Organic materials contained within the solid phase, although only a small percentage of the total soil weight, are extremely important in controlling chemical and physical processes in soil. Organic matter exists in the form of recognizable molecules such as proteins and organic acids, and in large polymers called humic materials or humus. Humus is dominated by acidic functional groups (?OH and ?COOH) capable of developing a negative charge and contributing substantial [Only registered users see links. ]. These large polymers possess a three-dimensional conformation that creates hydrophobic regions important in retaining nonionic synthetic organic compounds such as pesticides. Nonionic pesticides partition into these hydrophobic regions, thereby decreasing off-site movement and biological availability (see Figure 1).
A wide variety of organisms live in soil, including microorganisms not visible to the naked eye such as bacteria, fungi, protozoa, some algae, and viruses. Bacteria are present in the largest numbers, but fungi produce more biomass per unit weight of soil than any other group of microorganisms. Much of agricultural chemistry as it relates to nutrient cycles, pesticide transformation, plant growth, and organic matter degradation involves the participation of microorganisms. Microorganisms produce both intracellular and extracellular enzymes that increase reaction rates, oxidize and reduce organic and inorganic compounds, and synthesize organic molecules that modify soil chemical and physical properties.
Additional organisms in soil such as insects, nematodes, and earthworms also alter the soil ecosystem in a manner that directly or indirectly affects chemical reactions. These organisms physically process plant-derived organic materials prior to biochemical degradation by microorganisms. Nutrient release from organic materials is thus accelerated because the meso- and macrofauna expose more organic matter surface area to microbial breakdown and redistribute such materials in soil to areas of intense microbial activity.