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:
	 
     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.