Taxonomy is just the identification of organisms that live in the lake. While we can do taxonomy for fish and plants, typically when we talk about taxonomy we are meaning algae, zooplankton and macroinvertebrates. Algae are at the base of the food chain. Some types of algae are more edible than others. Some algae produce toxins and are more prone to bloom and create poor water quality. Zooplankton are microscopic organisms that feed directly on algae and keep their numbers down and water clarity up. Certain types of zooplankton are much more efficient than others at controlling algae. Newly hatched fish will eat zooplankton. Zooplankton "pass" energy from algae to fish because most fish do not eat algae directly. Some types of zooplankton are more edible than others for fish. Macroinvertebrates are clams, snails, worms, leeches, and larval form of some insects that live in lake mud or on surface of plants or rocks. They are fed on by some fish and they are very important in breaking down and decaying dead organisms in the lake. All three of these groups, algae, zooplankton, and macroinvertebrates are diverse, meaning there are many, many different species of each group. What species exist in any lake is not random. Each species has a unique set of environmental conditions in which it thrives. As such, there is a long history of using these organisms as bioindicators. We say algae, zooplankton, and macroinvertebrates integrate the environmental condition of the lake over long periods of time. We can take periodical samples for water conditions and chemistry and analyze it for a limited number of chemicals and nutrients we think are important but these samples are snapshots in time and may not reflect the overall "average" condition, and we might not be measuring the right chemicals for our purpose. For example, certain species are favored in lakes, which, on average, have high concentrations of nitrogen. They are found only in those lakes. A single set of water samples may indicate low nitrogen levels because of where the samples are taken, when the samples are taken, or the type of nitrogen we analyze for. In this case, we would misdiagnose a lake problem, not recognizing high nitrogen levels. By sampling biological communities and finding species of algae, zooplankton or macroinvertrebrates that thrive on high nitrogen levels that would be an indication that our water samples aren't telling us what we think they are about the average condition of the lake. And, if we monitor the types of organisms in a lake regularly we can see shifts in the types of species present, which may indicate changes in the underlying chemistry in environment of the lake.