All About Microbes and Plants

When you’re growing plants, it’s important to consider how microbes impact soil and plant health. While these small organisms are often invisible to the naked eye, they have visible impacts on plant growth and vigor.

Certain types of bacteria and fungi play a big role in soil/media health. Therefore, they largely impact plant health in ways such as increasing nutrient uptake, improving tolerance to drought, and protecting against disease.

In fact, organic production is impossible without microbes. While conventional production can rely on chemicals for nutrition and pests control, organic production cannot.

Plants in organic systems rely on microbes to convert organic nutrients into available forms. Also, plants rely on these beneficial organisms to boost their immune responses and overall plant health.

If you’re looking for a way to increase the beneficial bacteria and fungi in your soil, you can innoculate your growing media. Products such as Amplify provide your media with a broad spectrum of beneficial microorganisms.

What does Microbe Mean?

People often use the word microbe instead of saying microorganism. As you might guess, both words refer to small organisms. These organisms include bacteria, fungi, algae, and protozoa. It’s important to note that they do NOT include viruses.

Don’t forget that microbes are not inert chemicals, and they are not nutrients. Rather, they’re alive! Therefore, they can multiply and quickly take over an area.

Microorganisms in Soil: Why do They Matter?

Healthy soil is not an inert physical substance. Rather, it’s teeming with life. In fact, just one teaspoon of soil can contain over a million microorganisms! Talk about living soil.

So, why do these little organisms matter?

Soil bacteria and fungi play a huge role in nutrient cycling. They convert nutrients into forms that plants can take up. Even if you apply nutrients, they might not be available to plants. Microbes help make sure plants can take up the nutrients you apply, so they don’t go to waste.

They also help plants take up water. Additionally, they help ward off disease and improve soil structure.

When you put all these benefits together, it means healthier plants and higher yields.

Types of Soil Microorganisms

These organisms are can be broken into four main categories: bacteria, fungi, algae, and protozoa. Within each of these categories, there are hundreds of different species.

Soil Microbes: Bacteria

Soil bacteria are essential to plant health. With that said, soil contains both beneficial and harmful bacteria. By increasing beneficial bacteria, you can limit the harmful bacteria present in soil. So, if you’re dealing with bacterial diseases, consider adding beneficial bacteria to your soil or media.

Common Soil Bacteria

There are thousands of species of bacteria present in the soil. These include both aerobic and anaerobic bacteria as well as rod, sphere, and spiral bacteria.

However, some types of bacteria are more common in soil than others. The type of bacteria present in an area depends on factors like geography, aeration, temperature, and soil structure.

It’s important to note that you can change the microbial composition of soils. By doing so, you can create a soil filled with microbes that benefit plants.

Beneficial Bacteria for Plants

Mutualists form symbiotic relationships with plants. This means that the bacteria help the plant and the plant helps the bacteria.

One type of mutualist bacteria are nitrogen-fixing bacteria. These bacteria convert nitrogen gas from the atmosphere into a plant-available form. In return, the plant provides the bacteria with carbon sources.

Some of these bacteria live in root nodules on legume plants such as clover, peas, and alder trees. Other types of these bacteria live freely in the soil.

soil microbes facilitate nutrient uptake

Another type of mutualist are nitrifying bacteria. These bacteria convert ammonium (NH4) into nitrate (NO3). This benefits plants because nitrate is easily taken up by most plants. However, it also easily leaches from the soil.

Decomposers work to break down materials in the soil. These bacteria are essential to holding nutrients in the soil and making them available to plants. Furthermore, certain types of decomposing bacteria can break down toxic compounds such as pesticides

How Do Bacteria Help Plants Grow?

Bacteria help plants grow in a number of different ways. One way is by changing the soil structure, another is by increasing plant growth, and yet another is by increasing nutrient uptake uptake.

Improve Soil Structure

Bacteria are crucial for creating a proper soil structure. As decomposers break down larger materials to form small soil clusters called aggregates. When the number of aggregates in the soil increases, so does aeration and drainage.

Increased aeration leads to increased root growth in plants. As plants’ roots grow deeper and wider, they can better reach and take up nutrients. Increased drainage further increases aeration, and water does not settle in the soil. Therefore, bacteria help inhibit the growth of harmful soil fungi.

Increase Nutrient Uptake

As mentioned above, soil bacteria help stabilize nutrients in the soil and convert them to plant-available forms. Without bacteria, many nutrients in the soil would be unavailable to plants.

Protect Plants from Disease

Some bacteria, such as Bacillus amyloliquefaciens protect plants from harmful microbes that cause disease. Good bacteria can protect your plants from issues such as root rot and fusarium wilt.

Boost Plant Growth

Certain bacteria known as plant growth-promoting bacteria (PGPB) act as biostimulants to increase plant growth. As the plants’ roots grow, they are better able to reach and take up water and nutrients. In turn, this further increases plant growth.

What Types of Bacteria Help Plants Make Proteins?

The building blocks of proteins are nitrogen molecules. We know that nitrogen is a macronutrient that plants need in large amounts. However, not all nitrogen in soil or solution is available to plants.

As I’ve briefly mentioned above, certain types of bacteria convert gaseous nitrogen into plant-available nitrogen. Some of these types of bacteria are listed below.

  • Rhizobia: live on nodules on legumes
  • Cyanobacteria: form relationships with some plants or exist freely in the soil
  • Cereal associative bacteria: form relationships with grass plants

Another type of bacteria that helps plants form proteins are nitrifying bacteria. All of these organisms convert various forms of nitrogen into nitrate, a plant-available form of nitrogen.

Some types of these bacteria convert ammonia to nitrates. Other types of these bacteria convert toxic nitrites into nitrates.

Fungal Microbes in Soil

Besides bacteria, the other main type of beneficial soil microorganism is fungi. Fungi help plants by protecting them from disease and increasing nutrient uptake.

Are Fungi Microbes?

Yes, fungi are considered microorganisms. While you can see some stages of the fungi life cycle, they are still considered microbes.

Beneficial Fungi

Soil fungi help plants in a number of ways. One way is by protecting against pathogens. Another way is by increasing nutrient and water uptake.

Trichoderma hazarium is a fungus that helps protect plants against bad fungi. This fungus can help protect plants from Pythium, Rhizoctonia, and Fusarium.

T. hazarium protects plants through a number of actions. One way is by releasing an enzyme that attacks cell walls of harmful fungi. A second way is by releasing toxic compounds that impact the bad fungi. A third way it protects plants is by directly competing with pathogens for resources such as nutrients and root exudates. Exudates are small compounds, such as sugars and amino acids, that plant roots secrete.

The Role of Mycorrhizal Fungi

Many plants form symbiotic relationships with mycorrhizal fungi. In fact, scientists think that about 80% of plants form symbiotic relationships with these fungi.

In simple terms, these fungi work to extend the plant root system so plants can better take up nutrients and water. Even if a plant’s root system only extends five inches under the ground, mycorrhizal fungi can transport water and nutrients seven inches under the ground to the plant. In return, plants provide the fungi with carbohydrates formed during photosynthesis,

The relationships between plants and these fungi are species-specific. Therefore, a fungus that forms a relationship with one plant may not form a relationship with another plant.

In addition to increasing water and nutrient uptake, these fungi can help protect plants from heavy metals and high salinity.

Microbes, Soil, Plants, and Nutrients

Because it’s so important to plants, I’ll reiterate that plants rely on microorganisms in the soil to take up nutrients. You cannot examine nutrients in plants without examining soil and the tiny organisms that live in it.

Define Limiting Nutrient

Plants need a variety of macronutrients and micronutrients. To achieve maximum plant growth, you must provide the proper amount of nutrients to your plants. This involves determining what amount of nutrients plants need at various stages during their life cycle.

When a lack of nutrients stunts a plant’s growth, these nutrients are known as limiting nutrients. It’s important to note that nutrients can be present in soil yet unavailable to plants. Therefore, even if the proper amount of nutrients are present in soil, they can still be considered limiting nutrients.

The plant availability of nutrients is impacting by soil pH, soil temperature, and the presence of soil microbes. If the soil is too cold or your pH is too high, plants may exhibit signs of nutrient deficiency.

Root/Microbe Interaction in Facilitating Nutrient Uptake

Microbes play a major role in plants’ uptake of nutrients. As I mentioned above, both bacteria and fungi increase nutrient uptake in plants.

To review, fungi extend the roots’ reach, allowing plants to reach more nutrients. Bacteria help convert nutrients to plant-available forms, which increases plant nutrient uptake.

Adding Microbes with Microbial Inoculants

The best way to boost the beneficial microorganisms in your soil is to use a microbial inoculant. These substances provide a dose of organisms that then multiply and establish themselves in the soil.

Some inoculants provide only one or two species of bacteria, while others provide a whole suite of beneficial microorganisms. Some of the best microorganisms include Rhizobium species, Azospirillum species, Pseudomonas species, and Bacillus species.

One product that provides a dose of many species is Amplify. This product contains a full spectrum of both aerobic and anaerobic microorganisms.

How to Use Inoculants

Some innoculants come in a powder form and some come in a liquid form. Growers often apply powder inoculants, such as Rhizobium, dirrectly to seeds before planting. Other types of powder inoculants, such as compost tea powders, must be added to water prior to use.

Liquid innculants are diluted with water and then they’re ready to use.Remember, since microbes are alive, they can multiply. Therefore, you don’t need to apply a large amount of a microbial inoculant. This means that a little product goes a long way!

Most inoculants come in a liquid form that needs to be diluted before it’s applied. I always dilute the inoculant in water, so the microbes can cover a larger area. Make sure you follow the directions for the particular product you’re using.

Since inoculants contain microorganisms, most need to be stored out of extreme heat and cold. To be safe, a good practice is to store them in a refrigerated area or cool area like a basement.

However, some products are more stable than others. We’ve found that Amplify tends to remain effective longer than other products.

Helpful Microorganisms in Inoculants

Different microbial inoculants supply different species of organisms to the soil. Also, different products contain different concentrations of different species of microbes. So two products that contain the same species of microorganisms might be quite different products.

Some inoculants contain only one species. For example, some inoculants contain a certain type of Rhizobium that is compatible with a certain type of plant.

Other inoculants contain a mix of microbes designed for protecting against pathogens or increasing nutrient uptake. While the makeup of inoculant products differ, many products contain the species listed below.

Bacillus subtilis: helps protect plants against harmful fungi

Bacillus amyloliquefaciens: protects plants against pathogens

Streptomyces lividicus: controls against soil-borne fungal pathogens

Trichoderma harzianum: protects plants against fungal pathogens that cause issues such as root rot and damping-off

Some inoculants contain a secret, proprietary blend of microbes. So, it may be hard to determine exactly what you’re applying to your soil. However, it never hurts to contact a company directly and ask what makes their product different from the others.

Benefits of Microbes

If you’re on the fence about adding microbes to your soil, don’t be! By inoculating your soil or media with beneficial organisms, you’ll see the following benefits.

  • Increased plant water uptake and decreased drought stress
  • Decreased levels of soil toxins
  • Better plant resistance to pathogens and insect pests
  • Increased plant nutrient availability and nutrient uptake

Together, all these benefits lead to noticeably increased growth and healthier plants. When your plants are growing with biology, rather than in a sterile media, they will grow faster and larger. Consequently, you’ll see bigger yields and higher quality.

Not All Microbes are Friends

Now that we’ve covered all the benefits of beneficial microoganims, it’s time to remind you that not all of these organisms are good. Hundreds of different microbes cause disease within plants. 

For example, fungi cause issues including powdery mildew, root rot, and rust. Bacteria cause diseases such as various blights and wilts.

To prevent these pathogens from taking over, it’s important to have a proper environment. This includes good drainage and airflow. Anothe way to limit these pathogens is to introduce good microbes, as they can outcompete the unwanted species.

Microbes: A Key to Healthy Plants

Growing plants isn’t just about chemistry, but also biology. When you pay attention to the many tiny organisms present in your plants’ roots zones, you’ll experience big benefits.

So, along with providing the necessary nutrients, lighting, and environmental conditions, provide the proper biology. To boost the beneficial microbes in your soil and/or media, start using a soil inoculant such as Amplify.


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Biological Nitrogen Fixation

Soil Bacteria

Soil Microbiology: A Primer

What are Microorganisms?

Categorized as Nutrients

By Briana Yablonski

Briana grew up in Eastern Pennsylvania and currently resides in Knoxville, Tennessee. She holds a Bachelor of Science in plant sciences from Penn State University and has worked on produce farms in Minnesota, Pennsylvania, Virginia, and Tennessee. She now runs her own small farm and enjoys walking dogs at the local shelter, hiking, and riding her bike.