a gardener digging soil in his vegetable garden with a spade

What Are Soil Microbes: an introduction

Despite appearances, soils are filled with life. This life under the ground is part of a soil food web that decomposes organic matter, makes nutrients available, and ultimately enables plants to grow. The key to this are microbes -but what are soil microbes?

Even though we can’t see them, soil microbes are impressively abundant and include bacteria, actinomycetes, fungi, algae, and protozoa. For example, in a single teaspoon of healthy soil, you can find billions of microbes

Microbes are abundant in quantity, but also in diversity. Billions of different types of bacteria, for example, fill different roles. We’ll talk about the role of each type of microbe, but the important thing to remember is that the more microbes you have in your soil, the more they can self-regulate.

Scientists are still uncovering secrets below the soil and the more they learn the more questions arise. The more scientists discover about microorganisms in the soil, the more we realize how important they are to a healthy planet. If you’re curious about what’s happening inside your garden beds, keep reading for an introduction to what we do know about soil microbes.

What are Soil Microbes

Soil microbes are microscopic organisms that live in the soil. Microbes serve as decomposers, chemical processors, plant doctors, nutrient providers, pathogen controllers, and hormone creators. All of these actions give soil fertility, strengthens plant immune systems, and encourage plant growth.

You can find most soil microbes in the top layer of soil around the plant’s rhizosphere (the area around the roots). This concentration of microbes allows for the best uptake of nutrients and is one of the reasons why topsoil is so valuable.

Microbes can be as tiny as single-celled organisms, usually form colonies, and include bacteria, actinomycetes, algae, fungi, and protozoa. Their short life cycles of eating, pooping, reproducing, dying, and eating each other regulate harmful organisms and provide plants with a constant source of nutrients.

Complex ecosystems

Each category of soil microbes serves a different purpose and together they make up a complex ecosystem.  Within a healthy soil ecosystem, microbes maintain a mutually reinforcing closed loop. In this closed-loop, microbes create fertile soil through a rapid life cycle of eating, multiplying, and dying.  Fertile soil feeds plants, and encourages more microbes, and the cycle continues.

For me, soil microbes are the real farmers because they are the ones cultivating each other, fertilizing the plants, releasing antibiotics, and regulating pathogens.

Unfortunately, delicate soil life can be destroyed by unsustainable agricultural practices such as intensive chemical fertilizer, pesticide, and herbicide use as well as excessive tilling. Ironically, with healthy soil microbe life, there is less need for chemical fertilizers, herbicides, and pesticides.

tractor and sprayer spraying crops
Many chemical sprays used in agriculture can be harmful

In the next section, I’ll talk all about the role of microbes in the soil and why they are much more effective than conventional agricultural practices.

What is the role of microbes in the soil?

The main role of microbes in the soil is to recycle nutrients by decomposing organic matter and making those nutrients available to plants. However, specific microbes do so much more than this. Some process chemical toxins, others produce antibiotics, and some have even evolved to form symbiotic relationships with plants. 

Soil microbes, especially bacteria and fungi, are primarily decomposers. This small power creates an astonishing chain reaction. By decomposing organic matter and minerals, soil microbes allow plants to grow by making nutrients available to them.

Essential processes

When you add compost to the soil, the nutrients contained inside are not yet available to the plants. Bacteria and fungi feed on the compost and process it into humus which allows the plant to uptake nutrients. Without soil microbes, we could add as many nutrients to the soil as possible and the plants wouldn’t benefit from it.

Besides decomposing organic material into humus, soil microbes fix nitrogen found in the air into the ground in several ways. When protozoa eat and excrete nitrogen-fixing bacteria, the nitrogen becomes available to plants.

Nitrogen fixing

The rhizobia bacteria, for example, is responsible for one of the most important plant-microbe relationships which fixes nitrogen into the soil in partnership with legume plants. Fungi, on the other hand, form relationships with root systems to extend their reach, increase surface area, and facilitate nutrient transfer between plants.

Microbes also act as plant doctors by providing antibiotics, controlling diseases, and breaking down heavy metals. But more about their specific roles in the next section.

Each one of these roles is essential for sustaining plant life. Although we don’t know everything about the role of soil microbes, there is no doubt that they are absolutely essential for plant life on Earth.

What are the Five Types of Soil Microbes

Soil microbes are categorized into five types: bacteria, actinomycetes fungi, algae, and protozoa. Each of these categories plays a different but essential role in sustaining soil health. Let me break it down for you:

Fungi growing on a tree branch in a forest
Fungi start the decomposition process to make nutrients available to plants

In the soil, bacteria are responsible for decomposing organic matter, fixing nitrogen, and breaking down chemicals and metals. Without bacteria, the soil could be filled with essential nutrients but they would never be small enough for plants to uptake through their roots. By decomposing organic matter, bacteria recycle those nutrients into a form available to plants.


Nitrogen is the most in-demand nutrient in the soil. It is abundant in the air but isn’t available to plants in this state. Bacteria fix nitrogen from the air and protozoa make it available to plants.

Besides decomposing organic matter, bacteria also break down heavy metals and chemicals like pesticides which would otherwise build up in the soil. The buildup of heavy metals and chemicals can change the pH of the soil, inhibiting microbial life and nutrient uptake.


Actinomycetes can either be beneficial or harmful, so maintaining a healthy diversity of microbes ensures a balance. The beneficial actinomycetes are responsible for creating antibiotics that are just as important for plants as they are to humans.  


Fungi live around the plant roots and like bacteria, they help make nutrients available to plants by starting the decomposition process. Without fungi and bacteria, other microorganisms like protozoa couldn’t finish the job of decomposing organic matter. 

Fungi also play a unique role, colonizing plant roots and then serving as extensions. Extending plant roots means there is more surface area between roots and soil. It also means that the plant can access water and nutrients that would otherwise be unavailable. Fungal-root relationships also enable communication and nutrient transfer between plants.


Algae are both cooks and food for other microbes. They convert sunlight into sugars through photosynthesis and in doing so, introduce nutrients into the soil. When they die, the algae itself also become food for other microbes. Most algae are found on the soil surface where there is exposure to the sun. 

algae in swamp
Algae convert sunlight into sugars


Protozoa are single-celled organisms that feed off organic matter and other microorganisms. These secondary decomposers are thought to be responsible for releasing nutrients and minerals. When protozoa eat other microbes which are further down the food chain, they release the nutrients the bacteria consumed in a state available to plants.

Not all microbes in your garden are good. Diseases like powdery mildew, root rot, and damping-off, for example, all come from fungi. The key is to support a thriving and diverse microbial life, which can self-regulate.

Can I Damage Soil Microbes

Yes, most certainly. In fact, our poor treatment of soil microbes in agricultural practices has led to a huge world crisis. Due to excessive tilling, monocropping, and applying chemical fertilizers, pesticides, and herbicides our soil microbes are at risk. 


The most obvious destroyer of soil microbes is chemical agricultural treatments that are designed to kill specific harmful microbes but end up indiscriminately killing all soil life. Herbicides and pesticides designed to target a specific pathogen end up destabilizing the microbial balance by killing off the beneficial microbes.


Excessive cultivation of soil is another culprit to the destruction of microbial life because microbes are sensitive to soil structure. Microbes live in the top couple of inches of soil, so when that soil is turned over through tilling, most microbes can’t adapt. Eventually, they will bounce back, but if the land is tilled excessively and without regard for microbes they don’t have time to recover.

Plant diversity

Maintaining plant diversity is essential for hosting a huge diversity of microbes. When farms became highly specialized factories that produced only a single crop, the diversity of microbes on that land naturally decreased. To encourage greater diversity below the soil, increase diversity above the soil.

Exposed soil

The last major threat to microbial life is leaving the soil uncovered. When crops are harvested and the soil is between plantings it becomes exposed to the elements. Exposure to the hot sun causes an inhospitable environment for microbes and can cause the topsoil to blow away.

bare soil with no organic covering
Leaving soil exposed with no organic cover for long periods erodes and damages microbial life

Many conventional agricultural practices are promoted and implemented without regard for soil microbes. Ironically, it is this disregard for microbes that is making farmland around the world into uncultivable land. 

How do you Increase Soil Microbes?

Just like with microbes in the human body, soil microbes can be both good and bad. Having a diversity of each that balance each other out is the key to maintaining healthy soil.

Increasing the amount and diversity of microbes in your soil can have huge implications for preventing disease in your crops. You can increase your soil microbes by adding lots of organic manure to your soil, introducing soil samples from fertile soils, or buying them from a specialist.

Add compost

Organic manure is essentially food for microorganisms. This will feed the microbes that are already in your ground, allowing them to multiply. In exchange, they will decompose the compost making the nutrients available to plants.

compost heap with a bag of compost filled to be taken away
Organic manure is a great natural amendment for your soil

With very poor soil, you might want to consider introducing soil microbes from off-site fertile land. You add them to the soil, then they will feed on organic matter (like compost) and multiply.


You might not be able to see them, but we all owe soil microbes unending gratitude. It might sound dramatic, but without soil microbes life on earth as we know it wouldn’t exist. These microscopic organisms form a circular food chain that recycles nutrients and sustains plant growth.

Microbes in the soil break down organic matter, make essential nutrients available, control the ‘bad’ microbes, and form symbiotic relationships with specific plants. Additionally, their movements under the soil create natural tunnels through which air and water can circulate and roots can grow.

Without soil microbes, soils would just be dust and we wouldn’t be able to grow anything. Although life on earth relies on these unsung heroes, our actions threaten their existence. Overuse of harmful agricultural practices has decimated the populations in the most important agricultural regions.

Through regenerative soil practices, we can support a diverse and thriving soil microbe ecosystem while creating a more resilient food system. Start in your backyard by incorporating compost between seasons and avoiding chemical solutions.

Building up your soil microbes will pay off in the long run since your garden will be much more resilient to pests, diseases, and extreme weather conditions. Additionally, you’ll find your plants will grow faster and larger while being even more nutritious.