How to Use Beneficial Bacteria for Pest and Disease Control in the Grow Room

By Eric Hopper
Published: October 12, 2017 | Last updated: April 23, 2021 03:06:47
Key Takeaways

Though microorganisms in your soil are out of sight, they shouldn’t be out of mind. While certain beneficial bacteria strains can help with nutrient uptake, others are powerful allies in the fight against pests and disease.

A growing number of modern horticulturists are learning about and embracing the power of microorganisms. In fact, many of the modern growers who utilize organic gardening techniques put their soil’s microbial population at the center of their focus. After all, the main theology of organic horticulture is “feed the soil and the soil will feed the plants.”


Beneficial bacteria have been a part of horticulture since the beginning of time, though our understanding of how they work and how to use them continues to develop. Many gardeners today are familiar with beneficial microorganism products that inoculate a soil or medium.

Some of these products have specific strains of beneficial microorganisms that create synergistic relationships with the roots. These relationships aid in the breakdown of organic materials and speeds up nutrient uptake. There are other bacteria strains used in horticulture to protect plants from pest insects and pathogenic diseases.


Once used only by organic and natural horticulturists, some of these beneficial bacteria products for pest insect and disease control are now being embraced by large commercial operations. This is due to their effectiveness and the minimal negative impact most of these products have on the environment. In many cases, these beneficial bacteria products are safer and more effective than their chemical counterparts.

After all, many of the chemical pesticides and fungicides damage much more than just the pest insects or diseases they were designed to treat.

Bacteria for Insect Control

Few things are more devastating to a garden than a pest insect infestation. Pest insects can quickly destroy an otherwise healthy crop, which is why a grower must take immediate action whenever a pest insect problem is identified. Depending on the particular pest insect problem a grower faces, he or she may be able to implement a treatment with a beneficial bacteria strain.


Bacillus Thuringiensis

Bacillus thuringiensis (Bt.) is a naturally occurring, soil-dwelling bacterium that is used as a biological pesticide. It is most commonly used to treat caterpillars and is very effective at controlling cabbage loopers.


While there are many different strains of Bt. found throughout the world, some strains produce crystal proteins that have insecticidal properties. When ingested, these special crystal proteins disturb the insect’s digestive system. This causes the insect to stop eating entirely, so it will eventually starve to death.

Many biological insecticidal sprays and powders contain Bt. Application instructions vary, but it is imperative that the insects consume the Bt. or the treatment will not work. In most cases, crops should be treated with Bt. on hot, dry days when the insects are most actively feeding. This will ensure a high consumption rate among the pest insect population. It is also important to remember that a reapplication may be necessary as rain or wind can remove the active ingredient from the plants.

Bacillus thuringiensis is considered an all-natural pesticide and some products containing it are certified for use by organic certification institutions. Most Bt. sprays and powders are regarded as environmentally friendly and have little or no effect on humans, wildlife, pollinators, or most beneficial insects. New Bt. strains are being developed all the time.

Each strain used in horticulture is given a unique number and registered with the United States Environmental Protection Agency. Specific formulations and strains of Bt. that are approved for use in organic production are listed on the website of the Organic Materials Review Institute (OMRI).

Spinosad (Saccharopolyspora spinosa)

Spinosad is a biological insecticide based on chemical compounds found in the bacterial species Saccharopolyspora spinosa. The insecticide is a result from the fermentation of the bacteria, a process that creates different forms of spinosyns. Spinosyns occur in more than 20 natural forms and more than 200 synthetic forms have been created in a lab. The insecticide spinosad contains a mix of two specific spinosyns, spinosyn A and spinosyn D, in a roughly 17:3 ratio.

Unlike Bt., which must be consumed by the pest insect, spinosad is effective by both contact and ingestion. Spinosad affects receptors in the insect’s nervous system, making the insect unable to feed or reproduce. Spinosad is considered an all-natural product and is approved for use in organic horticulture by numerous nations. It is used to control a wide variety of insects, including caterpillars, flies, beetles, thrips, and spider mites.

Bacteria for Fungi/Pathogen Control

Another tragedy that can befall an otherwise healthy garden is a pathogen attack. Powdery mildew, grey mold, root rot (pythium), and botrytis can all quickly destroy a garden. Similar to a pest insect problem, immediate action should be taken whenever a pathogen is identified. One of the best ways to combat these fungi-based pathogens is with the use of bacteria.

Bacillus Subtilis

Bacillus subtilis is a naturally occurring bacteria commonly found in soil and in the gastrointestinal tract of humans. It has many different uses in many different industries, but in horticulture, Bacillus subtilis is used as a natural treatment for powdery mildew.

When sprayed directly on powdery mildew, the strain feeds on the pathogenic fungus. When the fungus is gone, the bacteria dies off as well since it no longer has a food source. Unfortunately, multiple applications may be necessary as airborne powdery mildew spores can settle onto plants after the first batch of Bacillus subtilis dies off. It is also difficult to apply Bacillus subtilis in the later stage of flowering in an indoor garden because spraying any liquid will increase the level of humidity.

Bacillus Amyloliquefaciens

Bacillus amyloliquefaciens is a species of bacterium in the genus Bacillus. Bacillus amyloliquefaciens is a fast-growing rhizobacteria and can quickly colonize roots. It has gained immense popularity among hydroponic and aquaponic growers due to its ability to destroy and keep away root rot. In horticulture, Bacillus amyloliquefaciens is used to treat multiple root pathogens, including ralstonia, fusarium, and pythium.

Streptomyces Lydicus

Streptomyces lydicus is a bacterium species from the genus Streptomyces and has been isolated from soil. In horticulture, Streptomyces lydicus is used as a biological fungicide. It can be used to treat various fungal pathogens, including fusarium, pythium, phytophthora, rhizoctonia, and verticillum. Streptomyces lydicus is most commonly found in powder form that can be mixed in a liquid for application or mixed directly in the soil or medium.

The way the microbial world affects our daily lives is something most people never think about. Even experienced horticulturists take the beneficial microbes that affect a garden’s performance for granted.

As the old saying goes, “out of sight, out of mind.” However, as we discover more about how the microbial world affects horticulture and how we can use certain microorganisms to help us achieve our goals, we will pay closer attention to the microscopic world around us.

The link between healthy microbial life and successful gardening is unquestionable. Although we are unable to see the microorganisms, gardeners can witness the undeniable results from using beneficial microbe products in the garden.

Using beneficial microbes in horticulture can go far beyond the inoculation of a soil or medium. When pest insects or pathogens try to take hold in the garden, a horticulturist can deploy an army of microscopic bacterial troops ready to defend his or her precious plants.


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Written by Eric Hopper | Writer, Consultant, Product Tester

Profile Picture of Eric Hopper

Eric Hopper’s past experiences within the indoor gardening industry include being a hydroponic retail store manager and owner. Currently, he works as a writer, consultant and product tester for various indoor horticulture companies. His inquisitive nature keeps him busy seeking new technologies and methods that could help maximize a garden’s performance.

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