The cycling of oxygen, nitrogen, water vapour, and carbon dioxide, as well as the trace gases—methane, ammonia, various oxides of nitrogen and sulfur, and non-methane hydrocarbons—between the atmosphere and the biosphere results in relatively constant proportions of these compounds in the atmosphere over time. Without the continuous generation of these gases by the biosphere, they would quickly disappear from the atmosphere.

The carbon cycle, as it relates to the biosphere, is simple in its essence. Inorganic carbon (carbon dioxide) is converted to organic carbon (the molecules of life). To complete the cycle, organic carbon is then converted back to inorganic carbon. Ultimately, the carbon cycle is powered by sunlight as green plants and cyanobacteria (blue-green algae) use sunlight to split water into oxygen and hydrogen and to fix carbon dioxide into organic carbon. Carbon dioxide is removed from the atmosphere, and oxygen is added. Animals engage in aerobic respiration, in which oxygen is consumed and organic carbon is oxidized to manufacture inorganic carbon dioxide. It should be noted that chemosynthetic bacteria, which are found in deep-ocean and cave ecosystems, also fix carbon dioxide and produce organic carbon. Instead of using sunlight as an energy source, these bacteria rely on the oxidation of either ammonia or sulfur.

The carbon cycle is fully coupled to the oxygen cycle. Each year, photosynthesis fixes carbon dioxide and releases 100,000 megatons of oxygen to the atmosphere. Respiration by animals and living organisms consumes about the same amount of oxygen and produces carbon dioxide in return. Oxygen and carbon dioxide are thus coupled in two linked cycles. On a seasonal basis, an enrichment of atmospheric carbon dioxide occurs in the winter half of the year, whereas a drawdown of atmospheric carbon dioxide takes place during the summer.

The nitrogen cycle begins with the fixing of inorganic atmospheric nitrogen (N₂) into organic compounds. These nitrogen-containing compounds are used by organisms and, through the process of denitrification, are converted back to inorganic atmospheric nitrogen. Ammonia and ammonium ions are the products of nitrogen fixation and may be incorporated into some organisms as organic nitrogen-containing molecules. In addition, ammonium ions may be oxidized to form nitrites, which can be further oxidized by nitrifying bacteria into nitrates. Though both nitrites and nitrates may be used to make organic nitrogen-containing molecules, nitrates are especially useful for plant growth and are key compounds that support both terrestrial and aquatic food chains. Nitrates may also be denitrified by bacteria to produce nitrogen gas. This process completes the nitrogen cycle.

The nitrogen cycle is coupled to both the carbon and oxygen cycles. Seventy-eight percent of the gases of the atmosphere by volume is diatomic nitrogen. Diatomic nitrogen is the most stable of the nitrogen-containing gases of the atmosphere. Only 300 megatons of nitrogen must be produced each year by denitrifying bacteria to account for losses. These losses mostly occur during lightning discharges and during nitrogen-fixation activities by blue-green algae and nitrogen-fixing bacteria. (The latter are found in the root nodules of certain plants called legumes.) Nitrogen-fixing bacteria use atmospheric nitrogen to produce oxides of nitrogen. Denitrifying bacteria convert nitrates in soils and wetlands to nitrogen gas, which is then returned to the atmosphere.

Nitrous oxide occurs in trace amounts (0.3 ppm) in the atmosphere. Between 100 and 300 megatons of nitrous oxide are produced by soil and marine bacteria each year to maintain this concentration. In the atmosphere, nitrous oxide is short-lived because it is quickly broken down by ultraviolet light. Nitric oxide (NO), a minor contributor in the breakdown of stratospheric ozone, is the by-product of this reaction.

Like nitrous oxide, ammonia is also produced in soils and marine waters by bacteria and escapes into the atmosphere. Nearly 1,000 megatons are added to the atmosphere each year. Ammonia decreases the acidity of precipitation and serves as a nutrient for plants when returned to the land via precipitation.

There are six major sulfur-containing biogenic atmospheric gases that are part of the sulfur cycle. They include hydrogen sulfide, carbon disulfide (CS₂), carbonyl sulfide (COS), dimethyl sulfide (DMS; C₂H₆S), dimethyl disulfide ([CH₃S]₂), and methyl mercaptan (CH₃SH). Sulfur dioxide (SO₂) is an oxidation product of these sulfur gases, and it is also added to the atmosphere by volcanoes, burning biomass, and anthropogenic sources (i.e., smelting metals and coal ignition). SO₂ is removed from the atmosphere and returned to the biosphere in rainfall. The increased acidity of rain and snow from anthropogenic additions of SO₂ and oxides of nitrogen is often referred to as “acid precipitation.” The acidity of this precipitation and other phenomena, such as “acid fog,” is partly cancelled by the release of ammonia in the atmosphere.

The concentration of methane at any one time in the atmosphere is only about 1.7 ppm. Though only a trace gas, it is highly reactive and plays a key role in the chemical reactions that control the composition of the atmosphere. Methanogenic bacteria in wetland sediments decompose organic matter and release 1,000 megatons of gaseous methane to the atmosphere per year. In the lower atmosphere, methane reacts with oxygen to produce water and carbon dioxide. Each year 2,000 megatons of oxygen are removed from the atmosphere by this mechanism. This loss of oxygen must be replaced by photosynthesis. Some methane reaches the upper stratosphere, where its interaction with oxygen is a major source of upper stratospheric moisture. Within wetlands, bacteria produce methyl halide compounds (methyl chloride [CH₃Cl] and methyl iodide [CH₃I] gases), whereas these same methyl halides are produced in forests by fungi. These gases, upon reaching the stratosphere, regulate the production of stratospheric ozone by contributing to its natural breakdown (see ozonosphere). Without the continual production of methane by methanogenic bacteria, the oxygen concentration of the atmosphere would increase by 1 percent in only 12,000 years. Dangerously high levels of oxygen in the atmosphere would greatly increase the incidence of wildfires. If the oxygen concentration of Earth’s atmosphere rose from its current concentration of 21 percent to 25 percent, even damp twigs and grass would easily ignite. Non-methane hydrocarbons of terrestrial origin are generally well mixed in the free atmosphere above the planetary boundary layer (PBL; see below). These organic particles weaken incoming solar radiation as it passes through the atmosphere, and reductions of 1 percent have been recorded.