The Science of Soil: Microbial Environments

 Soil is a suitable environment for vast amounts of microbes. Just one gram of soil may be home to 10 million to 10 billion bacteria.(Atlas, 367) This bacterial population consists of chemolithotrophic species and photoautotrophic species of cyanobacteria. Other microbes living in the soil are viruses, fungi, algae, and protozoa. According to Atlas(see below), there are autochthonous microorganism populations which have developed in soil habitats while others are allochthonous microorganisms which enter the soil habitat by means of animals and plants, and do not stay or take up the habitat as their own. For example, some species of fungi, especially yeasts, are presumed to be autochthonous because they have been found solely in the soil. Fungi, as natural inhabitants or as foreign bodies, take up a large amount of the biomass in the soil.

Microbes that live in soil are drawn to the soil environment because it is a source of abundant nutrients. Some are better equipped to survive in specific soil habitats, which are numerous and very different according to climate and acidity. Water is a determining factor because wet soil is limited in air supply, making it a poor environment for aerobic microorganisms. On the other hand, a dry soil environment is not suitable for many microorganisms unless they are equipped with endospores or cysts that keep them from drying out during droughts until it rains. Bacteria such as those of the genus Bacillus are an example of those that can form endospores.   

Areas of soil that are more acidic are more favorable for fungi because they thrive on such an environment, while they can also take advantage of the availability of more nutrients at their disposal due to the loss of bacteria which do not survive in acidic environments.

 Since organisms need organic molecules, and the top layers of soil contain plant and animal wastes which form organic material known as humus, microbes will naturally be drawn to such an environment and colonize. This is especially so in the areas of plant root growth known as the rhizosphere. Because root cells produce organic molecules, they are favorable targets for microbial colonies. Such microbes are beneficial to the soil because they act as agents to break down the organic matter and recycle it. Without microbes, plant and animal wastes would not be broken down into the humic material which is a major component of the soil. Microbes are necessary in the decomposition of the organic polymers into monomers such as amino-acids, sugars, quinones, and phenols. Microbial enzymes are also involved in polymerizing these monomers. Cellulose and lignin are among the plant polymers that are recycled by microbes, which are presumed to be the basis of humic material.(Atlas, 374)

Soil varies according to the type of rock it originates from, climate, location, biological activity, and time(Atlas, 362). It is studied as different layers or horizons – topsoil or the A horizon, subsoil or the B horizon, the C horizon or a layer of weathered bedrock, and the R horizon which is the lowest layer consisting of undisturbed bedrock(Nester, 766). The topsoil is rich in nutrients due to the accumulation of animal and plant matter that is being decomposed into humic material. This topmost layer of animal and plant matter can be recognized as is, while the second sub-layer can only be recognized as organic substances. Some call these topsoil layers the organic horizon. In this case the A horizon consists of a larger section of mineral soil that is mixed with the upper organic substances, and a similar section of mineral soil in which silicate clays, iron oxides and aluminum oxides are being leached. These substances collect deeper in the soil in what is known as the B horizon. Microbial activity is mostly limited to this depth.

Besides the differences in depth, the texture of soil is also a determining factor in the diversity of microbial life that will exist in a soil habitat. Microbes need enough surface area to grow in soil, which is determined by the ratio of clay, silt and sand in a given soil habitat. Clay particles are smaller than sand particles, and therefore can provide greater surface areas.

Soil atmospheres are also different among soils; some supply oxygen while others are filled with water, making them suitable for anaerobic microbes. The metabolic processes that can take place in the soil depend heavily on the amount of oxygen that is available in the soil atmosphere.

A troubling issue in agriculture that weakens productivity is soil erosion. Some agriculturalists use methods of food production that reduce the damaging effects of commercial farming. An increasingly favored practice is the use of cover crops to ensure sustainable growth. Crops such as rye, oats, and legumes are used for nitrogen fixation which is necessary for the growth of the desired crop. These cover crops reduce soil erosion by increasing topsoil residue. The residue can aid in incorporating rainwater into soils to add moisture and can also provide shelter against radiation. Rye is an adequate cover crop because it survives in the winter and protects the soil from the cold while maintaining a supply of nitrogen, which attract microbes to the soil. While most plants have a high C/N ratio, cover crops such as legumes have a C/N ratio as low as 10 and can easily decompose.(Lu, 124) Such planting rejuvenates the soil and keeps it ready for subsequent seasons.

 Recent studies have shown that bacteria from the soil have developed resistance to antibiotics. Experiments have shown that they can actually feed on antibiotics and grow rapidly among them. According to Dr. Galtum Dontez, hundreds of soil bacteria may be living on antibiotics which used to compete with them for their habitats.(NPR, 2008) Furthermore, bacteria can pass on these resistant genes through horizontal gene transfer to rapidly produce multi-resistant bacteria.(Amábile-Cuevas,138) This is likely to have harmful consequences for human life because some bacteria in the soil are related to human and other animal germs.   

References

Amabile-Cuevas, C. F. New Antibiotics and New Resistance, American Scientist 2003; 91 (2): 138-149.

Atlas, R. M., Bartha, R. Microbial Ecology: Fundamentals and Application. Menlo Park (CA): Addison Wesley Longman, Inc.; 1998. 694 p.

Lu, Y. Cover Crops in Sustainable Food Production, Food Rev. Int. 2000; 16 (2): 121-157.

Nester, E. W. Microbiology: A Human Perspective. San Francisco (CA): McGraw Hill; 2007. 811 p.

Study Finds Soil Bacteria Can Live on Antibiotic Diet. (news.) National Public Radio. 2008 Apr. 4. Available from: http://proquest.umi.com/pqdweb?did=1456931661&sid=8&Fmt=3&clientId=47479&RQT=309&VName=PQD