Soil microbiology

(microbiology) A study of the microorganisms in soil, their functions, and the effect of their activities on the character of the soil and the growth and health of plant life.

The study of biota that inhabit the soil and the processes that they mediate. The soil is a complex environment colonized by an immense diversity of microorganisms. Soil microbiology focuses on the soil viruses, bacteria, actinomycetes, fungi, and protozoa, but it has traditionally also included investigations of the soil animals such as the nematodes, mites, and other microarthropods. These organisms, collectively referred to as the soil biota, function in a belowground ecosystem based on plant roots and litter as food sources. Modern soil microbiology represents an integration of microbiology with the concepts of soil science, chemistry, and ecology to understand the functions of microorganisms in the soil environment.

The surface layers of soil contain the highest numbers and variety of microorganisms, because these layers receive the largest amounts of potential food sources from plants and animals. The soil biota form a belowground system based on the energy and nutrients that they receive from the decomposition of plant and animal tissues. The primary decomposers are the bacteria and fungi.

Microorganisms, especially algae and lichen, are pioneering colonizers of barren rock surfaces. Colonization by these organisms begins the process of soil formation necessary for the growth of higher plants. After plants have been established, decomposition by microorganisms recycles the energy, carbon, and nutrients in dead plant and animal tissues into forms usable by plants. Therefore, microorganisms have a key role in the processing of materials that maintain life on the Earth. The transformations of elements between forms are described conceptually as the elemental cycles.

In the carbon cycle, microorganisms transform plant and animal residues into carbon dioxide and the soil organic matter known as humus. Humus improves the water-holding capacity of soil, supplies plant nutrients, and contributes to soil aggregation. Microorganisms may also directly affect soil aggregation. The extent of soil aggregation determines the workability or tilth of the soil. A soil with good tilth is suitable for plant growth because it is permeable to water, air, and roots. See also Humus.

Soil microorganisms play key roles in the nitrogen cycle. The atmosphere is approximately 80% nitrogen gas (N₂), a form of nitrogen that is available to plants only when it is transformed to ammonia (NH₃) by either soil bacteria (N₂ fixation) or by humans (manufacture of fertilizers). Soil bacteria also mediate denitrification, which returns nitrogen to the atmosphere by transforming NO₃⁻ to N₂ or nitrous oxide (N₂O) gas. Microorganisms are crucial to the cycling of sulfur, phosphorus, iron, and many micronutrient trace elements.

In addition to the elemental cycles, there are several interactions between plants and microbes which are detrimental or beneficial to plant growth. Some soil microorganisms are pathogenic to plants and cause plant diseases such as root rots and wilts. Many plants form symbiotic relationships with fungi called mycorrhizae (literally fungus-root). Mycorrhizae increase the ability of plants to take up nutrients and water. The region of soil surrounding plant roots, the rhizosphere, may contain beneficial microorganisms which protect the plant root from pathogens or supply stimulating growth factors. The interactions between plant roots and soil microorganisms is an area of active research in soil microbiology. See also Biogeochemistry; Mycorrhizae; Nitrogen cycle; Nitrogen fixation; Nitrogen oxides; Rhizosphere.

The incredible diversity of soil microorganisms is a vast reserve of potentially useful organisms. Many of the medically important antibiotics are produced by filamentous bacteria known as actinomycetes. The soil is the largest reservoir of these medically important microorganisms. See also Antibiotic.

The numerous natural substances that are used by microorganisms indicate that soil microorganisms have diverse mechanisms for degrading a variety of compounds. Human activity has polluted the environment with a wide variety of synthetic or processed compounds. Many of these hazardous or toxic substances can be degraded by soil microorganisms. This is the basis for the treatment of contaminated soils by bioremediation, the use of microorganisms or microbial processes to detoxify and degrade environmental contaminants. Soil microbiologists study the microorganisms, the metabolic pathways, and the controlling environmental conditions that can be used to eliminate pollutants from the soil environment. See also Hazardous waste.

Microbiologists traditionally isolate pure strains of microorganisms by using culture methods. Methods that do not rely on culturing microorganisms include microscopic observation and biochemical or genetic analysis of specific cell constituents. The rates or controlling factors for microbial processes are studied by using methods from chemistry, biology, and ecology. Typically, these studies involve measuring the rate of production and consumption of a compound of interest. The results of these studies are commonly analyzed by using mathematical models. Models allow the information from one system to be generalized for different environmental conditions. See also Fluorescence microscope; Immunofluorescence; Microbiology; Molecular biology; Soil; Soil chemistry; Soil ecology.