B.03.00: Introduction to Soil Microorganisms

There are billions to hundreds of billions of soil microorganisms in a mere handful of a typical, garden soil. That single handful might well contain thousands of different species of bacteria (most of whom have yet to be classified), hundreds of different species of fungi and protozoa, dozens of different species of nematodes plus a goodly assortment of various mites and other microarthropods. Almost all of these countless soil organisms are not only beneficial, but essential to the life giving properties of soil.

The work of these soil microorganisms is exceedingly complex and extends into nearly every section of this FAQ. The ways the soil bacteria and fungi break down plant and animals residues and wastes are addressed in Section C, "Composting & Use of Compost". The ways the soil bacteria and fungi breakdown and then convert materials into plant nutrients as well as the ways the soil bacteria, fungi, and amoeba hold these nutrients in place and then make them available to the plants are addressed in Section D, "Plant Nutrition". The ways some of the soil microorganisms assist the plants in their physiology are addressed in Section F, "Botany for the Home Gardener". The ways some of the soil bacteria and SOME of the fungi both cause and control plant disease are addressed in Section G, "Plant & Soil Disease; Treatment and Prevention" and the ways some of the nematodes, some of the soil insects, and some of the various micro-arthropods such as mites attack and/or protect plants are addressed in Section H, "Plant & Soil Pests; Prevention and Treatment". This sub-section is limited to the ways the soil microorganisms impact on the physical, chemical, and bio-chemical properties of soil.

B.03.01: What do soil microorganisms do for the physical, chemical, and/or bio-chemical properties of soil?

Soil microorganisms breakdown a variety of organic materials and use a portion of these breakdown products to generate or synthesize a series of compounds that make up humus. See http://.rain.org/~sals/Petrik.html. The three major fractions of humus are humic substances, poly-saccharides and other non-humic substances, and humin. These materials impact on the physical, chemical and bio-chemical properties of soil in many important ways; See
B.03.04 regarding humic substances,
B.03.06 regarding humin, and
B.03.09 regarding polysaccharides.

In addition to producing humus, the soil microorganisms breakdown and/or bind a variety of organic and inorganic materials to clean up corrupted or polluted soils - petroleum products, synthetic pesticides, and heavy metals included. See B.03.10 regarding soil cleanup using bio-remediation.

B.03.02: What is humus?

The various soil organisms breakdown both organic and mineral materials in the soil partly by enzymatic action and partly by taking the materials in as nutrients and metabolizing them further. Most of the breakdown products are used by the plants as nutrients or are lost into the soil environment. A small portion of these breakdown products, however, perhaps 5% or so, becomes resistant to further decomposition and become more or less stabilized. Humus is that remaining, more or less homogenous mix of more or less stable material.

"Detritus" is the proper term for the recognizable debris from dead plants and animals. Humus is the dark colored, sweet smelling, goo. Humus is often called, "Black Gold" because of its great value to plants, soil, and the soil microorganisms.

B.03.03: What are humic substances?

The initial breakdown of organic and mineral materials by the soil microorganisms produces mostly simple chemical compounds. When the conditions are aerobic, most of these chemical compounds exist in the oxidized state. Humus, the remaining and more or less stable material, goes through a process in which the small 'bits and pieces' join together to form complex, chained structures called "polymers". Chemically, they are poly-phenolic acids. The synthesis or making of these polymers is partly the result of the enzymes from the soil microorganisms and partly the result of soil chemistry.

"Humic, Fulvic, and Microbial Balance: Organic Soil Conditioning" by William R. Jackson says, "During humification, all cellular makeup undergoes a pattern of transformations, modifications, and structural re-arrangements, resulting in highly complex polymeric humic compounds. Although some of these modifications are chemical, most are bio-chemical and develop through the enormous numbers of enzymes released by the microorganism population".

The relatively small and simple polymers, specifically those humic substances with a small molecular weight, are known as fulvic acids. The relatively large and complex polymers, specifically those humic materials with a high molecular weight, are known as humic acids. It is believed that fulvic acids become humic acids with more polymerization and that humic acids become humin with even more polymerization. Humic substances include fulvic acids, humic acids, the salts of both fulvic and humic acids, and humin.

B.03.04: What do humic substances do for the soil?

Humic substances perform at least five critical functions:
  1. They INCREASE ADSORPTION OF MINERALS and bring into solution mineral materials that would otherwise be inert and convert them into forms that can be taken up by the plants as nutrients;
  2. They INCREASE ADSORPTION OF ORGANIC COMPOUNDS which aids in plant nutrition, plant physiology, and in the cleanup of polluting or toxic materials in the soil;
  3. They INCREASE THE WATER HOLDING CAPACITIES OF THE SOIL which makes water more available to the plants for greater plant production;
  4. They INCREASE THE SOIL'S BUFFERING CAPACITY helping to stabilize the soil's pH to help the plants to take up mineral nutrients; and
  5. They DARKEN THE SOIL COLOR which increases the soil's adsorption of solar energy.
Fulvic acids are more chemically reactive than humic acids and are mostly involved in the chemical reactions that influence plant's growth and nutrition while the humic acids are mostly involved in altering the physical characteristics of the soil.

B.03.05: What is Leonardite and how is it used?

Leonardite is a mined product that can contain as much as 85%, by weight, humic substances dependent upon the source and the processing. Leonardite contains both humic and fulvic acids. It is processed and sold as a combination fertilizer, soil amendment, and biological stimulant. It can either be applied directly to the soil or used as a foliar spray. The rate of application is critical. More is not better and overapplication can tie-up soil nutrients reducing their availability to the plants.
See: www.humic.com
See: humatech-inc.com

B.03.06: What is humin?

Humin is a highly polymerized, highly condensed humic substance. It is an extremely stable material with a half- life that can extend into centuries. Humin is insoluble in both acid and alkali and it is also highly resistant to microbial attack.

B.03.07: What does humin do for the soil?

"The Nature and Properties of Soils" by Brady and Weil says, "Certain clays are known to attract and hold substances such as amino acids, peptides, and proteins, forming complexes that protect the nitrogen-containing compounds from microbial degradation". Apparently, humin is involved in this process but the mechanics are not clear.

B.03.08: What are soil polysaccharides?

Polysaccharides are non-humic polymers that have sugar like structures. About 25% of the humus in the soil is in this form. These substances are less complex and less resistant to microbial attack than the materials of the humic group.

B.03.09: What do soil polysaccharides do for the soil?

Soil polysaccharides help to stabilize soil aggregates and contribute to soil tilth. The acrylic polymers that are marketed as "water holding", soil amendments essentially try to emulate the work of the soil polysaccharides.

B.03.10: How do I clean polluted soil?

Problem materials such as: most synthetic pesticides and herbicides, petroleum products, organic toxins, heavy metals, and polyvalent metals such as lead, copper, zinc, etc. are subject to oxidation and once oxidized are increasingly vulnerable to attack by soil microorganisms. Fulvic acid, the most chemically reactive of the soil humates, is strongly surface active and it also an effective oxidizing agent.

Fulvic acid working in concert with the soil microorganism can bio-degrade most problem materials. Adding an abundance of organic material to the soil will elevate the levels of fulvic acid and it will also build larger and more active populations of soil microorganisms. In time, the combination will clean up most problem materials. Because, it is seldom self-evident as to when the problem materials have been degraded, it would be a good idea to have the soil tested before counting it as safe.

B.03.11: Is soil testing really necessary?

Even soils that have had the advantages of crop rotation, cover crops, ample feedings of manures or composts do not have immunity from mineral deficiencies and particularly deficiencies relative to trace elements. If the materials that are used to feed the soil are deficient in some mineral, the deficience will show up in the soil. These problems will show up in soil testing.

Problem areas in the garden where things just don't grow well may be the result of pH or toxic levels of metals. Soil testing, if done properly, should identify these problems as well.

One of the problems with soil testing is that the results are usually given strictly in terms mineral content and the recommended corrections assume the sole use of synthetic materials. The organic content, including the humic substance content, is critical to the fertility and function of the soil and this is largely ignored.

Dr. Elaine Ingham, Department of Botany and Plant Pathology, at Oregon State University tests soils for soil micro-organism populations. She measures the bio-diversity and the vigor of the microbe communities which is probably even more important. Her address is Cordley Hall 2082, Oregon State University, Corvallis, OR 97331-2902. The costs for this testing is said to be just a few dollars.