Prokaryotes are ubiquitous: There is no niche or ecosystem in which they are not present. Prokaryotes play many roles in the environments they occupy. The roles they play in the carbon and nitrogen cycles are vital to life on Earth. In addition, the current scientific consensus suggests that metabolically interactive prokaryotic communities may have been the basis for the emergence of eukaryotic cells.

Prokaryotes and the Carbon Cycle

Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle (Figure 1). The carbon cycle traces the movement of carbon from inorganic to organic compounds and back again. Carbon is cycled through Earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. In a way, the carbon cycle echoes the role of the “four elements” first proposed by the ancient Greek philosopher, Empedocles: fire, water, earth, and air. Carbon dioxide is removed from the atmosphere by land plants and marine prokaryotes, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including prokaryotes, fungi, and animals. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments, that carbon is not readily available.

Participants in the carbon cycle are roughly divided among producers, consumers, and decomposers of organic carbon compounds. The primary producers of organic carbon compounds from CO₂ are land plants and photosynthetic bacteria. A large amount of available carbon is found in living land plants. A related source of carbon compounds is humus, which is a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. (The term “humus,” by the way, is the root of the word “human.”) Consumers such as animals and other heterotrophs use organic compounds generated by producers and release carbon dioxide to the atmosphere. Other bacteria and fungi, collectively called decomposers, carry out the breakdown (decomposition) of plants and animals and their organic compounds. Most carbon dioxide in the atmosphere is derived from the respiration of microorganisms that decompose dead animals, plants, and humus.

In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane (CH₄). This methane moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that oxidize methane to carbon dioxide, which then returns to the atmosphere.

Figure 1. Prokaryotes play a significant role in continuously moving carbon through the biosphere. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

Prokaryotes and the Nitrogen Cycle

Nitrogen is a very important element for life because it is a major constituent of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds to ammonia, ammonium ions, nitrate, nitrite, and nitrogen gas by many processes, many of which are carried out only by prokaryotes. As illustrated in Figure 2, prokaryotes are key to the nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen (N₂) from the air, but this nitrogen is not usable by plants, which are primary producers. Gaseous nitrogen is transformed, or “fixed” into more readily available forms, such as ammonia (NH₃), through the process of nitrogen fixation. Nitrogen-fixing bacteria include Azotobacter in soil and the ubiquitous photosynthetic cyanobacteria. Some nitrogen fixing bacteria, like Rhizobium, live in symbiotic relationships in the roots of legumes.

Another source of ammonia is ammonification, the process by which ammonia is released during the decomposition of nitrogen-containing organic compounds. The ammonium ion is progressively oxidized by different species of bacteria in a process called nitrification. The nitrification process begins with the conversion of ammonium to nitrite (NO₂^–), and continues with the conversion of nitrite to nitrate. Nitrification in soils is carried out by bacteria belonging to the genera Nitrosomas, Nitrobacter, and Nitrospira. Most nitrogen in soil is in the form of ammonium (NH₄⁺) or nitrate (NO₃^–). Ammonia and nitrate can be used by plants or converted to other forms.

Ammonia released into the atmosphere, however, represents only 15 percent of the total nitrogen released; the rest is as N₂ and N₂O (nitrous oxide). Ammonia is catabolized anaerobically by some prokaryotes, yielding N₂ as the final product. Denitrifying bacteria reverse the process of nitrification, reducing the nitrate from soils to gaseous compounds such as N₂O, NO, and N₂.

Figure 2. Prokaryotes play a key role in the nitrogen cycle. (credit: Environmental Protection Agency)