Mycorrhizal Fungi | Rhizobium | Rhizosphere

The Root Cellar

A favorite habitat of microbes is near and in the roots of plants. Many microbes live in soil, but even more (up to 100 times more) live close to the roots of plants. This area near the roots is called the "rhizosphere" which is the thin layer of soil that sticks to the roots. The rhizosphere is a huge habitat in the soil, because plants have so many root fibers. An individual wheat plant, for example, may have a root surface area of 6 square meters (yards)!

Some microbes have very close relationships with plants. The plant and the microbes become so close that the microbe actually lives inside the plant! This association of microbes and roots often benefits both organisms. The plant gives the microbes food, such as sugars and amino acids, and the microbes give the plants minerals, some vitamins, nitrogen, and some amino acids.

One example of a microbe living inside plant roots is Rhizobium, which lives inside the roots of plants such as peas and clover. Another group of microbes living inside roots are mycorrhizal fungi. Rhizobia and the mycorrhizal fungi live with plants in symbiotic relationships. Symbiosis is the living together of two or more organisms. Often, this association helps both organisms.


Mycorrhizal Fungi

Most plants, including more that 90% of all trees, have special fungi associated with their roots. These fungi help plants absorb nutrients and water. These fungi form a symbiotic association with the roots of nearly all plants to help them grow. Sometimes these microbes become macrobes, large organisms, that you can see as mushrooms.

Mycorrhizal fungi live with and help the roots of nearly all plants. Mycorrhizae means "fungus root." In this association, the fungus extends itself into the soil and helps the plant by gathering water and nutrients, such as phosphorus and nitrogen. In return, the plant helps the fungus by giving it sugar produced by photosynthesis. This is an example of symbiosis, a win-win association.

Mycorrhizae allow plants to live in desolate areas that are poor in nutrients, such as road-sides, disturbed soil near mining operations and in tropical rain forests. Surprisingly, rain forests are often depleted of nutrients because there is so much competition by other plants for nutrients. In these nutrient-poor soils mycorrhizae can help plants to live where they otherwise might die.


The most common mycorrhizae grow inside the cells of roots. These are called "endomycorrhizae," (Endo means inside.) Many of these endomycorrhizae form tiny trees and little sacs inside root cells. These tiny trees, called "arbuscules" (Latin for tree) and tiny sacs, called "vesicles" (little sac) are connected to long threads of the mycorrhizae that lead out into the soil. These long threads, called hyphae, are analogous to the roots of plants. These hyphae extend beyond the length of roots, and allow the roots to absorb more nutrients than they would without the help of the fungus.


Another type of mycorrhizae grows between the cells of roots and on the outside of the root, not inside the cells. Because these fungi live outside the cells of the plant, they are called ectomycorrhizae (ecto = outside.) These fungi have a thick network of thin, fungal cells, or hyphae, that cover the roots of the plants. This covering protects the roots in a sheathe of ectomycorrhizal cells. These fungi are friends mostly with pine trees. Often, deforested lands are planted with tree seeds, together with mycorrhizal fungi, which help seedlings get a good start in life. Some ectomycorrhizal fungi associated with trees form mushrooms, such as Boletus, Aminita, and truffles. All conifer trees have mycorrhizal associations.

Try This!

Take a walk in the forest and notice all the trees and mushrooms. Can you tell whether certain mushrooms are found near certain trees? Could the two have a symbiotic association?



Rhizobia (singular is rhizobium) are bacteria that form a symbiosis with the roots of certain plants called legumes. These bacteria are found elsewhere in the Zoo in Ag Acres.

Nitrogen Fixers Help Make Protein:

 Where does our protein come from? It comes from nitrogen in the air which microbes, such as rhizobia, help turn into protein. Rhizobia live in the roots of plants called legumes such as peas, clover and peanuts, where they convert nitrogen in the air into a form of nitrogen called ammonia that the plants can then turn into protein. Rhizobia can live independently in soil, or in a special association with plants called a symbiosis. When they live with plants, Rhizobia live in special root tissues called "nodules". When Rhizobia are in root nodules, they gain a special ability to help fertilize the plants. Rhizobia convert nitrogen in the air into a form of nitrogen that the plants can use. This conversion of nitrogen is called "nitrogen fixation." The protein from plants is then used by animals, including humans, that eat them.

This is a cartoon of rhizobium fixing nitrogen (N2) from the air into ammonia (NH3) a form of nitrogen that plants can use.


Try This!

Next time you are out in a field, carefully dig up a small clover and see if you can see nodules of Rhizobium on its roots. Find a field that does not get fertilizer to find the best nodules. (Why do suppose a fertilized plant would have no nodules?)



Many microbes live near the roots of plants.

 The thin layer of soil next to the roots of plants is called the rhizosphere. The rhizosphere contains many more microbes than in the surrounding soil. This is because plants "leak" nutrients into the soil, which the microbes can use.


Try This!

Carefully dig a plant out of the soil (a weed from your lawn?) and observe the soil that sticks to the roots. Inside these particles are millions of rhizosphere microbes.



(Click on a term to return to the text you were reading before)


Amino Acid- a molecule which is the building block of protein. Amino acids contain nitrogen as well as carbon, hydrogen and oxygen, the basic atoms of life. All organisms contain at least 20 different types of amino acids. Some bacteria are able to make all amino acids, unlike humans which cannot make about 8 amino acids for which they must rely on other organisms, like microbes and plants, to make for them. One type of amino acid, glutamate, is made by bacteria which humans then use to make the flavor enhancer, MSG -- monosodium glutamate.

Legume- a flowering plant which bears its seeds in pods. All legumes looked at so far have a symbiotic association with root-colonizing bacteria called rhizobia. Legumes includes plants such as clover, peas, beans. Legumes contain seeds, such as peas and beans, that are rich in protein.

Nodule -a special structure of roots of certain plants which contain the symbiotic, nitrogen fixing bacteria Rhizobium.

Nutrients- the necessary components of food that microbes and all life require to exist and grow. Essential elemental nutrients include such basic molecules as nitrogen, carbon, oxygen, hydrogen, phosphorus, potassium and trace minerals.

Protein- an important molecule that is found in all life. Proteins are polymers, that is, long strings of individual amino acids.

Sugars -a sweet tasting substance produced by many organisms which is used as an energy storage molecule.

Symbiosis - dissimilar organisms living together. A symbiosis is an ecological relationship between two or more different species living together in direct contact. There are several types of symbiotic relationships, including parasitism, in which one organism hurts the other; commensalism, in which one organism benefits without hurting the other; and mutualism, in which both partners gain from the association. In microbial ecology when the term symbiosis is used, unless stated otherwise, it refers to mutually beneficial relationships.