Beneficial Microbes: A Closer Look at the Microbes Living Around Your Plants’ Roots

By Monica Mansfield
Published: March 4, 2020 | Last updated: December 7, 2021 10:40:15
Key Takeaways

There is an entire world living in the soil, with a complete cast of characters eating, reproducing, and providing food for the plants we grow. In fact, there are more microbes in a teaspoon of soil than there are people on Earth.

Microorganisms living in the rhizosphere have a symbiotic relationship with the plants who host them. Bacteria, fungi, nematodes, protozoa, and arthropods are all beneficial microbes connected in the soil food web and working together to feed the plants in our garden. As gardeners, it helps us to learn about these beneficial microbes and how to support them, so they thrive in the soil and work to give us a healthy garden.



One teaspoon of healthy soil contains between 100 million and one billion bacteria. These tiny, one-celled organisms are a minuscule 4/100,000 of an inch wide and only slightly longer in length. They are the first microbes to digest new organic matter in the soil. They recycle nutrients, suppress diseases, and improve the soil’s ability to hold water. There are four kinds of bacteria: decomposers, mutualists, lithotrophs, and pathogens.

Decomposers feed on carbons, such as root exudates and plant litter. After digesting them, their waste becomes food for other soil organisms in the food web. This way, nutrients such as nitrogen are kept in the root zone instead of leaching out into the groundwater.


Mutualists have symbiotic relationships with plants. For example, nitrogen-fixing bacteria make their home in the root zone of legumes and certain trees. They convert nitrogen from the air into a plant-available form. This nitrogen is then returned to the soil when the plant drops its leaves.

Instead of consuming carbon compounds, lithotrophs consume nitrogen, sulfur, iron, and hydrogen. They play a role in the nitrogen recycling process and can be helpful at degrading pollutants.

While bacterial pathogens can damage plants, they can be kept in check with a healthy and diverse microbial community in the rhizosphere. Other microorganisms will compete with the pathogens and keep their populations and check.



Fungi are another key player in the soil food web. These microscopic cells grow strands called hyphae that weave throughout the soil and bloom above the soil as mushrooms. They can be grouped as decomposers, mutualists, and pathogens.

Decomposers play an important part in nutrient cycling by breaking down hard-to-digest materials, such as cellulose and lignin, and retaining the nutrients in the soil. They also help create humus, which is resistant to degradation and holds water well.


Mutualists have a symbiotic relationship with plants. They colonize the root zone and send out their hyphae to create a vast underground network. The hyphae resemble roots and can travel miles underground. Plants can communicate with one another through this network and warn one another of potential threats. These mycorrhizal fungi will bring soil nutrients and water back to its host plant.

Pathogenic fungi, such as Verticillium and Pythium, can reduce a harvest or kill plants completely when they colonize their root zone. However, some pathogenic fungi help to control pests and disease. For example, certain strains will set traps for harmful nematodes. Some strains create sticky traps, while others make circular rings with their hyphae to constrict and kill their prey.


Protozoa are several times larger than bacteria and can be classified into three groups: ciliates, amoeba, and flagellates. Ciliates consume bacteria, amoebas, and flagellates. They can eat up to 10,000 bacteria per day, and then release nitrogen in a form plants and other soil organisms will dine on.

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Protozoa stimulate bacterial populations. When they graze on bacteria, much like when you prune a tree, growth is enhanced. They also suppress plant diseases by competing with and feeding on pathogens. They themselves are an important food source for other soil organisms.

Protozoa live in the rhizosphere next to roots, where there are plenty of bacteria to eat. Moisture is important for protozoa because they travel by water.


Nematodes are non-segmented worms that are only about 1/500 of an inch in diameter and 1/25 of an inch long. They feed on a wide variety of soil organisms. Some strains feed on bacteria and fungi while others consume plants, algae, and other nematodes. When they eat bacteria or fungi, ammonium is released into the soil in a form plants can use.

Their grazing stimulates bacterial growth, however, too many nematodes can reduce bacterial populations, which in turn decreases plant productivity. Predatory nematodes, soil microarthropods, insects, and parasitic bacteria and fungi keep nematode populations in balance.

While some nematodes can cause plant diseases, others suppress them by feeding on disease-causing organisms. In fact, you can purchase beneficial nematodes as a biocontrol agent at most garden centers.

Nematodes act as a taxi cab for other bacteria and fungi. They carry microbes on their surface and in their digestive system as they travel along roots in the soil.

How to Support Soil Microorganisms

Beneficial soil microorganisms thrive in soil that has plenty of organic matter and has not been tilled. While tilling initially releases a burst of nutrients, it also destroys established fungal networks. Over time, organic matter becomes depleted and microbial populations shrink because they have lost their food source. Under no-till conditions, small amounts of nutrients are released every year and high levels of organic matter are maintained.

Fall is the ideal time to add organic matter to your garden so that it can decompose over the winter. For great results, simply mulch with compost, straw, leaf litter, manure, or wood chips. You can also chop and drop your spent plants, and either leave them on top of your soil or turn them under. Doing this with legumes will add plenty of nitrogen to your soil.

Cover crops also feed soil microbes. There are 1,000 to 2,000 times more microbes living around roots then there are living in bare or tilled soil. Planting a winter cover crop to a no-till field will prevent nutrients from being lost through erosion and leaching, and give beneficial microbes a place to call home with plenty of food nearby.

Synthetic fertilizers and pesticides can do serious damage to microbe populations. The salts in fertilizers and chemicals in pesticides harm microbes. Better to add organic matter and amendments to the soil if you want a thriving microbial population. When your soil contains a diverse population of microorganisms, you'll find pests tend to be less of a problem. However, if problems do arise, organic pesticides such as neem oil or soap sprays will effectively treat infestations without harming soil biology.

If you create an environment that is favorable to beneficial microbes in your soil, they will do many of your garden chores for you. They will recycle nutrients and create rich soil that will grow a happy, healthy garden.


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Written by Monica Mansfield | Homesteader, Owner & Writer of The Nature Life Project

Profile Picture of Monica Mansfield

Monica Mansfield is passionate about gardening, sustainable living, and holistic health. After owning an indoor garden store for 5 1/2 years, Monica sold the business and started a 6.5-acre homestead with her husband, Owen. She writes about gardening and health, as well as her homestead adventures on her blog at

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