more deeply and we grew a real appreciation for it.

It is now known that soil health is hugely important for growing happy plants. By getting the soil right, a multitude of problems can be avoided. You are giving your plants the environment to not only survive but actually thrive.

In this article, the important aspects of soil health will first be covered, followed by the best ways to incorporate this information into container gardening. End result: happy, hearty, homegrown plants.


a leave and a lizard in on the ground showing good health of soil
Photo by Carlin Roland


Health of soil: what exactly is going on in soil?

In order to choose the best soil for our plants and be able to manipulate it to optimum health, it is important to understand exactly what it is. There is so much going on in soil that is invisible to the naked eye, and a healthy helping of dirt consists of the right levels and proportions of “going-ons”.  Four key components compose the soil: mineral solids, water, air, and organic matter, all equally important and worth understanding.


Mineral solids

The mineral solids are what you might picture when you initially think of soil; this is the part you can actually see.

They consist of sand, silt, and clay. Which are mostly made up of silicon, oxygen, aluminum, potassium, calcium, and magnesium. Sand particles are the largest and clay particles are the smallest.

Texture is the term for the proportions of sand, silt, and clay in the soil. Technically sand by itself is a soil, but it alone will not grow many plants because water drains through the large particles too quickly.

Loam is a mixture of sand, silt, and clay, and equal proportions is considered the best for growing plants. A sandy loam will have all three but with majority sand. A sandy clay contains no silt. These three solids bind together in the various proportions along with organic matter to form what are called peds – aka tiny clusters of soil. The more structured these peds are, the more space there is in the soil for water, oxygen, microorganisms, etc. Peds are also affected by conditions like temperature, moisture, and compaction.

The texture of the soil combined with the structure of the peds texture create what is known as the soil behavior. By understanding the behavior of our soil, we understand how our soil will hold nutrients and water and how it will act as a growing agent.

drawing that explains health of soil with soil particules and ped


Water and air

Water and air are essential for almost all living beings to exist and are particularly important for plants. A plant takes in water and air primarily through its roots. Therefore, the available amounts in the soil directly affects a plant’s intake.

A typical soil contains 50% solid particles and 50% porous space, in terms of volume. The porous space is where the water and air hang out, and in a healthy soil there will be near equal amounts of each.

If there is too much water, little gas exchange between the soil and the atmosphere can occur. Carbon dioxide that is produced by respiring roots gets trapped and oxygen from the atmosphere cannot enter. This leads to anaerobic (no oxygen) conditions, which will lead to plant death as a plant needs oxygen for numerous processes.

On the other extreme, if there is little water, easy gas exchange can occur, but a plant will dry out and die.

The soil structure and water/air content are closely linked. The bigger the pores in the soil, the faster water will drain through but the more room there is for air. In soil with small pores, water will stick around but there will be less room for air. Water doesn’t simply take up all the room in big pores because the force of gravity wins out over the bonds it can form with the minerals, which are relatively far away.

Therefore, a soil with pores of medium size is ideal for getting the right balance of water and air.


Organic matter and the soil food web

Organic matter in soil consists of the wastes, residues, and metabolites of plants, fungi, bacteria, and small animals.

Without organic matter, soil would be a sad, cold domain, and would be uninhabitable for plants. This is where the oh-so important compost comes into play for gardening and the health of soil.

Compost is, in essence, the organic matter part of the soil equation. It is made of decomposed organic material, mostly plants, and the fungi, microbes, and tiny animals that thrive on that material, forming a food web. Each being plays its own role but they are all important to soil and plant health.



tree developing large roots in healthy soil
Source: Mycorrhizal Applications


Fungi and plants have been linked ever since they worked together to inhabit the land that nothing else could. From my experience, we often overlook this relationship when it comes to gardening and the health of soil.

Roots do their job of absorbing nutrients and water from the soil, but sometimes they are limited in how much they can absorb. Enter mycorrhizae, another brilliant relationship between the Plant and Fungi kingdoms.

Over 95% of plants have these relationships. It works through the bonding of certain soil fungi with the roots of a plant. Some types of fungi go inside of the root’s cells (endomycorrhizal aka arbuscular) while some grow around the root, creating a covering (ectomycorrhizal).

Once the relationship has been established, the fungus sends out tiny threads called hyphae into the soil, searching for water and nutrients which are then transferred right through the bonds into the plant. In exchange, the plant gives the fungus energy in the form of sugars, which the fungus needs to grow. Plants usually have plenty of carbon to spare, so it is no sweat for them.

In agricultural land, there are several meters of hyphae per teaspoon of soil. In a healthy forest, up to 64 kilometers in a single teaspoon! Whilst that amount is hard to wrap one’s head around, it shows how drastically mycorrhizae can increase the surface area through which water and nutrients can be absorbed.

Almost all of the veggies, herbs, fruits, and flowers that we grow do best when engaged in these relationships. Vegetables that do not form relationships include broccoli, brussels sprouts, cauliflower, cabbage, kale, beets, mustard greens, and spinach. If you are growing these, no need to worry about fungi.



Going back to the teaspoon measurement for visualization, there are 50 billion microbes in one teaspoon of healthy soil. These microbes, along with tiny animals, create a food chain and add in metabolic processes that turn our soil from a stagnant world to a breathing one.

Most bacteria found in soil are decomposers. They feed on simple carbon compounds, breaking them down into forms that then plant can reuse. They also increase nutrient availability, for example dissolving phosphorus so that it is more widespread in the soil.

One of the most important functions of soil bacteria is to make nitrogen available. Plants need nitrogen to make amino acids and proteins.  But they cannot use nitrogen in its gas form, the form in which it exists in the atmosphere and soil. Luckily, some bacteria are able to convert nitrogen from a gas into a mineral form that plants are able to use. This conversion process is called nitrogen fixation.

Plants form relationships with certain bacteria that both “fix” nitrogen and then immobilize it in the plant’s root zone. That enables the plant to absorb it before it escapes. If you are growing any legumes, you can rest easy. Legumes contain bacteria attached to their roots that fix nitrogen for the legume while the legume gives the bacteria sugars. Just like the mycorrhizal relationships.


infographics about the soil food web and health of soil
Source: Natural Resources Conservation Service


Next come the tiny animals that help make soil healthy.

Protozoa are single celled animals that feed on bacteria, fungi, and other protozoa. They then excrete the wastes, releasing nutrients back into the soil in a form that can be used by plants.

Nematodes, tiny animals resembling non-segmented worms, are the next size up in the food chain. They can be pests, feeding on plants, but they’re also highly beneficial. They feed on bacteria, fungi, and protozoa and therefore release nutrients. In addition, they help with converting nitrogen into a plant-friendly form. About 50% of mineralized nitrogen comes from nematode feeding.

The last size up (at least as far as container gardening goes) in the food chain are earthworms. They are a good, non-microscopic way to tell if you have healthy soil in a garden and can be a good addition to container gardening.  They eat their way through the soil, mixing organic matter (leaves, etc.) with minerals, bacteria, and enzymes in their digestive systems. It all comes out the other end in worm casts which are high in available plant nutrients. In addition, earthworms make small tunnels up to 1 meter into the soil, allowing roots to penetrate more easily and water to get further into the ground. For container gardening, soil will not be this deep, but the created space is equally as beneficial.  

Health of soil for plant health

Soil is a beautiful and complex world that, like so many things in gardening, takes time and patience to understand. I hope this article has helped shed light on how soil is not static but dynamic. And how focusing on the life forms within it should be given priority. The health of the fungi, microbes, and animals are what maintain the health of soil.

More gardeners and farmers have begun to understand that the best way to keep disease away from plants is to have thriving communities of microorganisms.

Just like our immune system, microbes in particular help keep the plant strong and able to fight disease. In addition, insects are more likely to attack a weak, unhealthy plant.

On farms, insecticides are often unnecessary when soil health is improved. Changing from a fix-the-problem mindset which often results in unhealthy mechanisms like insecticides, to a prevent-the-problem one is as easy as starting with the base of all growth – soil. By creating the healthiest base possible for plants to grow in, many problems can be prevented in an organic, healthy way.




Building Soils for Better Crops: Sustainable Soil Management by Fred Magdoff and Harold Van Es

Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web by Jeff Lowenfels

One comment

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