The Benefits of Using Soil Inoculants and Microbes in the Garden

Hopefully you don’t think of soil as just dirt.

Soil is actually an incredibly complex ecosystem, with billions of organisms found in a single teaspoonful. These organisms range from fungi and bacteria to earthworms, nematodes, and insects.

Good soil health is critical for plants to survive and thrive, so the survival of humans indirectly rests on the health of the soil.

This is so important that there are government programs working today to improve soil health. A number of these projects are specialized for urban areas and include funding to study heavy metal toxicity in the ground in New York.

A cut away of the soil structure showing green grass above and healthy roots down in the soil.

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Some of the many benefits of good soil health include:

Soil that is composed of aggregates (smaller fragments) will be less likely than individual particles to be blown away by the wind or taken up by water – both major causes of soil erosion.

Ideally, these aggregates stick together, and fungi can make this happen. They do so by secreting a sticky gel that glues the organic particles and the minerals together, helping to form humus. In addition, their hyphae thread through the small particles.

The fine roots of plants also help aggregates form by growing through the smaller fragments and helping them stick together.

A major advantage of humus is that it holds onto nutrients as water travels through the soil. This benefits both plants and the environment.

Adding soil inoculants like mycorrhizae will help ensure that your plants grow in healthy soil that provides them ready access to nutrients, so they will thrive!

The Process of Soil Inoculation

Fortunately, you can take steps to improve the earth that your plants grow in.

The process of soil inoculation involves taking specific microbes or nematodes and incorporating them into the soil, or applying them directly on seeds and plant roots.

In addition, you can implement practices that will improve the microbial diversity of your soil in general. Simple measures like incorporating compost into the ground and growing cover crops can do wonders to improve the numbers of beneficial microbes in the soil.

The Plant Rhizosphere

In addition to living dispersed in the soil, many microbes (both beneficial and destructive) live in an active zone around plant roots known as the rhizosphere.

A cut away of the earth showing tall, healthy grasses above ground and the root structure in the rhizosphere below ground.
The rhizosphere consists of the area around the plant roots where many forms of beneficial microbes live.

This is the area in the soil where the plants secrete compounds like sugars and amino acids.

In fact, up to 44 percent of the compounds that plants make from photosynthesis can end up in the rhizosphere. This makes the rhizosphere a relatively lush area for microbes.

In addition to microbes, other organisms like protozoa and nematodes live in the rhizosphere. They feed on the fungi and bacteria that live there and release their remains as waste products. This “waste” is a great source of nutrients for plants.

Types of Soil Inoculants

Microbes in the ground help plants in many different ways. Some limit the growth of pathogens. They can do this by outcompeting the pathogens or even parasitizing them.

Other microbes have symbiotic associations with plants. That means the microbes and plants have a mutually beneficial relationship. This includes bacteria that fix nitrogen or fungi that live as mycorrhizae and provide the plants with nutrients that may be otherwise unavailable.

Yet others stimulate a plant’s immune system, through what is known as acquired resistance. (You know that plants have immune systems, right?) The plants may grow more robustly as a result, or they may produce chemicals to fight off pathogens or insects.


Biofertilizers are products you can buy that contain microbes that will live in the rhizosphere or on roots, and increase the supply of nutrients to the plants.

A wooden compost bin with aged compost with fungi (mushrooms) growing on top and supporting a plethora of microbial life.
Compost is a prolific breeder of beneficial microbial organisms. Yes, mushrooms growing in your compost bin (or garden soil) is a good thing. They help break down the soil into compounds your plants can digest. Just don’t eat them (unless they are edible and you know for sure what you are harvest – bad things, including death, can occur if you harvest poisonous varieties).

This is an extremely valuable contribution to plant health. Often the soil can be full of plant nutrients, while the plants in that soil suffer from serious nutrient deficiencies.

A paradox indeed. This is a particular problem with potassium (K).

Up to 98 percent of the K in the soil is tightly bound to minerals like feldspar and mica. In fact, it so tightly bound that it is unavailable to plants.

While geological weathering will slowly release the potassium, making it available to plants, they commonly suffer from a deficiency of K.

Here is where microbes come into the picture. Both fungi and bacteria can help release this trapped potassium.

However, so many types of bacteria release K that there is even a term for them – KSB – potassium solubilizing bacteria.

Much research remains to be done on these special bacteria, but it appears that they secrete types of acids that release K from the minerals.

Your immediate and logical response to a deficiency identified by a foliar nutrient analysis may be to add more fertilizer to the ground. However, that can make the problem even worse.

A close up horizontal image of a cover crop growing in the garden.
Cover crops such a crimson clover (show), hairy vetch, and other legumes use Rhizobium bacteria to help trap nitrogen. The use of cover crops is particular effective when they are tilled back into the soil. If you follow no till techniques, using a mulching mower such as a flail can also provide benefits.

Many soil microbes can help the plant absorb such previously unavailable nutrients, but when you fertilize, you frequently inhibit these microbes. Such inhibition is primarily a problem with large quantities of chemical fertilizer.

However, it is possible to over-fertilize if you incorporate too much of a particular type of plant matter. Just be judicious and incorporate a variety of types of organic matter.

Cover crops, compost, or crop residues result in a diversity of microbes, which enhances soil health.

Nitrogen-Fixing Organisms

You are probably well aware that some microbes live closely with a plant and help to make nitrogen available to it. This is how legumes can live in such poor quality soil.

Microbes such as the highly specialized bacterial genus Rhizobium live in an intimate association with their host legumes in root nodules. They are able to take nitrogen from the air and change it into forms that plants can use.

Close up a pea roots with bacteria root nodules.
Bacterium from the Rhizobium bacterium develop root nodules in legumes that that of peas (shown), beans, and alfalfa and have a beneficial symbiotic relationship with the plant and help it affix nitrogen in return for nutrients.

Only some plants can harbor the bacteria that carry out this reaction, although researchers have been trying to enable crops like corn or wheat to carry out this reaction for many decades.

In fact, DuPont was performing this type of research in the 1960s.

A close up square image of bags of soil inoculant for peas and beans set on a gray surface. To the bottom right of the frame is a white circular logo with text.

Inoculant for Peas and Beans via True Leaf Market

Applying soil inoculants like Rhizobium is particularly important if you are planting a crop like beans or peas in earth that has not previously been used for legumes. Such soil is likely to lack a good population of nitrogen-fixing bacteria, but you can change that!

A square image of a pile of powdered inoculant set on a light gray surface. To the bottom right of the frame is a white circular logo with text.

Alfalfa and Clover Inoculant via True Leaf Market

Fortunately, wheat and corn can be helped by other kinds of bacteria that live freely in their rhizosphere and fix nitrogen.

Nutrient-Solubilizing Microbes

Mycorrhizal fungi are the most well known of this class. They live in close association with plant roots, and their hyphae extend way out from the roots.

This enables them to obtain nutrients from a wide span of the earth (and also from the tiny little soil pores that phosphorus can hide in).

Phosphorus in the ground is often found in forms that are unavailable to plants. But when they have mycorrhizae on their roots, the plants obtain phosphorus from the fungi in exchange for carbohydrates like sugars.

In addition to improving the supply of nutrients to the plants, the extensive webs of mycrorrhizal mycelia absorb water. So, they in turn can improve the drought resistance of the plants.

Different types of mychorrhizae are specialized for different plants. You can either buy a mixture of them to apply to your garden, or buy ones that are specialized for the particular type or types of plants that you are growing.

Potassium, as mentioned above, and iron are other important nutrients that can be abundant in the soil but unavailable to plants. Some types of fungi and bacteria secrete organic acids that make them more soluble.

A contain of ARBICO Organics™ Root Build 240 on a white, isolated background.

Arbico Organics™ Root Build 240 (Beneficial Mycorrhizal Fungi)

Other types of fungi and bacteria produce specialized compounds called siderophores that bind with iron and make it unavailable to other microbes. The good thing about it for us is that plants can use the iron that the siderophores make available.

These organisms perform best in soil that hasn’t been heavily fertilized. Scientists think that a plant doesn’t want to part with its precious nutrients if it isn’t getting something in return.

Therefore, the plants are more inhospitable to these microbes when the earth has a lot of nutrients freely accessible, like those released by chemical fertilizers.

Microbes that Produce Plant Growth Hormones

Some microbes produce chemicals that directly stimulate plant growth. This can be so beneficial to the plants that they can sometimes outgrow the pathogens!

One example of this is fungi that produce a hormone called gibberellin that helps seeds germinate and improves plant growth.

This compound was identified from an organism that caused a rice disorder called “foolish seedling disease.” The infected rice elongated unnaturally and had pale yellow leaves.

Japanese scientists isolated gibberellin from the fungal pathogen Gibberella in 1938. Their research came to prominence after the end of World War II and led to the discovery of gibberellins first in fungi, and then in plants.

In addition to gibberellin, soil microbes can produce the important hormone auxin. Many strains of bacteria in the earth produce auxin, which has an enormous effect on plants. It helps to:

  • Stimulate the elongation of shoots.
  • Control the orientation of seedlings.
  • Stimulate roots to branch.
  • Promote the development of fruit.

Many microbes that make auxin are good biocontrol agents and can compete against plant pathogens.


Other microbes will help keep pathogens in the soil in check. There are even types of earth called suppressive soils that are so full of these microbes that plants generally grow disease-free in them.

Bacillus thuringiensis growing in a petri dish.
The bacteria Bacillus thuringiensis provides a safe and organic means of attacking problem insects in the garden or orchard.

One of the problems with soil-borne fungal pathogens is that they can sap the growth of your plants without showing other visible symptoms, so you might not even realize they are there! But your plants will.

Biofungicides are a type of biopesticide. They are microbes that help control plant pathogens. One advantage of using biofungicides instead of chemical fungicides is that they can frequently combat pathogens, while allowing beneficial plant microbes to continue thriving.

The microbes can restrain the growth of pathogens in two ways. One is to directly prevent their growth. They can do this by producing chemicals like antibiotics that will kill other bacteria. Some bacteria even produce compounds called bacteriocins that kill other strains of the same species.

Another way to limit the growth of a pathogen is to feast on it! Some microbes parasitize others and live inside of them. Most fungi contain chitin in their cell walls. Many plants and some fungi produce an enzyme called chitinase that degrades the fungal cell walls.

Crustaceans also have chitin in their cell walls. Many years ago people used to spread crab shells on their fields to draw out the organisms that break down chitin.

However, times have changed, and you can now buy microbes to do the job for you!

Other microbes just outcompete the offending pathogens by efficiently colonizing the roots.

Bacillus Species

Species of Bacillus are types of bacteria that produce spores and survive efficiently in the earth.

The most famous one used as a biopesticide is Bacillus thuringiensis. These bacteria are certified for organic gardening and produce a toxin, known as Bt for short, which naturally kills insects.

A close up of a bottle of Bonide Thuricide isolated on a white background.

Bonide Bt Liquid Concentrate via Arbico Organics

If you’ve heard of Bt, it might be because a common class of GMOs has been engineered to produce this toxin and produce plants that are naturally resistant to insects.

Bacillus subtilis is widely used as a biofungicide.

This organism participates in a powerful combo of activities. It produces antibiotics, limits plant pathogen spore germination, and is thought to trigger an immune response in plants.

A close up square image of CEASE Biological Fungicide isolated on a white background.

CEASE Biological Fungicide (Bacillus subtilis)

You can find CEASE available from Arbico Organics.

Another species that is a common soil inhabitant that is used as a soil inoculant is Bacillus amyloliquefaciens (BAA).

BAA can grow on roots and form a physical barrier that prevents other microbes from colonizing the roots. Because of this tendency, it can prevent many types of diseases.

Two different sized plastic bottle of BONIDE® Revitalize® Biofungicide on a white, isolated background.

Bonide® Revitalize® Biofungicide (BAA) via Arbico Organics

There is also evidence that BAA can cause a plant to ramp up its defense mechanisms. That is another way it can help plants to resist disease.

And yet another factor that makes BAA such a useful soil inoculant is that some strains produce enzymes that break apart (lyse) other kinds of bacteria.

Unlike B. subtilis, BAA will not overwinter in the ground. If you use this type, you will have to reapply it each year.


This is a rather odd organism that is a bacterium but produces mycelia-like threads. Specific types of this genus, including Streptomyces lividicus, are sold as biofungicides.

A microscopic vie of the Streptomyces bacteria.
Streptomyces bacterium. Image credit: CDC/Dr. David Berd. CC0 1.0.

Many species of Streptomyces produce antibiotics that help them compete against other microbes in the earth. They were the source of such classic antibiotics as streptomycin, tetracycline, and chloramphenicol that have been widely used in medicine.

Conveniently, they also produce antifungal compounds that have been used in medicine, and help to control soil-borne fungi.

S. lydicus is no exception and produces the antifungal compound natamycin, which is used to treat eye infections.

This species is also highly effective at outcompeting fungi in the rhizosphere because it feeds off plant byproducts. This deprives pathogenic soil fungi of an important source of nutrients.

Actinovate® AG Fungicide (Streptomyces lydicus) via Arbico Organics

In addition to the plentiful fungal pathogens in the earth, S. lydicus can also protect against leaf pathogens, such as powdery mildew and rust.

Trichoderma Harzianum

This section would be incomplete without a description of Trichoderma. These fungi are widespread in the soil and live on plant roots.

Trichoderma fungi growing in a petri dish. Top down view with a black background..
Trichoderma fungi grows on plant roots and attacks various other fungi that cause root rot.

They are so important that two volumes of books were published on them in 1998. The monographs were edited by two prominent researchers in the field – Gary E. Harman and C. P. Kubicek.

A number of species of Trichoderma have been sold commercially. However, a 15-year breeding program at Cornell University produced a powerhouse strain of T. harzianum that works well in the field. (Many microbes work well in the lab but peter out in the field.) It is commonly sold as strain T-22.

Living on the roots puts the fungus in a good position to prey on the kinds of fungi that rot roots, including Pythium (damping off), Fusarium (wilts), and Rhizoctonia (root rot). T-22 releases a large amount of chitinase into the soil that breaks down the cell walls of the other types of fungi.

A micro view showing light green Trichoderma Fungi.

Once it has breached the walls, it can grow inside the fungi and parasitize them! This phenomenon is known as mycoparasitism (with “myco” meaning fungi).

In case you wonder why Trichoderma’s chitinases don’t dissolve itself, scientists have asked that same question.

An enzyme like chitinase can only act on a compound if it can access it. Austrian scientists believe that the mycelia may be protected by proteins that block access to the organism’s chitinases.

RootShield® WP (T-22) via Arbico Organics

Trichoderma has an advantage over many other soil inoculants because it grows well on plant roots. You only need to apply a little bit, and it will colonize the roots for a whole growing season. Other microbes need to be applied directly to the seeds for them to be able to colonize roots.

One caveat is that Trichoderma improves the growth of plants that are weakened. So you may not see as much of an effect if your plants are already in their prime.

Read our complete guide to using Trichoderma in the garden here.


While you may think of nematodes as plagues in your garden, other types of these roundworms are highly effective at controlling a broad of array of insect pests.

Microscopic view of Steinernema nematodes.
Steinernema nematodes are prolific hunters of many pest insects. Photo courtesy of Tony Coulson via CCO 2.0.

Part of the reason that nematodes are such effective killers of pests (but not beneficial insects) is that specialized bacteria live in their guts and can kill insects within 24-48 hours.

Whatever your soil type, you can find nematodes to help you in your quest to rid your garden of pests. Nematodes can live in areas as diverse as deserts and even ocean beaches.

Boxes of Arbico Triple-Threat nematode treatment on a white isolated background.

Triple Threat Nematode Bundle via ARBICO Organics

Their use in controlling insects is so promising that hundreds of researchers from more than 40 countries are working to make new insect-killing nematodes available.

Read on to choose the right nematode to control particular insects.

Tips for Using Soil Inoculants

Remember that while the bag of microbes that you buy may look like any other product, it contains living organisms. Be careful with how you handle them.

The best place to keep them is in the refrigerator. It is not a good idea to leave them in the sun in a hot car or truck, for instance.

Follow the manufacturer’s instructions! The best practices for the applications of soil inoculants can vary depending on what part of the country you are in, so there are no one size fits all instructions.

A pair of human hands using a pump sprayer to apply beneficial soil microbes.
Many, but not all, beneficial micro-organisms are applied via a pump sprayer. Read and follow all storage and application instructions for best results.

Also, you should be careful when handling them. While these organisms are pathogens of other microbes and generally not humans, people with compromised immune systems could conceivably be infected.

Mining New Types of Soil Inoculants

You probably know that scientists are constantly discovering new and highly unusual microbes in extreme environments.

This research fundamentally advances the knowledge of biology, since some of them are radically different from what was previously known. For example, bacteria in deep sea vents don’t need oxygen and use other compounds instead!

This same approach is used to identify new strains of fungi or bacteria that could help crops in the future.

Microbiologists go to extreme sites like the high desert or cliffs surrounding volcanoes to isolate bacteria from plant roots. The idea is that a microbe that helps a plant grow in an extreme environment could do so with crops as well.

These scientists perform detailed genetic tests that reveal genes that produce antibiotics, or plant growth hormones like auxin. In addition, they test these bacteria against other bacteria in the lab to find ones that are good at outcompeting other organisms.

While it can take a while to transition from lab research to direct uses in agriculture, this approach is likely to provide new and exciting types of soil inoculants down the road.

Microbial Competition Benefits Humanity

The antibiotics produced by many bacteria to help them compete against others in the soil revolutionized medicine. And microbial conflict in the soil has led to the use of soil inoculants to benefit crops.

With an increasing knowledge of microbial ecology in recent years, scientists have been better able to select strains of microbes that benefit plant growth and harness them to our advantage.

A pair of human hands holds a mound of healthy garden soil toward the viewer.

This area is booming with many companies that are developing their own proprietary strains of microbes to use as soil inoculants. Another trend is developing mixtures of microbes to add at once that act synergistically to improve soil health.

The next few years are likely to bring a huge increase in the variety of soil inoculants available to improve your plants – exciting news for the gardener!

Have you applied soil inoculants to your garden? What were the results? Share your stories and questions with us in the comments below.

And for more information about all things soil, check out the following articles next:

Photo of author
One of Helga George’s greatest childhood joys was reading about rare and greenhouse plants that would not grow in Delaware. Now that she lives near Santa Barbara, California, she is delighted that many of these grow right outside! Fascinated by the childhood discovery that plants make chemicals to defend themselves, Helga embarked on further academic study and obtained two degrees, studying plant diseases as a plant pathology major. She holds a BS in agriculture from Cornell University, and an MS from the University of Massachusetts Amherst. Helga then returned to Cornell to obtain a PhD, studying one of the model systems of plant defense. She transitioned to full-time writing in 2009.
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Pamela Stafford
Pamela Stafford (@guest_4731)
4 years ago

I loved this article. Thank you!

Cathleen Caffrey
Cathleen Caffrey (@guest_5355)
4 years ago

I’m delighted to find this post. I’ve been reading a lot about soil and plants and the ways they communicate. I also have a smallish patch of lawn behind my mobile home that has one huge silver maple with roots growing near the top of the lawn. The rest of the lawn hasn’t been well treated for years. I’m trying to improve the soil with very little money so I can put in some other trees and plants before the silver maple (quite old) bites the dust. I don’t have a lot of money so I’m trying an experiment: the… Read more »

Allison Sidhu
Allison Sidhu(@allison-sidhu)
Reply to  Cathleen Caffrey
4 years ago

Thanks for your message, Cathleen. We prefer to communicate via the comments section of our articles since this helps us to share our advice with you as well as other readers. You can feel free to contact us via the contact form for our website as well. Be careful with the donated grass clippings- depending on where the gardener gathered these from, they may come from treated lawns. An overabundance of nitrogen can affect other plants, introducing nutrients that your trees and other plants may not need, and the clippings may be sprayed with herbicides or pesticides as well. We… Read more »

Cathleen Caffrey
Cathleen Caffrey (@guest_5448)
Reply to  Allison Sidhu
4 years ago

Thanks. Since I’m mixing a lot of dried leaves with the grass clippings and know that no poisons are used on the local grass, I’m hopeful that this will help balance the nitrogen. I’ve also been wondering if it would help to add some of one or more of the micronutrient materials, like Azomite or microrhyzai (sp?). The soil has not been enriched for years and is very hard packed, so it needs more life. And the latest wisdom from my master gardener housemate is that the soil should not be tilled as has been the long-standing recommendation. Any thoughts… Read more »

Sarah Marino
Sarah Marino (@guest_9992)
3 years ago

I am just entering the organic gardening realm and am so excited but a little overwhelmed with the information. I tend to go overboard so I was just wondering if there is any damage that could be done from adding multiple inoculants or using too any in your garden. Should I spread out the additions? Thanks so much ! I really enjoyed the read!

Katie Gill
Katie Gill (@guest_10692)
3 years ago

What a wonderfully insightful article! Thank you!
I looked up Serenade with BAA, but it looks like it’s not manufactured anymore. Do you know of another product that you’d recommend?

Katie Gill
Katie Gill (@guest_10738)
Reply to  Helga George, PhD
3 years ago

Thanks Helga for the reply. I’m interested to know the name of the textbook, because you’ve really sparked in interest in me. The idea of using beneficial microbes to protect and defend sounds more holistic then pesticide use.
I thought I read on one of the Amazon reviews that Serenade hasn’t made that particular product for years, and was concerned about the the bacterial colony health in the product if it’s been sitting somewhere (with unknown conditions) for many years.
What are your thoughts?

Katie Gill
Katie Gill (@guest_10739)
Reply to  Katie Gill
3 years ago

Oh sorry, you’re right regarding the BAA and B subtilis. I did get some BAA through Bonide Revitalize. BTW, do you think it’s overkill with both types of bacteria? I’ve noticed the Japanese flowering cherry tree in our new house has fire blight (it looks like it’s been an ongoing problem sincethere’s multiple tree limbs cut off and I’ve since cut off a few myself with the discovery) and a few others on the property has powdery mildew. I thought I’d try the biologics when the temperatures get a little warmer (or do you think it’s ok to apply now?… Read more »

Katie Gill
Katie Gill (@guest_10755)
Reply to  Helga George, PhD
3 years ago

Thank you for your thoughtful replies Helga! It is much appreciated. I’ll check out both Teaming with Microbes and Cease. Thanks again! Stay safe!

Trevor Barnhill
Trevor Barnhill (@guest_11864)
3 years ago

Helga, I am so glad I found this site; What a gold mine! Your article was so informative and useful. However, I am left with a question, which is similar to other comments below concerning beneficial[s] out competing or even killing each other. I have read that B. amyloliquefaciens among other bacteria kill fungi. This makes me wonder if it kills endo/ecto mycelium. Currently, I am about to spray nematodes everywhere for fire ants, and B. Amylo…(Southern Ag D747) all over grass, garden and trees (hopefully it controls what i think is fireblight and a probable but unidentified fungal[?] in… Read more »

Last edited 3 years ago by Trevor Barnhill