Bacteria and Fungi: Mighty Microbes

By Kyle Ladenburger
Published: March 15, 2019 | Last updated: December 7, 2021 10:36:43
Key Takeaways

Before plants, there were soil microbes, or micro-organisms. As a vital part of the soil food web, microbes help to cycle energy and nutrition throughout the land by breaking down organic matter and converting it into a form that is readily available to plants. Here’s more on why something so small has such a large impact.

Nearly every living creature and organism on Earth relies on others within its ecosystem to perform certain tasks and help fuel the natural progression of life.


Think of it this way: a coyote hunts down and kills a rabbit. After the coyote consumes its fill of flesh and protein, it leaves the carcass behind and moves on. Though the coyote has discarded what remains of the dead rabbit, this is only the beginning of the story. As the rabbit carcass sits, it will begin to attract smaller animals and insects that will continue to break down what remains, including bones, tendons, vascular tissues and proteins.

This decomposition continues all the way down to the smallest microscopic organisms in the soil that consume the last of the deceased rabbit’s organic matter and release the remaining carbon and nutrients into the soil. Just as many animals, insects and soil microbes have relied on the consumption of the rabbit to obtain vital nutrients for survival, plants rely on tiny soil microbes to further break down organic matter, eventually improving soil fertility by converting the organic matter into a form that is readily available to the roots of a needy plant.


The following is a brief overview of two kinds of soil microbes that can directly affect the growth of a plant—bacteria and fungi.


Bacteria are the most populous micro-organisms found in healthy soils. These tiny, single-celled creatures are microscopic in size and anywhere from 300,000-500,000 of them can fit into a period at the end of a sentence. Bacteria are the oldest, most primitive forms of life and come in three styles or shapes: spiral, coccus (oval) and bacillus (rod-shaped), all of which are active in the soil. In nature, bacteria serve as one of the main decomposers of organic matter, second only to fungi, making them a vital part of the soil food web.

By decomposing dead plant and animal materials, the bacteria, in turn, ingest organic carbon compounds, nitrogen and any other elemental nutrients present. The nutrients are then held or immobilized within the bacteria and released when it dies. The process by which the nutrients are converted and released in plant-accessible forms is called mineralization. A favorite food source for soil bacteria is fresh, young plant material, or green matter, which the bacteria can easily break down because of its high sugar content.


The older plant material (brown matter) contains more complex organic carbon compounds that require initial decomposition by other organisms before bacteria can benefit. The green matter they consume contains the carbohydrate cellulose, which is comprised of chains of carbon-based glucose.

Half of a plant’s mass is made up of cellulose, so bacteria have a plentiful food source when they colonize the soil near it. Another popular food source for bacteria is root exudates—the compounds roots excrete—and large numbers of them will populate a plant’s rhizosphere, where they break down organic matter, such as dead root cells, and help feed the plant.


Bacteria help make nitrogen available to plants. Through the decomposition process, specialized bacteria have the ability to change the amino acids found in the organic material into ammonia in a process termed ammonification. Plants can take in nitrogen from ammonia in the form of ammonium nitrogen.

Other specialized bacteria can convert the ammonia to nitrite, which in turn is oxidized by nitrite-oxidizing bacteria, finally converting it into the nitrate form of nitrogen, a form that is also readily taken in by a plant’s roots. This transformation is collectively referred to as part of the nitrogen cycle, in which bacteria play a crucial role.

Bacteria are found in larger numbers than fungi in gardens or fields that are tilled on a regular basis because fungi are much more delicate and need more time in undisturbed soil to grow and populate.


Like bacteria, fungi play an important role in the decomposition of organic matter and the recycling of nutrients in the soil food web. Though larger in size than bacteria, fungi are still microscopic cells, but they grow in long, hair-like structures called hyphae that join together and form mycelium that can colonize the roots of a plant. The visible part of a fungi is the mushroom, which is simply the fruiting body that contains the spores for reproduction.

A big difference between bacteria and fungi is that fungi not only decompose cellulose, the main food source for bacteria, but they can also decompose more complex plant tissues, such as lignin and pectin, which are more fibrous and require specialized enzymes from fungi to break down.

After the fungi break down the organic matter, they help to immobilize the nutrients within the soil. This initial decomposition of complex organic matter makes it possible for smaller organisms like bacteria to feed from it as well. When fungal hyphae grow in length, they have the ability to traverse the surrounding soil in search of more organic matter to consume.

The same cannot be said about bacteria, which are more or less immobile in the soil. In nature, fungi are heavy consumers of organic matter such as dead leaves, plants and animal material. Without fungi and their ability to effectively decompose and recycle these materials, organic matter would just continue to accumulate on the forest floor.

Some fungi even have the ability to form symbiotic relationships with the roots of vascular plants, called mycorrhizae. This mycorrhizal relationship is mutually beneficial to both the plant and the fungi. After colonizing the roots, the fungi receive a steady and direct supply of carbohydrates, such as glucose and sucrose, from the plants.

In return, the plant receives elemental nutrient ions that its own roots, for a variety of reasons, may not be able to uptake. The fungal hyphae have the ability to access these hard-to-reach nutrients, such as the often-elusive phosphate ion, and deliver them directly to the roots. Plant roots colonized by mycorrhizal fungi greatly benefit from the fungi’s ability to enhance and expand the surface area and reach of the original root structure.

As was eluded to earlier, fungi are slower growing and more delicate than their bacterial counterparts and they thrive in soil that is relatively undisturbed such as no-till and permaculture gardens. As they live and work on decomposing organic matter, fungi also release nitrogen in the ammonium form which, given the presence of specialized bacteria, can be converted to nitrate in two steps.

Microbes and Organic Gardening

Outdoor gardeners growing organically benefit from or rely on the presence of soil microbes in their gardens, many without even knowing the role these microbes play. Every living creature requires a food/energy source to survive and reproduce, and soil microbes feed and obtain energy primarily from the organic matter in the soil.

Luckily, most organic fertilizers and amendments come in a form where further decomposition is required before they will be of any benefit to the plant. The microbes feed on this organic matter, breaking down the complex carbon bonds and, for lack of a better word, releasing the elemental nutrients held within the bond.

However, if the soil does not contain enough organic matter for microbes to feed sufficiently, their numbers will undoubtedly be lower and they will likely congregate within a plant’s rhizosphere, consuming any root exudates and dead root cells that they can.

Outdoor soil gardeners are not the only growers that can benefit from microbes in the soil, both outdoor and indoor container growers can as well. Growers who use an organic, soilless potting mix and some form of organic fertilizer stand to benefit greatly from the inoculation of beneficial microbes to the rooting media.

Most organic fertilizers contain small amounts of elemental nutrients that are readily available to plant roots, but most of the nutrients will still be trapped within a carbon bond. The addition of soil microbes to the rooting medium will help the grower obtain a higher level of soil fertility and plant development. Soil microbes also help with water retention and disease suppression within the root zone.

Natural evolution has embraced both competition and reliance as a way to cycle energy and nutrition throughout the land, sea and sky. The micro-organisms in the soil and the plants we grow are constantly involved in an often mutually beneficial game of give and take. And it is relationships like the ones between soil microbes and plants that helps keep life complex and perpetual.


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Written by Kyle Ladenburger | Director of Regulatory Affairs for Age Old Organics & ENP Turf, Freelance Garden Writer

Profile Picture of Kyle Ladenburger
Kyle L. Ladenburger is a freelance garden writer who has worked in the gardening/hydroponics industry for over 15 years. As an avid indoor and outdoor gardener he is well versed in nearly all types of growing methods with an overall focus on sustainability and maintaining healthy soils. He holds a strong conviction that growing one’s own food is a powerful way to change our lives and our world for the better.

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