Garden & Greenhouse


Increasing Microbial Population in a Soil or Medium

Posted May 20th, 2018 by Garden & Greenhouse in , ,

Within every soil or growing medium there is a world of living, microscopic organisms. It is these organisms who are responsible for the breaking down of organic matter into absorbable nutrients for plants to uptake. These microorganisms can provide other benefits to plants as well, including heightened protection from pest insects or pathogens. Our current understanding of plant physiology and beneficial microbes has many horticulturists adding and/or supplementing the beneficial microorganisms in the growing medium.

Increasing the beneficial microbial population in a soil or medium is a tactic that will automatically increase efficiency and productivity throughout the entire garden. There are a few different ways for a gardener to increase the population of beneficial microorganisms in his or her soil. There are also many different species of microorganisms that are considered beneficial to plants. These beneficial microbes are generally categorized into one of two categories: beneficial fungi or beneficial bacteria.

Beneficial Fungi – Trichoderma

Trichoderma are specialized fungi that feed on other fungi. However, it is actually the enzymes released by the trichoderma that make these microscopic organisms so beneficial. Trichoderma release particular chitinase enzymes that break down chitin. Pathogenic fungi’s cell walls are made primarily of chitin. The chitinase

enzymes released by trichoderma microbes feed on the pathogenic fungi; protecting the plant’s roots from being attacked. Increasing the population of trichoderma is a way for indoor horticulturists to better prevent soil borne pathogens. In fact, when a large population of pathogenic fungi exists in the soil, trichoderma will increase their chitinase production and feed almost exclusively on the pathogen.

In addition to chitinase, trichoderma release another enzyme, cellulases, which is beneficial to plants. Cellulases aid in breaking down organic material in the soil and convert it into readily available nutrients for the plant. Cellulases also can penetrate the cells in the plant’s roots. When cellulases enzymes penetrate the root’s cells, they trigger the plant’s natural defenses (similar to a human’s immune system). This stimulates the plant metabolism without causing any real harm to the plant and/or its functions. As the trichoderma feed on sugars secreted by the plant’s roots, the plant creates a stronger resistance to pest insects and pathogens.

Beneficial Fungi – Mycorrhizae

The beneficial microorganisms that most hobbyists are familiar with are beneficial fungi known as mycorrhizae. Mycorrhizae are naturally occurring fungi that form symbiotic relationships with over 90 percent of the world’s plant species. In other words, almost every plant on the planet has a relationship with these microorganisms. Essentially, mycorrhizae fungi become an extension of the root system and further the root system’s reach into the depths of the soil. This extension broadens the plant’s access to vital nutrients. Mycorrhizae have synergistic relationships with the plant’s roots. The extending web of mycorrhizae fungi assimilate nutrients for the plant and, in return, the plant’s roots secrete sugars or carbon for the fungi to feed on. Like the trichoderma, it is the enzymes produced by the mycorrhizae fungi that make this microbe such an asset to the plants. There are two types of mycorrhizae fungi: endomycorrhiza and ectomycorrhiza.


Endomycorrhizas are the type of mycorrhiza whose hyphae (long, branching filamentous structure of the fungus) penetrates the plant cells. Instead of penetrating the interior of the cell, the hyphae manipulates the cell membrane, turning it inside out, and thereby increasing the contact surface area between the hyphae and the cytoplasm. This helps facilitate the transfer of nutrients between them as it requires less energy than would otherwise be needed by the plant to do so. Put another way, this specialized relationship between fungi and plant increases the efficiency of nutrient uptake.


Ectomycorrhiza are a group of fungi that have a structure which surrounds the root tip. Ectomycorrhiza essentially surround the outer layer of the root mass. In nature, vast networks of ectomycorrhiza extend between plants (even plants of different species) and allow the plants to actually transfer nutrients to one another.

Beneficial Bacteria

There are many different strains of bacteria that live in the soil and provide benefits to plants. Various beneficial bacteria can help to break down organic matter (aid in composition), facilitate nutrient uptake, or help protect the plant (more specifically the plant’s roots) from pathogens. Inoculating beneficial bacteria into the soil or medium gives the bacteria a chance to colonize and quickly multiply. A large population of beneficial bacteria equates to the faster break down of organic matter. This break down converts the organic matter into soluble compounds which are readily available to the plants. A continuous large population of beneficial bacteria in the soil or medium will increase the plant’s ability to feed and, in turn, accelerate growth.

Increasing the Beneficial Microbes Population in the Soil or Medium

There are a couple of straightforward methods a horticulturist can use to increase the population of beneficial microorganisms in his or her soil. First, and foremost, is to provide the microbes (and plants) with a balanced, well-aerated soil, in other words, a soil with plenty of compost or organic matter to feed the microbes. Just like any other living creature, beneficial microorganisms need food, water, and oxygen to survive and thrive. Put another way, simply having a well aerated soil with a wide variety of organic ingredients is a great start to promoting a healthy population of beneficial microorganisms. In addition to a quality soil mixture, horticulturists can increase the population of microorganisms by supplementing them into the soil or medium. This is done by either a compost tea or a specific microorganism supplement product.

Compost Tea

Compost tea accelerates the process of composting organic material and returning it back to the soil. Any hobbyist thinking about brewing his or her own compost tea should understand the most important part of the brewing process is aeration. It is the rigorous aeration used in the compost tea process that accelerates the growth of beneficial microorganisms and the breaking down of organic matter. Most beneficial microorganisms are aerobic, meaning they live and thrive in oxygen-rich environments. On the contrary, pathogenic microorganisms are almost always anaerobic, meaning they live and thrive in an environment depleted of oxygen. When brewing compost tea, the goal is to build up a large population of beneficial microorganisms, hence the need to add oxygen or aerate rigorously.

Although the exact process will differ from garden to garden, most gardeners start their compost teas by adding a specific compost catalyst. The catalyst is a mixture of specific nutrients that initially stimulates the beneficial microorganisms within the compost material to “wake-up” and begin to multiply. The next stage of the process is the aeration. For 24 hours or more air should be pumped through the compost solution (a lot of growers use Rubbermaid containers or five gallon buckets to make a “compost tea brewer”). A healthy compost tea will appear as a frothy brew. The froth or foam indicates the nutrients, bacteria, fungi, and other goodies are ready to go to work in the garden. Compost tea can be used as a soil drench or as a foliar spray. The soil drench is the best method to increase the microbial population within the soil.

Microorganism Supplements

There are a wide array of beneficial microorganism supplement products available which allow horticulturists to quickly increase the population of beneficial microbes in a soil or medium. Powder and liquid concentrates of mycorrhizae fungi are available and give a horticulturist the ability to inoculate virtually any soil or medium. There are also many trichoderma and beneficial bacterial supplement products available. A closer look at the product’s label will reveal the percentage of each type of beneficial microorganism it contains. The label of any beneficial microbe product should also include an expiration date. Although supplements in powdered form will generally have a longer shelf life, microorganisms are living creatures that will die off over time. Liquid formulations tend to have a shorter shelf life which means a horticulturist should plan on using these formulas more quickly.

The form (liquid or powder) and the specific type of beneficial microorganism will determine how often a gardener supplements his or her medium. Although some liquid formulas call for weekly applications, it is usually possible to supplement less frequently and still get the desired results. Each microbe formulation will have its own set of application instructions. These application instructions should be used as the initial guideline for use. However, experimentation is the best way for a gardener to determine the most effective type of microbial supplementation and the rate at which it should be applied.

Protect the Microbes

A living soil is an amazing balance of organic matter and microbial life. In order to get the most out of a soil or medium, a gardener should do everything in his or her power to promote and protect the beneficial microorganisms. Chemical fertilizers can leave behind salts that hinder the growth of beneficial microorganisms. Growers who are serious about keeping a healthy living soil should stick to natural and organic fertilizers and supplements.
As previously mentioned, beneficial microbes need an oxygen-rich environment to survive. The most common way hobbyist horticulturists damage the population of beneficial microorganisms is by overwatering their plants. An overwatered soil will not have time to properly dry out and will not provide enough oxygen for beneficial microorganisms to live and reproduce. The best way for horticulturists to increase the population of beneficial microbes in his or her soil is to remember that beneficial microorganisms, although unseen by the naked eye, are living creatures that require food, water, and oxygen to thrive. A conscious effort to provide these essential components to a soil or medium will be the best initial step toward creating a healthy soil that is brimming with life.

Eric Hopper resides in Michigan’s beautiful Upper Peninsula where he enjoys gardening and pursuing sustainability. He is a Garden & Greenhouse senior editor and can be contacted at

Some of the photos for this article were provided by Synergy Agricultural Products

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