The Good, The Bad and The Ugly: Managing Microbes in the Garden

By Frank Rauscher
Published: October 22, 2019 | Last updated: December 7, 2021 10:38:40
Key Takeaways

Plants need to receive a number of nutrients to thrive. Adding nutrients to a soil or hydroponic solution is an effective method for seeing that this happens at first. But another important step is keeping the bad bacteria at bay, along with establishing and maintaining the presence of the good bacteria. This way, you can create a living soil, boost the performance of your organic hydroponic system, and take a closer step towards greater yields. Managing microbes in the garden is vital!

Using beneficial micro-organisms on plant roots to cure problems and boost growth is nothing new. In the 1950s, more than 135,000 square miles of croplands were treated with strains of Azotobacter and various species of Bacillus. Farmers reported that more than 50% of the crops they tested experienced yield increases ranging from 10-20%. We now know that the applied bacteria were busy converting inorganic nutrients to usable nutrients and improving plant immune systems.


Since then, hydroponics has steadily become more popular. This method of gardening was initially developed in part to help growers control the root diseases that often occur in soil. While it did to some degree, hydroponics also introduced growers to other types of diseases.

For instance, pythium and the many phytophthora species of micro-organisms are well-adapted to aquatic environments, so they are major offenders when it comes to disease outbreaks in a hydroponic garden. Fortunately, a lot can be done to help limit such outbreaks. The key is using the good microbes against the bad ones.


Disinfection methods can help ensure each crop starts with a clean slate, so to speak, and active treatments help eliminate the harmful micro-organisms, but they tend to take the good out with the bad. The art of microbe management in hydroponics is learning how to minimize the bad guys, while maximizing the good guys.

The science of micro-organisms and how they affect the plant root systems they inhabit, whether that’s beneficially or detrimentally, is quite complex. Reports or summaries you might review may be covering methods of growing that are quite different from the methods you plan on using. So, many of the published results you come across may not be applicable. A better understanding of the overall science is helpful. The following is an overview to help you get started.

Microbe Behavior

Traditional gardeners know that a living soil is one of the keys to having healthy, vigorous, productive crops. The same is true in organic hydro systems. But just what is meant by the term living? Micro-organisms! We all want a large, diverse population of beneficial microbes present in our crops, especially if we intend to use organic nutrients.


These beneficial bacteria or fungi, which are also called endophytes, live within the small region of the soil/grow media surrounding plant roots called the rhizosphere. Rhizobacteria, which populate the rhizosphere, are the good bacteria that are living and functioning in the soil or soilless grow media of our crops. They can enhance plant growth through their ability to improve the availability of many nutrients.

Many factors influence the behavior and health of beneficial micro-organisms, such as total dissolved solids (salts), oxygen content, the type of grow media used, pH and various nutrient levels, just to mention a few. The benefits one type of endophyte provides can be different in various grow media or soil.


For example, in hydroponic cultures, each new crop often starts out from scratch with new water and new or sterilized grow media, so there really is not much of a microbial ecosystem to mineralize or convert organic compounds into the inorganic nutrients plants can actually uptake and use. Without a microbial culture being introduced to the system prior to the addition of the organic nutrients, there will typically be phytotoxic effects, which will cause poor plant growth or even failure.

The Microbe-Nutrient Relationship

Phosphorus, a vital macronutrient, is often a difficult nutrient for plants to uptake. A reason for this is its interaction with iron, aluminum and calcium, which cause it to precipitate out and become unavailable. Certain rhizobacteria can convert these into a more plant-available form (orthophosphate) and others can help make the iron more available. Making unavailable nutrients accessible to root systems is a key part of a healthy, living soil.

On the nitrogen side, organic sources of this macronutrient need to break down to create ammonia. Nitrification is the process that converts this ammonia into nitrites and then into nitrates. Plants can directly uptake and use nitrates, so this process of nitrification is essential in a hydroponic system that does not have inorganic nitrates added directly.

This process requires specialized bacteria. These indispensable microbes (like cyanobacteria, discussed later) must be added to the grow media or nutrient tank and cared for to survive and thrive. Ask the staff at your hydro shop for application rates and methods.

Many products on the market these days are inoculated with beneficial microbes, which colonize on the many surfaces within the system, including plant roots, the grow media, the tank, and the line walls. There are many other benefits microbes can and do provide. Let’s get to know them a little bit better, shall we?

Meet the Good Guys: Beneficial Microbes

The good-guy microbes are also known as plant growth-promoting rhizobacteria and probiotics. A good way to look at the different benefits of these endophytes is to review a few particular microbes as they pertain to improvements you may want to see take place. Here’s what to apply to your garden to:

  • Decrease toxins in the grow media – Arthrobacter globiforms and A. micotianae are basic soil bacteria that help degrade pesticides as well as reduce concentrations of a toxic form of chromium. In conjunction with Bacillus streptomyces, they are capable of completely neutralizing diazinon, a toxic pesticide.
  • Add some free nutrients – Cyanobacteria (blue-green algae) and Azotobacter vinelandii are examples of non-symbiotic microbes that help fix nitrogen in the soil, while species of rhizobia are symbiotic microbes that do the same job working with the root systems of certain plants such as legumes. There are many endophytes that will accomplish nitrogen fixation on many plants other than legumes. The bottom line about nitrogen fixing is that when these micro-organisms are present, your nutrient bill shrinks.
  • Multiply the effectiveness of the root system – Mycorrhizal fungi create a mutually beneficial relationship with plant roots. They colonize the root system and feed on the plant roots, making use of available carbohydrates that are generated through photosynthesis in the leaves. In turn, the plant roots see the benefits of increased water and nutrient uptake. It’s a win-win. When inspecting a root system where mycorrhizal fungi are present, you will notice a much thicker root structure. These types of fungi can also generate an immune response within the plant, making it more resistant to infections.

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

Who else is considered a good guy in the garden? It’s time to meet:

  • Bacillus thuringiensis – An effective organic pesticide safe to use for maintaining living soil.
  • Bacillus subtilus - Helps plants better cope with stress-related growing conditions.
  • Rhizobium japaonicum – A nitrogen-fixing, root-nodulating super bacterium.
  • Rhizopogan spp – A part of the mycorrhizae family used as soil fungal inoculants as it colonizes roots.
  • Glomus intraradices and other G. species – Soil fungal inoculants that boost the extensive networking of plant roots.

Controlling pathogenic microbes is one of the vital roles the good microbes play in the garden. Having a better understanding of how a plant’s immune system works (see QR code at the end of this article for reference) will reveal how some bacteria help strengthen a plant’s immune system through microbial antagonism to fight off diseases caused by the bad guys.

Meet the Bad Guys: Harmful Mircrobes

Who are the bad guys you are likely to come across in the garden?

  • Pythium describes a large number of fungi that cause root rot. Infected roots will look brown rather than have that nice, bright beige of a healthy root. Pythium is a moist-soil inhabitant. It doesn’t require much oxygen to thrive, so a well-oxygenated system will help keep these guys at bay.
  • Phytophthora are aggressive mold and plant pathogens that will keep plants from getting the nutrients is needs.
  • Fusarium oxysporum is a common fungus found primarily in soil that can cause plants to wilt, hence the term fusarium wilt. Certain types of yellowing of the leaves (chlorosis) are also symptoms.

Read more: Dealing with Pythium Root Rot

Microbes & Substrate Management

Microbes perform differently in different types of growing media, and their vigor will vary depending on parameters like pH and TDS levels, nutrient availability and temperatures, all of which vary according to the grow media being used. Controlling these aspects within your grow system is vital for success. Just adding microbes without managing your culture is asking for disappointment. Be sure to research the grow media you’ve chosen to determine best practices for managing the good and bad bacteria.

A culture medium, which is a solid or gas designed to support the growth of micro-organisms or cells, is used to feed the microbes and keep them in healthy concentrations. Aim to create a culture that enables the beneficial microbes and discourages the malevolent ones.

Nutrient broths can be important in developing a living soil. The wrong media or even an empty media will threaten the existence of the vigor you are hoping to achieve with your crop. Again, chat with the staff at the hydro shop or consult the expert growers in your life for more advice on culture media and how they interact with your selected growing medium.

Microbes & Organic Matter Management

For ultimate success, you can’t ignore the breakdown of organic matter in your system. As it decomposes, organic matter creates natural acids, which will impact the micro-organisms in the system.

When pH levels swing wildly, this can indicate that a root disease may be present, as there is a high count of malevolent, sometimes anaerobic, bacteria present creating all this acid. This will generally be accompanied by a rotten odor.

Spoiler alert: The organic material that’s decomposing is actually the root system of your plants. Pythium is often the culprit here. Rhizobacteria—the good guys—help bring the pH back down.

Read more: Bacteria? Virus? Fungi? Diagnosing Common Cannabis Diseases

Beyond Endophytes: Plant Hormones

Plant hormones such as auxins and ethylene are not endophytes, but they are another important factor to consider when discussing micro-organisms in the garden. Auxins have a major role in the coordination of plant growth processes. Plant body and cell production depend on these hormones in helping to direct plant growth behavior, their reaction to the environment, and the development of things like leaves and flowers.

Some auxins assist in the development of lateral roots, which in turn are key for better uptake of nutrients. Keeping ethylene levels low typically helps plant root growth, and many rhizobacteria contain an enzyme that has a key role in separating and isolating plant-produced ethylene and can help strengthen and improve plant vigor.

There are other classes of phytohormones that participate in providing similar benefits. Is it any wonder that we often encounter one plant doing well, while other plants, when given the same light/sun, water and nutrition, are failing? It all has to do with the interaction between microbes, plant hormones and the like.

Read next: Build the Best Organic Soil for Your Growroom


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Written by Frank Rauscher | Writer, Owner of Garden Galaxy

Profile Picture of Frank Rauscher
During his many years of service in horticulture, product development and sales, Frank has performed innumerable visits to landscapes to facilitate a correction for struggling plants or assist with new design. He also writes for Southwest Trees and Turf and The Green Pages, is the owner of Garden Galaxy and manages several websites. He has four children and eight grandchildren.

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