Soil microbiology

However “dead” soil may appear, it is in fact teeming with millions or billions of microbial cells per gram, depending upon soil fertility and the environment. Dead vegetation, human and animal wastes, and dead animals are deposited in or on soil. In time they all decompose into substances that contribute to soil, and microbes are largely responsible for these transformations.

Two great pioneer soil microbiologists were Martinus W. Beijerinck (1851–1931), a Dutchman, and Sergey N. Winogradsky (1856–1953), a Russian. These researchers isolated and identified new types of bacteria from soil, particularly autotrophic bacteria, that use inorganic chemicals as nutrients and as a source of energy. The relationship between legumes and bacteria in the nodules of legume roots was discovered by other scientists in 1888. The nodules contain large numbers of bacteria (Rhizobium) that are capable of fixing atmospheric nitrogen into compounds that can be used by plants.

The ecology of fertile soil consists of plant roots, animals such as rodents, insects, and worms, and a menagerie of microorganisms—viruses, bacteria, algae, fungi, and protozoa. The role of this microbial flora can be conveniently expressed in Earth’s natural cycles. In the nitrogen cycle, for example, microorganisms capture nitrogen gas from the atmosphere and convert it into a combined form of nitrogen that plants can use as a nutrient; the plant synthesizes organic nitrogen compounds that are consumed by humans and animals; the consumed nitrogen compounds eventually reach the soil; microorganisms complete the cycle by decomposing these compounds back to atmospheric nitrogen and simple inorganic molecules that can be used by plants. In similar cycles for other elements such as carbon, sulfur, and phosphorus, microbes play a role; this makes them essential to maintaining life on Earth.

Microbiology of water supplies, wastewater, and other aquatic environments

Long before the establishment of microbiology as a science, water was suspected of being a carrier of disease-producing organisms. But it was not until 1854, when an epidemic of cholera was proved to have had its origin in polluted water, that contaminated water was considered more seriously as a source of disease. Since that time there has been continuous research on the microbiology of public water supplies, including the development of laboratory procedures to determine whether the water is potable, or safe for human consumption. At the same time, purification procedures for these supplies have emerged.

A highly standardized and routine laboratory procedure to determine the potability of water is based upon detecting the presence or absence of the bacterium Escherichia coli. E. coli is a normal inhabitant of the intestinal tract of humans; its presence in water indicates that the water is polluted with intestinal wastes and may contain disease-producing organisms.

The principal operations employed in a municipal water-purification plant are sedimentation, filtration, and chlorination. Each of these operations removes or kills microorganisms, and the microbiological quality of the treated water is monitored at frequent intervals.

The used water supply of a community, commonly referred to as sewage, is microbiologically significant in two ways. First, sewage is a potential carrier of pathogenic microorganisms, so measures such as chlorination must be implemented to prevent these microbes from contaminating drinking-water supplies. Second, sewage-treatment plants purify water by exploiting the biochemical abilities of microbes to metabolize contaminants. Raw sewage is processed through large tanks, first for anaerobic degradation of complex substrates and later for aerobic oxidation of soluble products. This “activated sludge” treatment is dependent upon incubation conditions that favour the growth and metabolic activity of appropriate microorganisms.

Another aspect of the microbiology of water pertains to natural bodies of water such as ponds, lakes, rivers, and oceans. Aquatic microbes perform a host of biochemical transformations and are an essential component of the food chain in these environments. For example, the microbial flora of the sea comprises bacteria, algae, fungi, and protozoa. The microorganisms inhabiting aquatic environments are collectively referred to as plankton; phytoplankton refers to the photosynthetic microbes (primarily algae), whereas protozoa, and other small animals, are zooplankton. Phytoplankton is responsible for converting solar energy into chemical energy—the components of plankton cells that serve as food for higher aquatic life. The magnitude of this process can be appreciated by calculations indicating that it takes 1,000 tons of phytoplankton to support the growth of one ton of fish.

Large populations of archaea live in volcanic ridges 2,600 metres (8,500 feet) below the ocean surface in areas immediately surrounding hydrothermal vents (deep-sea hot springs). The vents spew superheated water (350 °C [662 °F]) that contains hydrogen sulfide (H₂S); the water surrounding the vents has a temperature range of 10–20 °C (50–68 °F). Many bacteria concentrate in this region because of the availability of H₂S, which they can use for energy. The abundance of animal life that also inhabits this region is completely dependent on the microbes for food.

There is a growing interest in other ecological aspects of aquatic microbiology, such as the role of microbes in global warming and oxygen production. Experimental approaches are being developed to study the complex biology and ecology of biofilms and microbial mats. These assemblages of microbes and their products, while potentially useful in several ways, are complex. In many instances the microbial flora involved must sometimes be studied in its natural environment because the environment cannot be reproduced in the laboratory.