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Chapter: Essential Microbiology: Microorganisms in the Environment

Microbiology of soil

In the following section it will be necessary to generalise, and treat soil as a homogeneous medium.

The microbiology of soil


In the following section it will be necessary to generalise, and treat soil as a homogeneous medium. In fact, it is no such thing; its precise make-up is dependent upon the un-derlying geology, and the climatic conditions both past and present. In addition, the microbial population of a soil will vary according to the amount of available wa-ter and organic matter, and different organisms colonise different strata in the soil.


The organic content of a soil derives from the re-mains of dead plants and animals. These are broken down in the soil by a combination of invertebrates and microorganisms (mainly bacteria and fungi) known as the decomposers. Their action results in the release of substances that can be used by plants and by other mi-croorganisms. Much organic material is easily degraded, while the more resistant fraction is referred to as hu-mus, and comprises lignin together with various othermacromolecules. The humus content of a soil, then, is a reflection of how favourable (or otherwise) conditions are for its decomposition; the value usually falls between 2 and 10 per cent by weight. The inorganic fraction of a soil derives from the weathering of minerals. Microorganisms may be present in soils in huge numbers, mostly attached to soil particles. Their numbers vary according to the availability of suitable nutrients. Bacteria (notably actinomycetes) form the largest fraction of the microbial population, together with much smaller numbers of fungi, algae and protozoans. Published values of bacterial numbers range from overestimates (those that do not distinguish between living and dead cells) and underestimates (those that depend on colony counts and therefore exclude those organisms we are not yet able to grow in the laboratory – 99 per cent according to some experts!). Suffice to say that many millions (possibly billions) of bacteria may be present in a single gram of topsoil. In spite of being present in such enormous numbers, microorganisms only represent a minute percentage of the volume of most soils. Fungi, although present in much smaller numbers than bacteria, form a higher proportion of the soil biomass, due to their greater size. The majority of soil microorganisms are aerobic heterotrophs, involved in the decomposition of organic substrates; thus, microbial numbers diminish greatly the further down into the soil we go, away from organic matter and oxygen. The proportion of anaerobes increases with depth, but unless the soil is waterlogged, they are unlikely to predominate.


Other factors affecting microbial distribution include pH, temperature, and mois-ture. Broadly speaking, neutral conditions favour bacteria, while fungi flourish in mildly acidic conditions (down to about pH 4), although extremophiles survive well outside these limits. Actinomycetes favour slightly alkaline conditions. Bacterial forms occur-ring commonly in soils include Pseudomonas, Bacillus, Clostridium, Nitrobacter and the nitrogen-fixing Rhizobium and Azotobacter, as well as cyanobacteria such as Nostoc and Anabaena. Commonly found actinomycetes include Streptomyces and Nocardia. As we have noted elsewhere, actinomycetes are notable for their secretion of antimicro-bial compounds into their surroundings. This provides an example of how the presence of one type of microorganism in a soil population can influence the growth of oth-ers, forming a dynamic, interactive ecosystem. In addition, bacteria may serve as prey for predatory protozoans, and secondary colonisers may depend on a supply of nutri-ents from, for example, cellulose degraders. Important fungal genera common in soil include the familiar Penicillium and Aspergillus; these not only recycle nutrients by breaking down organic material, but also contribute to the fabric of the soil, by bind-ing together microscopic soil particles. Soil protozoans are mostly predators that ingest bacteria or protists such as yeasts or unicellular algae. All the major forms of proto-zoans may be present (flagellates, ciliates and amoebas), moving around the water-lined spaces between soil particles. Algae are of course phototrophic, and are therefore to be found mostly near the soil surface, although it will be recalled  that some forms are capable of heterotrophic growth, and may thus survive further down.

The surface of soil particles is a good natural habitat for the development of biofilms, complex structures comprising microbial cells held together in a polysaccharide matrix. The microorganisms themselves produce the polysaccharide, which also allows the pas-sage of nutrients from the environment. Biofilms can form on almost any surface, and are often to be found in rapidly flowing waters. Biofilms may be beneficial (e.g. wastewater treatment – see below) or harmful (e.g. infections resulting from growth in catheters) to humans.


Although we have emphasised the importance of organic matter in soil ecosystems, microorganisms may also be found growing on or even within rocks. The growth of such organisms, together with the action of wind and rainfall, contribute to the weathering of rocks.


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