By Alfred R. Conklin, Jr.

Soil scientist define soil microorganisms as any organism in soil which requires a microscope to observe. These organisms ranges from bacteria to nematodes and includes diverse species of algae and protozoa. Soil microorganisms are responsible for the breakdown of organic matter, including hydrocarbons, conversion of inorganic components from one form to another and the production of humus. Although this group is large and diverse, soil microorganisms are thought of as being of three distinct types: fungi actinomycetes, and bacteria. Soil microorganisms form a robust community capable of surviving and functioning under extremes of temperature, water availability, pH, energy resources, nutrient availability and salt concentration.

There has long been interested in enumerating the number and types of microorganism in soil. This arises from a desire to use such measurements to indicate the health and productivity of a soil. The task of enumerating microorganisms in soil however, is extremely difficult and indeed may be impossible in any absolute sense. Direct observation is impossible because much of the organic and inorganic matter in soil is opaque. Direct observation in soil would also involve three-dimensional movement through a solid medium, which would certainly destroy any microscope objective.

Isolating individual microorganisms and allowing them to grow and produce colonies is another method of enumerating microorganisms in soil. However, this method is also problematic. Growing these organisms is difficult because different organisms from soil grow under different conditions of light, temperature, nutrients and oxygen. Some organisms grow attached to solid surfaces while others only grow unattached in solution. Some bacteria can grow under two vastly different sets of conditions. Facultative anaerobes for instance can grow in both the presence and absence of oxygen. In addition some fungal hypha can break apart and form reproductive fragments, or propagules, thus leading to an over estimate of their abundance.

Another approach is to look at an extract of some characteristic component of microbial cells and relating that back to the number of cells, the biomass or number of organisms in soil. We could break open the cells and look at the amount of DNA or RNA or measure the amount of ATP released. Each method is fraught with problems. Is the DNA from living or dead cells or is it only from microorganism? ATP only comes from living cells but is it only from microorganism and if so is it from all or only some microorganisms?

Another approach is to measure some aspect of metabolic activity and relate this to microbial numbers or amount of microbial biomass. One might think that measuring the amount of carbon dioxide given off by soil microorganisms would be a good measure of their abundance and activity. Although some microorganisms in soil do produce carbon dioxide others take it up. Unless one knows the number or amount of biomass of each type of organism the use of carbon dioxide production as a measure of microbial numbers or activity is not very useful.

In spite of all these problems soil scientist generally agree on the probable numbers or amounts of biomass in surface soils. Bacteria are present in numbers of 108 to 109 organisms per gram or 300 to 3000 grams of biomass per m3 of soil. Actinomycetes are less common perhaps 107 to 108 organisms per gram but still 300 to 3000 grams of biomass per m3 of soil. For fungi the figures are 105 to 106 propagules per gram or 600 to 10000 grams of biomass per m3 of soil. In the case of both the actinomycetes and fungi the larger masses are due to the larger size of the organisms. All in all these three groups of organisms represent a sizable amount of living matter in the soil.

The fungi are the largest of this group of common soil microorganisms. They are also the more familiar since we can often see colonies of fungi growing on food, particularly bread and cheese. Although larger than other soil microorganisms, in soil they are so small that they cannot be seen without a microscope. Because of their filamentous structure fungi can live in very harsh conditions. They can grow on hydrocarbons and can live and grow under conditions where there is a very high osmotic potential such as sugar or syrup. In soil they breakdown highly complex and resistant compounds such as cellulose, starch, gums and lignins.

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The actinomycetes are smaller than fungi but are also filamentous and have short branches. They are perhaps best known for production or antibiotics. Streptomycin, actinomycin and neomycin are but three examples of antibiotics produced by this group of soil microorganisms. More generally actinomycetes are involved in the decomposition of complex organic compounds such as phospholipids. They are abundant in soils in which the easily decomposed organic matter has already been decomposed and only the more resistant compounds remain.

The bacteria are the smallest, most diverse group of microorganisms. They are diverse in shape, the methods by which they get energy, in the types of compounds they can decompose and the conditions under which they can live. Some bacteria can live in the absence of oxygen while others can only live in the presence of oxygen. Still others can live either with or without oxygen. All can survive in hostel oxygen environments. There are bacterial that can grow at low, medium and high temperatures and some can survive and grow in extremes of pH and water availability.

Some bacteria need only the simplest of inputs to live grow and reproduce. They can live using sunlight for energy, carbon dioxide as a sole carbon source and inorganic ions from their surroundings. From these simple components they to produce all the molecules
necessary for life. Other bacterial have quite demanding needs. They need organic material as an energy source and as a source of carbon to build cellular materials. In some cases they even need preformed organic compounds such as amino acids, vitamins etc. for growth and reproduction.

In the soil environment microorganisms produce a large variety of byproducts some of which are quite surprising. A whole host of microorganism can decompose nitrogen containing organic compounds and release ammonia and ammonium into the soil solution. This in turn is oxidized for energy by other bacteria producing nitrite and nitrate. The rate of nitrate production is faster than nitrite production so nitrite build up in soil is rare. Some free living and some symbiotic bacteria can take nitrogen from the air and combine it with organic compounds to produce amino acids. At the other end of the cycle there are bacteria that can break down nitrate and convert it back to nitrogen gas.

During the decomposition of organic matter in soil a number of products are produced. In aerobic soils this process is oxidation and the chief products are carbon dioxide and water. Microorganisms carry out this process not for either of these products but for the energy they can get from the process. In anaerobic soils microorganism also break down organic compounds for energy but in this case the final products are water, carbon dioxide methane and energy.

An interesting characteristic of soil is that even under the best aerobic conditions when lots of oxygen is readily available methane can be produced. Methane is and can only be produced under anaerobic conditions. So how can it be formed in aerobic soils? The answer is pores. In all soils including those that are air dry, there are small water filled pores. Organisms in the openings use up oxygen as it diffuses into the pore leaving the interior anaerobic. Methane produced in the interior of the pore diffused out into the soil air.

During the decomposition process compounds resistant to decomposition are released into the soil solution. These compounds are synthesized into a complex material called humus. This is a colloidal material, which is dark in color and very complex in construction and structure. It is very resistant to decay sometimes lasting as long a 1000 years. Humus has a high water holding capacity and a high cation exchange capacity. It is important in absorbing organic molecules and inorganic compounds added to soil by either natural or unnatural means.

Knowing the variety and complexity of the soil microbial community one should expect and can find microorganisms, including bacteria, actinomycetes and fungi, which can degrade hydrocarbons. The question is how to encourage the growth and increase the rate of decomposition carried out by these organisms. Most often this is done by the judicious application of fertilizer, particularly nitrogen and making sure that the soil has an adequate supply of base cations, calcium, magnesium, potassium, and water.

Knowing the complexity of the microbial community and organic matter in soil it should not be surprising to find any organic molecule in it. Every soil sample I have ever analyzed for hydrocarbons has been positive. In some cases these were soils, which could not have been exposed to a hydrocarbon spill. When analyzing soils for hydrocarbons one must always be careful to be sure that the results do not represent the natural hydrocarbon content of the soil in question.

The presence of a large, active, diverse microbial population in soil is an indication that the soil is in good condition. The opposite is indicative of toxic or poor soil conditions. A poor soil can have a very narrow range of microorganism individuals. It would also be indicated if a large or large and diverse microbial population is present not active. Large numbers of diverse species of microorganisms can survive in soil in an inactive or resting state. It is important that the population be not only large but also diverse and highly active for the soil to be in good condition.

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