Beneficial Microbe Populations in the Indoor Garden

By Matt LeBannister
Published: March 20, 2019 | Last updated: December 7, 2021 10:37:59
Key Takeaways

Millions of beneficial microbes live in and around your plants’ roots and root zone. Even though you can’t see them, these little guys can make or break your garden.

There are so many factors to keep track of when gardening indoors. We must make sure the lights are the proper strength, color and distance from the foliage; the leaves are healthy, green and free of harmful insects; and the nutrient solution being fed to the plants is pH balanced, not too strong or too weak, and designed for their specific stage of growth.


It is no wonder that we tend to focus on the things that we can see, generally the part of the plant above ground, when gardening indoors. We can’t help but occasionally neglect the vital part of the plant that is below the surface: the roots and the root zone.

Down there is a whole world of microbes, many of which have a symbiotic relationship with your plants. This symbiotic relationship is important to maintain in order for your plants to be healthy and strong, especially if you are using organic nutrients and trying to go pesticide free.


These beneficial bacteria and fungi break down nutrients, aerate soil and fend off disease. They can make the difference between an okay harvest and a stellar one. Beneficial microbes exist naturally in nature, but they will not be present in adequate numbers in your indoor garden unless you help to introduce and maintain sufficient populations.

(Think of this process in comparison to baking bread: You could leave the dough out in the open and hope that the right type of yeast will land on your dough, or you could introduce bread yeast to the equation and be certain of the outcome.)

Beneficial Bacteria and Protozoa

Beneficial bacteria and protozoa are very important to your plants overall health, especially when gardening using organic methods in soil or soilless potting mixes.


One benefit is that the beneficial bacteria eat exudates, simple sugars, carbons and carbohydrates that the plant excretes through its roots (these sugars can also be added to the soil in the form of carbo/sugary supplements, molasses or humic acid in order to increase available food for these bacteria).

The beneficial bacteria are then eaten by beneficial protozoa, single-cell organisms that then excrete plant-available nutrients.


Beneficial bacteria also help break down organic matter. This is extremely important when gardening using organic nutrients since most organic nutrients need to be digested by bacteria and fungi before the nutrients can become available to the plants. If the plants are slow-growing house plants, then there is no rush; but if you are gardening indoors to harvest, then time is money.

The longer it takes before you can harvest, the more you have to spend on electricity, replacement light bulbs, nutrients, etc. Adding beneficial bacteria to your soil and soilless mixes can greatly accelerate the plants’ ability to absorb and convert nutrients into what they need to grow.

Beneficial bacteria can also help condition and aerate soil, and allow for better drainage. Another benefit of beneficial bacteria is their ability to covert non-soluble phosphates (calcium phosphate) into a type plants can use. Some beneficial bacteria also have the ability to break down toxins (oil-based chemicals, pesticides, etc.) present in the soil or soilless mix, turning it into plant food, air and water.

Beneficial Fungi

Beneficial fungi, or mycorrhizae, are fungi that have a symbiotic relationship with plants. There are two classifications of mycorrhizae: endo-mycorrhizae, which live on or partially within plant roots and share their sap with the plants; and ecto-mycorrhizae, which live entirely outside the roots of the plant they share their symbiotic relationship with.

There are numerous advantages to gardening with beneficial fungi. Mycorrhizae protect plants from harmful bacteria, fungi and pathogens by producing anti-biotics. In fact, penicillin was derived from common bread mold.

Beneficial fungi also create pathways in the soil and soilless medium that brings water and nutrients to the plants. Beneficial fungi works in conjunction with beneficial bacteria to break down organic matter and turn it to plant-available nutrients. Also, like beneficial bacteria, mycorrhizae help convert non-soluble phosphates that are present in the soil into a more plant available form.

Things to Avoid if You Are Trying to Build Up Your Garden's Beneficial Microbe Population

There are a few things that should be avoided if your want to keep the populations of beneficial microbes healthy and strong.

Chemical fertilizers will not provide any nourishment to the microbes. Chemical fertilizers are made up of salts, and salts pull the water out of the microbes, either killing them or causing them to go into a dormant state.

Hydrogen peroxide should not be used in conjunction with beneficial microbes. Hydrogen peroxide is used for various purposes in gardening. H2O2 adds oxygen to water, lower algae levels and can help suppress diseases within plants. It helps sterilize water and growing medium to kill harmful microbes, but it will also kill the good biology.

Pesticides get sprayed onto leaves to kill harmful insects, but they also kill beneficial microbes that are present on the leaves. If the pesticides are washed into the medium, they will kill any beneficial microbes in the soil or soilless potting mix.

Fungicides will destroy harmful bacteria, as well as any beneficial fungi.

Over-tilling and compaction can decimate beneficial microbe populations since microbes need air to survive.

Cultivate Beneficial Microbes Using Actively Aerated Compost Tea (AACT)

The difference between compost tea and AACT is that both the nutrients and microbe population has been extracted with AACT. Creating your own AACT and adding billions of beneficial microbes to your garden can be an easy process once understood. Ideally, you would first make some compost tea using homemade compost that has been fermenting for at least a year.

Take your compost and wrap it in cheese-cloth or a stocking to filter out large bits from the mix. The microbe-rich compost must then soak in chlorine-free water for three to 14 days in a relatively warm space. During this time, you must aerate the compost tea with an aquarium air-pump and air-stone.

By aerating the water, you will kill off the harmful bacteria while promoting the oxygen-loving beneficial microbe populations. While the solution aerates and soaks, you must also add other ingredients—such as store-bought sugary supplements or molasses, kelp meal or extract, worm castings, humic acid, guano and other organic nutrients—that will help feed and boost the populations of the good biology.

After soaking and aerating, the AACT is ready to be used. It should be applied every one to two weeks onto growing medium and foliar sprayed onto leaves to keep beneficial microbe levels high where it is needed most (the leaves and root zone).

If you don’t have year old compost just lying around—most of us who are raising fast-growing plants indoors don’t—there is another way to cultivate beneficial microbes using AACT. Take the ingredients that you would add to a basic compost tea, such as bird or bat guano, kelp, fish emulsion, worm castings, coffee grinds, etc., and follow the process above.

To make sure that the beneficial microbes make it into the mix, add some topsoil into your compost tea. Dig down 2 to 4 in. below the surface of the soil. This layer of soil will have many beneficial microbes, which will then multiply as the AACT is made. Keep in mind that the concentrations of different compost teas vary, so you might have to dilute and adjust over time.

Now that there are beneficial microbes present in your soil or soilless medium, it is up to you to maintain their populations. The best way to accomplish this is to top-dress your plants with compost, mulch and feed them organic nutrients.

Every so often, adding molasses or a store-bought sugary supplement will boost beneficial microbe populations. And, of course, watering and foliar feeding your plants with your AACT will ensure that there are always sufficient levels of beneficial microbes present to break down organics, prevent disease and aerate and condition soil. With the help of billions of microscopic friends, your plants can reach their potential and stay healthy and strong.


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Written by Matt LeBannister

Profile Picture of Matt LeBannister
Matt LeBannister developed a green thumb as a child, having been born into a family of experienced gardeners. During his career, he has managed a hydroponic retail store and represented leading companies at the Indoor Gardening Expos. Matt has been writing articles for Maximum Yield since 2007. His articles are published around the world.

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