Understanding Microbial Activity in Plant Rooting Media

By J. Benton Jones Jr
Published: August 22, 2018 | Last updated: December 7, 2021 10:26:58
Key Takeaways

Microbial activity involving bacteria and fungi in a rooting medium, whether it is soil or a soilless organic mix, has important implications on plant growth.

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Microbial activity requires three things to be present: microbes such as bacteria and fungi, a suitable energy (food) source and sufficient essential plant nutrient elements, particularly nitrogen. In addition, pH, temperature, moisture content and level of aeration will determine the degree of microbial activity.


These physiochemical factors will determine which micro-organisms will exist and at what levels. In the following examples, it is assumed that the above-listed parameters are optimal for active microbial activity.

The one exception might be pH, which can affect the level of either bacterial or fungal activity, with acidic conditions favoring bacteria and neutral to alkaline conditions favoring fungal activity.


One can take a moderately fertile rooting medium and add a carbohydrate substrate, such as molasses, and the evolving CO2 created by microbial activity will last until either the added substrate is totally consumed, or one of the essential plant nutrient elements becomes insufficient. At that point, microbial activity will subside, or may even totally cease.

Nitrogen-deficient rooting media

In a nitrogen-deficient rooting media, following the addition of a carbohydrate substrate, there will be little stimulus in microbial activity until nitrogen is added, ideally in an easily available form, such as ammonium nitrate. Depending on the amount of nitrogen added, the level of microbial activity will continue until either the energy source is depleted or nitrogen is used up.

Repeat the above experiment, replacing the mineral nitrogen source with an organic nitrogen source at the same total nitrogen application rate, and there will be little microbial activity as microbes require a soluble nitrogen source to function. It could be that even over an extended period of time, the organic nitrogen-containing substance may not be easily decomposed since the level of microbial activity is low due to nitrogen deficiency.


However, if there is some mineral form of nitrogen in the organic substance, microbial activity will occur, and depending on the level of activity, decomposition of the organic substance will begin to occur, the extent depending on the quantity of the energy source and available nitrogen.

Such studies need to be conducted to determine what level of microbial activity does occur if the source of an essential plant nutrient element, particularly nitrogen, is as an organic form. In addition, the level of microbial activity in a rooting medium is determined by the available energy supply necessary for the micro-organisms to function and multiply.


When plants are being grown in a rooting medium, the root itself can be the source for energy substances, which then gives rise to what is referred to as the rhizosphere, a narrow cylindrical zone around the plant root where there exists an active microbial population. This is not the case in the whole soil, which might be essentially sterile by comparison because of the lack of an energy source.

Adding a composted material to the soil will not stimulate increased microbial activity since composts are the end product of microbial decomposition devoid of substances that would serve as an energy source.

Inoculating a rooting medium with either bacteria or fungi, or a mixture of both, will not create microbial activity, unless the rooting medium contains an energy source. There is also what is known as an intensity factor that needs to be taken into consideration when adding compost, energy source or inoculum to a rooting medium in terms of what already exists and what is being added, for it is the intensity added that determines the effect.

All micro-organisms in a rooting medium are competing for the same essential nutrient elements as the plant, so their active presence can result in a plant nutrient element deficiency. A good illustrative example is what can happen when wheat straw is plowed under followed by the planting of corn with a high nitrogen requirement.

The wheat straw becomes an energy source for soil micro-organisms, which will then absorb much, if not all, of the available nitrogen from the soil, leaving little for the emerging corn plants. The result can be a severe nitrogen deficiency. Therefore, farmers are advised to add a fertilizer source of nitrogen, sufficient to provide adequate nitrogen for both the corn plants and micro-organisms.

Microbial species found in a rooting medium are primarily determined by the plant species growing in the rooting medium, since it is the organic substances sloughed off plant roots that are the primary energy source.

Populations will be significantly affected by whether the growing system is a monoculture or a mix of plant species growing together or being rotated. In the monoculture of field crops, such as corn, soybeans and wheat, there will be few microbial species existing at fairly high populations, while in a rotational culture system, there will be a wide range of microbial species in relatively low populations.

In a monoculture growing system, microbial activity can be potentially pathogenic to the growing plants. It is recommended that plants be grown in rotation, whether in the field or in the home garden. Farmers attempting to re-establish an alfalfa stand by reseeding into an already existing alfalfa field will not be successful since existing microbes in the soil will be pathogenic to the newly germinating seedlings.

Microbial activity in a rooting medium is determined by a complexity of interacting factors. The results from the addition of a compost, energy-type substance and bacteria-fungi inoculum, whether singularly or in combination, will not always give consistent results without considering those factors that determine what can occur—both beneficial and detrimental.

Trying to manipulate microbial populations and their activity can be ineffective in terms of changing the fertility status of a rooting medium when applying an organic-bound plant nutrient element source to sustain plant growth when meeting the requirement for an organically-grown designation.

Let’s Talk Organic

After conversing with a gardener wanting to grow organically awhile ago, it became evident to me that any gardener who wishes to grow organically needs to have some degree of understanding of soil microbiology and the biochemical characteristics of those organic sources selected for supplying the essential plant nutrient elements. Without either, it would be difficult to make those determinations essential for success.

Many believe the soil is a cauldron of microbiological activity. However, soil tends to be essentially sterile, with the area around plant roots known as the rhizosphere being the place where there is active microbiological activity.

If one wishes to stimulate active microbiological activity in the whole soil, one ought to turn under a cover crop, sometimes referred to as a green manure crop, and the micro-organisms around the plant roots will use the turned under fresh plant vegetative material as an energy (food) source to multiply and function. However, when the food-energy source is exhausted, the micro-organisms will die and the soil will become relatively sterile again.

The bio-degradability of added organic materials for supplying essential plant nutrient elements is essential information since some sources may be quite stable and therefore will remain in the soil intact for long periods of time.

Adding a food-energy source for those micro-organisms present in the soil might be of limited benefit in terms of their ability to stimulate decomposing of other organic substances that have been added to the soil. It is fresh organic materials, such as un-composted animal manure and fresh plant debris—not dead plant tissue or composts—that will provide the food-energy source needed by soil micro-organisms to function.

Any composted material will not stimulate microbiological activity as all of the food-energy materials will have been exhausted in the composting process. Adding micro-organisms to the soil will be of no benefit if there isn’t a food energy source available for them in order to survive and function.

That may mean adding the organisms plus a food energy source, hoping that the combination fits the requirements. In addition, whatever microbiological activity that occurs may be with the added food energy source and not involving other organic substances in the soil. In addition, the microbiological activity may be competitive, thereby reducing plant growth for lack of sufficient essential plant nutrient elements that are being used by the micro-organisms.

It is not uncommon for plants to be nitrogen deficient when there is active microbiological activity in the rooting medium—the degree of deficiency related to the available nitrogen supply within the rooting medium.

A colleague and I once worked for more than two years trying to grow greenhouse tomatoes organically, searching for organic sources of the essential plant nutrient elements that would provide what was needed to promote sustained plant growth and fruit yield. We were unable to find an organic material as a source for nitrogen that would supply that level of required nitrogen necessary to sustain plant growth and fruit yield. We abandoned the project.

For those growing plants hydroponically, adding an organic substance to the nutrient solution is an open invitation for the potential occurrence of root disease occurrence. Anyone who has dealt with the root disease phythium can attest to its occurrence being ushered in when there is an accumulation of organic substances in the applied nutrient solution.

For the grower reusing a nutrient solution, removing the suspended organic materials by filtering, followed by sterilization, are essential steps to prevent phythium invasion. So, adding back an organic substance might defeat the filtering and sterilization steps, opening the nutrient solution to disease.

Those who see the advantage in having some level of organic substances, such as humic acid and other similar substances, in the rooting medium would expect to find that best plant growth should occur with the use of a soilless organic rooting medium that contains peat moss, or other similar substances or composts, as these materials are good sources for humic acid and similar compounds.

There is no evidence that plant growth is enhanced when using such a rooting medium as compared to other media. So, the question is, why would the inclusion of humic acid or other similar substances added to a rooting medium enhance plant growth when, occurring naturally, it doesn’t enhance plant growth?

For the organic grower, there is much that needs to be known about the rooting medium selected and the bio-chemical characteristics of substances being recommended, pertaining to their potential benefit to plant growth.

For the soil grower, knowledge of the biological physio-chemical characteristics of the soil needs to be present so that when additions are made, whether organic or inorganic, one can anticipate the effects on plant growth, either beneficial, of no effect or detrimental. Presently, much of the talk about organics is more speculation than fact.


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Written by J. Benton Jones Jr

Profile Picture of J. Benton Jones Jr
Dr. J. Benton Jones, Jr. has 50 years of experience growing plants hydroponically. He is an Emeritus Professor at the University of Georgia, Athens, and has authored eight books and written articles for magazines that deal with hydroponic issues. He currently has his own consulting company, Grosystems, Inc. Dr. Jones lives in Anderson, South Carolina.

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