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
"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
The ways some of the soil microorganisms
assist the plants in their physiology are addressed in
"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.
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
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
"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
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.