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Aerobic microorganisms require the presence of oxygen for growth. Molecular oxygen functions in the respiratory pathway of the microbes to produce the energy necessary for life. Bacteria , yeasts, fungi , and algae are capable of aerobic growth.

The opposite of an aerobe is an anaerobe. An anaerobe does not require oxygen, or sometimes cannot even tolerate the presence of oxygen.

There are various degrees of oxygen tolerance among aerobic microorganisms. Those that absolutely require oxygen are known as obligate aerobes. Facultative aerobes prefer the presence of oxygen but can adjust their metabolic machinery so as to grow in the absence of oxygen. Microaerophilic organisms are capable of oxygen-dependent growth but cannot grow if the oxygen concentration is that of an air atmosphere (about 21% oxygen). The oxygen content must be lower.

Oxygen functions to accept an electron from a substance that yields an electron, typically a substance that contains carbon. Compounds called flavoproteins and cytochromes are key to this electron transport process. They act as electron carriers. By accepting an electron, oxygen enables a process known as catabolism to occur. Catabolism is the breakdown of complex structures to yield energy. The energy is used to sustain the microorganism.

A common food source for microorganisms is the sugar glucose. Compounds such as glucose store energy inside themselves, in order to bond their constituent molecules together. When these bonds are severed, energy is released. In aerobic bacteria and other organisms, a compound called pyruvic acid retains most of the energy that is present in the glucose. The pyruvic acid in turn is broken down via a series of reactions that collectively are called the tricarboxylic acid cycle, or the Kreb's cycle (named after one the cycle's discoverers, Sir Hans Krebs). A principle product of the Kreb's cycle is a compound called nicotinamide adenine dinucleotide (NADH2). The NADH2 molecules feed into another chain of reactions of which oxygen is a key.

The energy-generating process in which oxygen functions is termed aerobic respiration . Oxygen is the final electron acceptor in the process. Anaerobic respiration exists, and involves the use of an electron acceptor other than oxygen. One of the most common of these alternate acceptors is nitrate, and the process involving it is known as denitrification.

Aerobic respiration allows a substrate to be broken down (this is also known as oxidation) to carbon dioxide and water. The complete breakdown process yields 38 molecules of adenine triphosphate (ATP) for each molecule of the sugar glucose. ATP is essentially the gasoline of the cell. Electron transport that does not involve oxygen also generates ATP, but not in the same quantity as with aerobic respiration. Thus, a facultative aerobe will preferentially use oxygen as the electron acceptor. The other so-called fermentative type of energy generation is a fall-back mechanism to permit the organism's survival in an oxygen-depleted environment.

The aerobic mode of energy production can occur in the disperse cytoplasm of bacteria and in the compartmentalized regions of yeast , fungi and algae cells. In the latter microorganisms, the structure in which the reactions take place is called the mitochondrion. The activities of the mitochondrion are coordinated with other energy-requiring processes in the cell.

See also Carbon cycle in microorganisms; Metabolism