Physiology and Biochemistry of Organisms in Soil

After reading this article you will learn about the physiology and biochemistry of organisms present in soil.

Soils are nature’s integrators; they form on the surface of the earth where the cycles of matter and the transfer of energy all meet. Soils interact reciprocally with the biosphere, hydrosphere, lithosphere and atmosphere (Fig. 18.46)

Only in soils do all four fundamental spheres interact. Such interactions entail biological, chemical, biochemical, and physical transformations and biological and physical translocations. Soil organisms and especially soil micro-organisms are intimately involved in biological and biochemical transformations. They are both sinks for elements and catalysts to speed transformations of elements.

Hence physiology and biochemistry of soil organisms is fundamentally important to understanding earth systems. Such a myriad or interactions may appear chaotic, random, or complex beyond understanding. Three groups of cycles are useful – geochemical cycles, biogeochemical cycles, and biochemical cycles.

Biogeochemical cycles relate to mesoscales, typically exchange materials within ecosystems, are dominant in soil landscapes, and are represented by element cycles such as the N cycle. Biochemical cycles operate within individuals or single cells, come close to the micro scale, and dominate within soil profiles or aggregates and can be represented by the tricarboxylic acid cycle (TCA cycle).

How can organisms, their physiology, and their functions be organized? Criteria with which to classify soil microorganisms include size, morphology, molecular genetics or physiology, and metabolism. A metabolic classification based on source of energy, electrons, and C has practical value (Tables 18.9 and 18.10). Phototrophs use light as an energy source; contrast, chemotrophs use chemical forms of energy.

These fundamental groups may be subdivided into organotrophs, for which the electron source is organic; lithotrophs, for which the electron source is inorganic; or aquatrophs, for which it is water. Organisms that use an organic form of C are referred to as heterotrophs; those that use CO₂ as C source are called autotrophs.

Most heterotrophs are chemoorganotrophs (e.g. Pseudomonas spp., but some such as Rhodospirillaceae are chemophototrophs). Most autotrophs are chemolithotrophs or photolithotrophs. Some such as the H₂-oxidizing bacteria (6H₂ + CO₂ + 2O₂→ CH₂O + 5 H₂O), are facultative chemolithotrophs capable of growing on carbohydrates under aerobic conditions.