The Full Guide to Gardening Microbes (Explained)

Milosh Potikj | 28 septembre 2023 | 11 MIN READ

As gardeners, we understand that having the perfect soil is essential for optimal plant growth. But we may not be aware of the incredible capabilities of the microbes lurking within it. Bolstering their presence by cultivating a microbial-rich environment means fewer disease-causing pathogens, more nutrient-rich soils, and better overall health for your plants.

In this comprehensive blog post, you’ll discover all there is to know about gardening microbes – from introducing healthy bacteria populations to identifying signs of unhealthy soil and finally delving into ways you can use beneficial microorganisms to power your green thumb success! Read on for a full guide to gardening microbes explained.

Basics of Gardening Microbes

Like the earth under our feet, there's more than meets the eye when it comes to soil. Hidden within it are countless tiny workers, known as microbes, playing a crucial role in our gardens. This section will introduce you to these minute powerhouses and explore their significant contribution to your garden's health.

What are Microbes?

Microbes, short for microorganisms, are tiny life forms often too small to be seen with the naked eye. They include a wide range of organisms such as bacteria, fungi, and viruses. In the context of gardening, Jeff Lowenfels and Wayne Lewis, authors of the book "Teaming with Microbes", highlight the importance of microbial communities present in the soil.

These communities, which include beneficial bacteria and fungi, help create healthy soils by breaking down organic material into nutrients that plant roots can absorb. This interaction forms a vital part of the soil food web, an intricate network of soil organisms working together to maintain soil health. The diversity in soil microenvironments, from the edges of soil mineral particles to environments without soil disturbance, can support different microbial populations.

These conditions affect the fertility of soils, making them more conducive for plant growth. From fixing atmospheric nitrogen to decomposing plant material, microbes play a critical role in maintaining the health and wellness of our gardens.

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The Critical Role of Microbes in Soil Health

Healthy soils teem with life, not just plant roots and insects, but also a multitude of microbes: bacteria, algae, fungi, and protozoa. According to Lowenfels and Lewis, a single teaspoon of good garden soil can contain a billion or more microbes. These microscopic organisms play a crucial role in soil health, performing a myriad of functions that help sustain life on Earth.

One of the key roles of these microbes involves the conversion of nitrogen. Nitrogen, a core component of amino acids and proteins, is essential for plant growth. Nitrogen-fixing bacteria, a type of beneficial microbe, can convert atmospheric nitrogen into forms of nitrogen that plants can use.

Moreover, microbes can help enhance soil structure. Some soil bacteria produce a sticky substance that binds soil particles together, creating aggregates that improve soil structure. This process allows for better water retention and easier plant root penetration. Other microbes, like fungi, excrete chemicals that can dissolve hard-to-access nutrients in the soil, making them available to plants.

What's more, the diversity of microbial communities in the soil can influence environmental conditions and contribute to the resilience of soils. For instance, certain microbes thrive under aerobic conditions, while others prefer anaerobic conditions. This diversity helps to maintain the overall health of the soil, even under varying environmental conditions.

Identifying Healthy and Unhealthy Soil

Identifying Healthy and Unhealthy Soil

To the naked eye, soil may just seem like dirt, but it's actually a complex ecosystem teeming with life. The health of this ecosystem can significantly impact the health and productivity of your plants. In this section, we'll delve into how to identify healthy and unhealthy soil, to ensure your plants are growing in the richest and most beneficial medium possible.

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Characteristics of Microbe-Rich Soil

Microbe-rich soil, often regarded as 'living soil', is teeming with a diverse range of soil organisms that contribute to its structure, fertility, and overall health. Microbe-rich soils tend to be dark in color, indicating a high organic matter content which is ideal for microbial activity. The soil should be crumbly and loose, making it easy for plant roots to penetrate and for water to infiltrate.

Healthy soil also exhibits a pleasant, earthy smell. This aroma is due to the activity of beneficial microbes and the presence of geosmin, a chemical produced by a type of soil bacteria. Moreover, healthy soils are often bustling with earthworms and other soil fauna - a good sign of a thriving microbial community.

Microbe-rich soil also possesses an optimal pH level, usually near neutral, which encourages diverse microbial communities. It is also well-aerated, allowing oxygen to reach the microbes that require it for their metabolic processes. If your soil fits this description, it's likely rich in beneficial bacteria and fungi, creating an environment where plants can flourish.

Jeff Lowenfels and Wayne Lewis in their book "Teaming with Microbes", promote the idea of nurturing these microbial communities rather than resorting to chemical fertilizers which may do more harm than good. By maintaining the soil's health through natural means, we create a sustainable environment that benefits not just our gardens, but the planet as a whole.

View our Microbes in store 

Signs of Unhealthy, Microbe-Deficient Soil

Unhealthy or microbe-deficient soil often exhibits a number of identifiable characteristics. Firstly, it may appear light in color or even grayish, lacking the deep, rich hue associated with high organic matter content. The soil may also have a hard, compacted texture, making it difficult for plant roots to penetrate and for water to absorb efficiently.

In addition, unhealthy soil often has an unpleasant odor, which may indicate the presence of anaerobic conditions or an imbalance in microbial populations. A lack of visible soil fauna, such as earthworms, may also signal a deficiency in beneficial microbes.

Furthermore, poor plant health can be a sign of unhealthy soil. Stunted growth, yellowing leaves, or a lack of vigor in your plants could mean the soil lacks the necessary microbial activity required for nutrient cycling.

Testing your soil can also provide insights into its health. Unhealthy soils often exhibit extreme pH levels, either acidic or alkaline, which can inhibit the growth of diverse microbial communities.

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Benefits of Microbial Life in Your Garden

The presence of a vibrant microbial life provides invaluable benefits to your garden, fostering a fertile and robust ecosystem where plants can thrive. Understanding these benefits can help us appreciate the unseen world under our feet and guide our efforts to nurture and maintain the biodiversity of our soils. Let's explore some of the key benefits of soil microbes in your garden.

Enhancing Plant Health and Growth

Soil microbes, especially beneficial bacteria, play a crucial role in enhancing both plant health and overall growth. By doing so, they establish a symbiotic relationship with the plant roots, assisting in the absorption of essential nutrients and water, and also protecting them from harmful pathogens. Some microbes, such as nitrogen-fixing bacteria, convert atmospheric nitrogen into a form that plants can easily absorb. This process is vital because nitrogen is a primary component of amino acids and proteins, crucial for plant growth.

Furthermore, fungi, a significant part of the soil microbial community, form networks known as mycorrhizal networks around plant roots. These fungal hyphae extend far beyond the plant's root system, effectively increasing the roots' surface area and, thus, its access to nutrients and water.

Natural Pest and Disease Control

Soil microbes also contribute significantly to pest and disease control in the garden environment. Certain types of bacteria and fungi have been recognized for their antagonistic properties against common garden pests and diseases. By producing various natural compounds, these microbes inhibit the growth of harmful pathogens in the soil.

Not only do these beneficial bacteria and fungi crowd out the disease-causing organisms, but they also produce substances that can directly act against these microbes. Some of these substances include antibiotics, fungal cell wall-degrading enzymes, and other bioactive compounds. In addition, certain predatory soil organisms, such as nematodes, can help regulate pest populations in the soil.

Improved Soil Fertility and Structure

Maintaining a thriving microbial community in your garden soil not only enhances plant health and natural pest control but also significantly improves soil fertility and structure. Microorganisms break down organic matter, releasing essential nutrients into the soil that plants can readily absorb.

Certain microbes, such as nitrogen-fixing bacteria, convert atmospheric nitrogen into forms that plants can use, boosting the soil's nitrogen content and overall fertility. Moreover, the activities of these soil organisms help improve soil structure. As they move through the soil and decompose organic matter, they create small channels and pockets.

These create spaces for plant roots to penetrate, promote better water retention, and improve aeration, which is vital for oxygen-dependent, or aerobic, microbial life. Healthy soils with good structure allow plant roots to grow deep and wide, leading to more stable plants and enhanced access to water and nutrients.

Cultivating a Microbe-Friendly Garden Environment

Cultivating a Microbe-Friendly Garden Environment

Creating a garden environment that is friendly to microbes is one of the best ways to ensure a healthy and productive garden. An environment rich in microbial life enhances soil fertility, promotes plant health, and boosts overall garden productivity. Let's delve into how to cultivate such an environment.

Adding Organic Matter: Compost and Green Manure

Adding organic matter to your garden is one of the most effective ways to enhance the biodiversity of microbes in your soil. Organic matter, in forms such as compost and green manure, serves as a source of food for soil microbes, promoting their growth and activity.

  1. Compost: Compost is a rich, nutrient-dense organic matter produced from household waste like vegetable scraps, coffee grounds, and yard debris. It acts as an excellent food source for beneficial soil microbes. As these microbes consume and break down the compost, they convert the nutrients into forms that plants can readily absorb, effectively recycling waste into plant food. This process fosters a thriving soil ecosystem teeming with microbial life.
  2. Green Manure: Green manure, on the other hand, refers to specific crops grown with the sole purpose of being incorporated back into the soil. These crops, often legumes, are rich in nitrogen and are excellent at improving soil fertility. They also support the growth of a special group of bacteria known as nitrogen-fixing bacteria. These bacteria convert atmospheric nitrogen into forms that plants and other soil organisms can use, enhancing soil nitrogen levels. By plowing these green manure crops back into the soil, you're not only adding valuable organic matter but also providing a feast for your garden's microbial populations.

More: How To Grow Hydroponic Plants Organically Without Soil.

Soil Conservation Practices: Mulching and No-Till Gardening

Mulching: Mulching is the practice of spreading organic matter, such as straw, leaves, or wood chips, on the surface of the soil. This serves multiple purposes that benefit both your plants and the soil microbes. Mulch helps retain soil moisture by reducing evaporation, providing the stable, moist conditions that soil microbes love. It also helps moderate soil temperature, and protects the soil from erosion, and as it decomposes, it adds organic matter back into the soil, providing additional food for your soil microbial communities.

No-Till Gardening: No-till gardening is a conservation practice that involves leaving the soil undisturbed by not tilling or turning it over. This method helps preserve the structure of soil aggregates and the complex network of fungal hyphae, both of which can be damaged by tilling. The undisturbed soil provides a stable environment for soil bacteria, fungi, and other organisms, allowing them to thrive and enhance the fertility of soils.

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The Role of Biofertilizers and Microbial Inoculants

Biofertilizers and microbial inoculants play crucial roles in enriching the soil with beneficial bacteria and other microbes. They are especially vital in urban soils which often lack a thriving microbial community due to soil disturbance and poor environmental conditions, when compared to rural soils.


Biofertilizers are preparations of living beneficial microbes which, when applied to seeds, plant surfaces, or soil, colonize the plant roots and promote growth by increasing the availability of primary nutrients to the host plant. Unlike chemical fertilizers, biofertilizers do not cause harm to the soil and are a natural means of improving soil fertility. They populate the soil with beneficial bacteria such as nitrogen-fixing bacteria, which can convert atmospheric nitrogen into a form that plants can absorb. This enhances the nitrogen content in the soil, improving plant growth and productivity.

Microbial Inoculants

Microbial inoculants, on the other hand, are substances that contain soil bacteria or other microorganisms. These substances are introduced to the soil to promote plant health. The microbes in these inoculants can form symbiotic relationships with plant roots, leading to improved nutrient uptake. They create healthier conditions for plant growth by enriching the soil's microbial communities. This diversity helps to suppress plant diseases and can speed up the breakdown of organic matter, making more nutrients available to the plants.

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Troubleshooting Common Microbial Issues

When cultivating a microbe-friendly environment, you may encounter several common issues. Here's how you can identify and address these problems:

Poor Microbial Activity

If your plants seem lackluster and soil fertility is low, it may be due to insufficient microbial activity. In such cases, adding organic matter or applying microbial inoculants can stimulate microbial communities in your soil. It's also crucial to limit the use of chemical fertilizers, which can harm beneficial microbes and disrupt the soil food web.

Anaerobic Conditions

Although some microbes thrive in low-oxygen or anaerobic conditions, these conditions can also encourage harmful bacteria and create an unhealthy soil environment. If your soil is staying wet for too long or has a foul smell, it may be too compact or poorly drained. Adding organic matter can improve soil structure and drainage, and turning the soil occasionally can help introduce oxygen.

Nitrogen Deficiency

If your plants are showing signs of nitrogen deficiency, such as yellowing leaves, it might mean that there are not enough nitrogen-fixing bacteria in your soil. Incorporating leguminous green manure or applying a biofertilizer that contains nitrogen-fixing bacteria can help improve nitrogen levels.

Poor Soil Health in Urban Soils

Urban soils can often be compacted, nutrient-poor, and low in microbial activity. Adding organic matter, practicing no-till gardening, and using biofertilizers can all help improve the health of urban soils.

Unhealthy Plant Roots

If your plant roots look unhealthy, it could be a sign that they're not benefiting from a symbiotic relationship with soil microbes. Microbial inoculants can introduce beneficial bacteria and fungi that form these symbiotic relationships, improving plant health.

Frequently Asked Questions

What are microbes in gardening?

Microbes in gardening refer to the microscopic organisms present in the soil, including bacteria, fungi, and protozoa. These beneficial microbes play a critical role in nutrient cycling and soil health, forming symbiotic relationships with plants to aid in nutrient uptake and disease resistance.

What are the 4 types of microbes?

There are four main types of microbes beneficial to gardens: bacteria, fungi, protozoa, and nematodes. Each type plays a crucial role in maintaining soil health, aiding in decomposition, nutrient cycling, and disease suppression. They interact symbiotically with plant roots, enhancing nutrient uptake and promoting plant growth.

How do you use EM1 on plants?

EM1, or Effective Microorganisms, is a beneficial microbial inoculant made up of a diverse mix of species. To use it on plants, simply dilute the EM1 with water according to the manufacturer's instructions, and then apply it directly to the soil or spray it onto the plant leaves.

Does EM1 work?

The effectiveness of EM1 is largely dependent on the conditions of your garden's soil. It can enhance soil health, promote plant growth, and reduce disease, especially when applied consistently as part of a holistic soil management approach.


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