Ecosystems are organizations of living populations in specific habitats. Each ecosystem requires a continuous outside source of energy for survival and nonliving habitat consisting of soil, water, and air.

A living community is composed of populations that show a pattern of energy and nutritional relationships called a food web. Microorganisms are essential producers and decomposers in any ecosystem.

The relationships between populations in a community are described according to the degree of benefit or harm they pose to one another. These relationships include mutualism, commensalism, predation, scavenging, and competition.

The Natural Recycling of Bioelements
Nutrients and minerals necessary to the communities and ecosystems must be continuously recycled. These biogeochemical cycles involve transformation of elements from inorganic to organic forms usable by all populations in the community and back again. Specific types of microorganisms are needed to convert many nutrients from one form to another.

Elements of critical importance to all ecosystems that cycle through various forms are: carbon, nitrogen, sulfur, phosphorus, and water. Carbon and nitrogen are part of the atmospheric cycle. Sulfur and phosphorus are part of the sedimentary cycling of nutrients. Water circulates in a hydrologic cycle involving both the atmosphere and the lithosphere.

The sun is the primary energy source for most surface ecosystems. Photosynthesis captures this energy and utilizes it for carbon fixation by producer populations. Producers include plants, algae, cyanobacteria, and certain bacterial species.

The lithosphere, or soil, is an ecosystem in which mineral-rich rocks are decomposed to organic humus, the base for the soil community. Soil ecosystems vary according to the kinds of rocks and amount of water, air, and nutrients present. The rhizosphere is the most ecologically active zone of the soil.

Aquatic ecosystems are classified according to the amount of light present as the photic and profundal zones. The shoreline is the littoral zone, and the soil at the bottom of the water comprises the benthic zone. The food web of the aquatic community is built on phytoplankton and zooplankton. The nature of the aquatic community varies with the temperature, depth, minerals and amount of light present in each zone.

Aquatic ecosystems are readily contaminated by chemical pollutants and pathogens microbes because of industry, agriculture, and improper disposal of human wastes.

Significant water-borne pathogens include protozoans, bacteria, and viruses. Giardia and Cryptosporidium are the most significant protozoan pathogens. Campylobacter, Salmonella, Shigella, Vibrio, and Mycobacterium are the most significant bacterial pathogens. Hepatitis A and Norwalk virus are the most significant viral pathogens.

Water quality assays assess the most probable number of microorganisms in a water sample and screen for the presence of enteric pathogens using E. coli as the indicator organism.

Wastewater or sewage is treated in three stages to remove organic material, microorganisms, and chemical pollutants. The primary phase removes physical objects from the wastewater. The secondary phase removes the organic matter by biodegradation. The tertiary phase disinfects the water and removes chemical pollutants.

Applied Microbiology and Biotechnology
The use of microorganisms for practical purposes to benefit humans is called biotechnology.

Microorganisms can compete with humans for the nutrients in food. Their presence in food can be detrimental, beneficial, or of neutral consequence to human consumers. Food intoxication or poisoning is caused by microbial toxins produced as by-products of microbial decomposition of food. Food infection occurs when pathogenic microorganisms in the food attack the human host after being consumed.

Heat, radiations, chemicals, and drying are methods used to limit numbers of microorganisms in food. The type of method used depends on the nature of the food and the type of pathogens or spoilage agents it contains.

Food fermentation processes utilize bacteria or yeast to produce desired components such as alcohols and organic acids in foods and beverages. Beer, Wine, yogurt, and cheeses are examples of such processes.

Some microorganisms are used as a source of protein. Examples are single-cell protein, mycoprotein, and Spirulina. Microbial protein could replace meat as a major protein source.

General Concepts in Industrial Microbiology
Industrial microbiology refers to the bulk production of any organic compound derived from microorganisms. Currently these include antibiotics, hormones, vitamins, acids, solvents, and enzymes.