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Many interesting chemical processes take place in the environment, in our bodies an in the food we eat. In almost all cases microbes play an important roll in these chemical conversions. Here are a few examples

• When mines are abandoned they leave underground tunnels exposed to air and water. This encourages the growth of sulfur-oxidizing bacteria that catabolize iron sulfide present in the rock into sulfuric acid. The high concentration of acid produced will drop the pH of the water to below 2.0, creating a very corrosive liquid that then exists the mine.

• One result of urban pollution from cars and smokestacks is the releases ammonia and other reduced nitrogen compounds into the air. This can be used as a substrate by ammonia-oxidizing bacteria, forming nitric acid, which corrodes the surface where theses microbes live. Ammonia-oxidizing bacteria are often found on the surface, and deep in the crevasses, of stone, and are thus found with statues and natural stone buildings. The build up of nitric acid causes the decay of these statues and structures. An example of this type of stone decay is found in the Cölonge cathedral in Germany.

• Microbes contribute to the global cycling of elements, converting carbon, oxygen, nitrogen, sulfur and phosphorous into their various inorganic and organic forms. In some cases only microbes are capable of certain conversions. For example, only microbes can convert nitrogen gas into ammonia using a process called nitrogen fixation.

• The decay of dead animals and plants depends upon the action of microorganisms, releasing the elements lock in the deceased so that they can be reused by other life forms.

It is worthwhile to understand all of these processes and the microbes involved in them. However, it is also just as important to know the population of microbes carrying out these conversions. Just because a microbe has been found that carries out a process does not mean that it is the major actor on any chemical conversion. It may be at too low a concentration to contribute significantly. Therefore, it is often vital to determine the number of microbes as well as their identity.

There are also many other reasons one might need to known the population of microorganisms in a given sample. For example, determining the rate at which a microbe is killed by UV light or heat requires analysis of the number of viable cells before, and at various times during treatment. In other experiments, it is important to know that you have the right density for a procedure, such as required for transforming a plasmid constructed in vitro into an E. coli strain. Assessment of microbial populations in applied industries is also important. Many food-processing plants will measure the level and type of microorganisms present in their food by doing counts on selective medium. In addition, viable cell counts will be performed when optimizing heat treatments for processing food. Sewage treatment plants will routinely sample and count the microbes present in their treatment systems to insure the correct type and numbers of bacteria are present. The microbial count can be determined using a wide array of techniques. Note that these assays all require somewhat different information and in different time frames, as explained below. In this chapter we summarize some of the more common methods and then do some virtual experiments performing them.

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