Garden & Greenhouse


Soil Microorganisms – Friends and Foes

Posted August 10th, 2011 by Robin Nichols in ,

Most soils are teaming with microorganisms, sometimes referred to as microflora, their variety and population depending on:

  • climatic conditions (temperature and rainfall)
  • soil physical characteristics (texture, structure, cation exchange capacity, aeration)
  • soil fertility (pH, level of essential elements, organic matter content)
  • degree of human activity (land use, cultivation, crop rotation, liming, fertilization)
  • crop cover (specie, annual, perennial)

No one factor defines what microorganisms exist in terms of specie, population and level of activity. With

Close-up mid section of woman holding soil

Close-up mid section of woman holding soil

increasing temperature, the rate of microorganism activity also increases. As for any biological organism, its degree of activity is determined by the availability of an energy source (food) and its quantity, a source requirement that varies with specie. In addition, there exists both competitive and synergistic activity among microorganisms. Some microorganisms are “free-living” (autotrophic), able to provide their own food source while others (chemosynthetic) are dependent on available food sources provided by that added to the soil by human activity, and that derived from plant roots and other soil biological sources. Inoculating a soil with a single specie or mixture of microorganisms will have little or no affect on specie population and microorganism activity.

Soil microorganisms can be divided into various categories, one system being based on physical size (megafauna, macrofaune, mesofauna, microfauna) and another grouped by their biological characteristics, the main groupings being bacteria, acetinomycetes, and fungi.

Fungi play key roles in soil biological activity, some as decomposers of organic materials releasing plant nutrient elements (major elements and micronutrients) as ions into the soil solution. In many soils, nitrogen N and boron B primary exist in the soil organic matter, therefore unavailable for plant root absorption until organic matter decomposition occurs. Other decomposition products, such as amino acids, enzymes, and hormones have little effect on root growth and function since these large molecules can not be absorbed by the plant root. Their presence in a soil, however, does affect microorganism activity for those species requiring such substances for their own metabolism.

Soil microorganism types and populations are mostly determined by the plants growing in the rooting medium. With a diversity of plant species, many different microorganism types exist at moderate populations. In a mono-culture plant growing system, the variety of microorganism types decreases with their individual populations being high. Under such conditions, plant growth may be partially impaired. For example, with continuous corn culture grain yields are consistently 10% lower as compared to when corn is grown in rotation with other crop plants. Similar situations exist with other field crops, such a soybean, alfalfa, sorghum, etc. For the home gardener, growing the same plant specie in a fixed location in the garden will lead to reduced yield, with the possibility that some microorganism may reach populations that can be pathogenic. Varying types of plants in rotation support a more diverse range in microorganism species at moderate population levels compared to that when monoculture is practiced. A way to maintain a more diverse microorganism population in a monoculture system is to plant a cover crop between seasons that will be turned under prior to planting.

Microorganisms are strong competitors for most of the same nutrient elements required by plants. For example, adding an easily decomposable organic substance to a soil can create a nutrient element deficiency in a growing crop plant as microorganisms take in those elements needed for their own metabolism from the soil solution, depriving the growing plants. Appling a highly carbonaceous substance to a soil can create a N deficiency in a growing crop, particularly if that crop has a high N requirement and there is an insufficient quantity of ionic forms of nitrogen, either or both the nitrate anion and ammonium cation, in the soil solution.

Around the plant root exists a cylindrical zone known as the “rhizosphere” [the narrow region of soil that is directly influenced by root secretions and associated soil microorganisms (]. It is an active biochemical zone that has both enhancing and protective aspects. Substances absorbed by the root are taken from the rhizosphere, its bio-chemical characteristics quite different from the rooting media itself, normally more acidic and a zone within which various elemental interactions occur, both preventing as well as enhancing root elemental absorption. The formation and stability of the rhizosphere vary with root medium conditions and the characteristics of the plant root itself.

Within the rhizophere, there exists what are called “mycorrhiza” [is a symbiotic (generally mutualistic, but occasionally weakly pathogenic) associations between a fungus and the roots of a vascular plant (], unique fungi, having specific association with a plant specie. Mycorrhiza play a major role in the growth of many plant species, particularly woody-stem plants and trees. A common practice when planting tree seedlings is to treat the roots with a mycorrhiza organism in order to enhance survival and stimulate initial plant root growth, particularly when planting into a relatively infertile soil, or when the soil has less than desirable physical and chemical properties. With time, mycorrhiza fungi will continue to exist around the roots as they advance into the soil mass.

As stated earlier, the types and populations of microorganisms are mostly determined by the plants growing in the rooting medium, with some modification associated with the rooting medium’s physio-chemical properties. Therefore, the addition of a microorganism inoculant to the rooting media will not alter its microbial makeup and accompanying biological activity. In addition, the function and activity of microorganisms are the result of competitive activities, with numbers and types of microorganisms being determined by survival criteria. For rooting media that is relatively sterile, such as a freshly prepared organic soilless mix, inoculation with a particular microorganism, or group of microorganisms can be beneficial to the plant to be rooted into that medium. Since all microorganisms require an energy source to survive and grow, that energy source must be present in the rooting media. With time, that energy source may be provided by the roots of the growing plant, thereby supporting those mcroorganisms that correlate with that plant specie. Without an energy source, inoculant microorganisms will not survive. Therefore, the bio-chemical properties of both the rooting medium and plant roots become major factors influencing microorganism population and activity.

Soil inoculants may consist of a single organism or a mix of organisms, being either or both bacteria and fungi.  Many inoculates contain organisms that commonly exist in soils and other types of rooting media. If the rooting medium has an existing stable biological character, inoculate microorganisms will not change what already exists, and may not be able to survive or compete with those microorganisms already present.

Microorganisms, such a Phytium, Fusarium, Aphanomyces, Verticillium, are commonly occurring root diseases, attacking plant roots in order to meet their energy needs. Some root disease microorganism thrive under anaerobic conditions and frequently are competitive under less than optimum temperatures than those that are non-pathogenic. Many of these root disease microorganisms are present in the soil at less than pathogenic populations, but increase in population when conditions occur that favor their biology. Many root disease organism can be controlled by altering cultural practices that would support a diverse microbial character in the rooting medium.

Microorganisms can be your friend or foe depending on how a rooting medium is managed; therefore, the need to know what procedures will keep a diverse and moderate populations of microflora functioning that contributes to successful plant production. No need to attempt to modify the microflora by the use of inoculants – let Mother Nature do it for you by being good stewards in your cultural practices.

J. Benton Jones, Jr. has a PhD in Agronomy and is the author of several books including Hydropopnic Handbook: How  Growing Systems Work available on Dr. Jones has written extensively on hydroponic growing and has been outdoor vegetable gardening employing sub-irrigation hydroponic growing systems (see:, and using domestic water for making his nutrient solution.

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