Prokaryotic Metabolism

Identify the metabolic needs of prokaryotes

Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans. The very broad range of environments that prokaryotes occupy is possible because they have diverse metabolic processes.

Learning Objectives

  • Identify the macronutrients needed by prokaryotes, and explain their importance
  • Describe the ways in which prokaryotes get energy and carbon for life processes
  • Describe the roles of prokaryotes in the carbon cycle
  • Describe the roles of prokaryotes in the nitrogen cycle

Needs of Prokaryotes

The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available nutrients, acidity, salinity, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of nutrients and conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.


Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they need certain substances, collectively called nutrients. When prokaryotes grow in nature, they obtain their nutrients from the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS.)

Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other compounds. Carbon accounts for about 50 percent of the composition of the cell. Nitrogen represents 12 percent of the total dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic (N2) nitrogen, however, can be converted into an organic form only by certain organisms, called nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and function of the prokaryotic cell.


In addition to these macronutrients, prokaryotes require various metallic elements in small amounts. These are referred to as micronutrients or trace elements. For example, iron is necessary for the function of the cytochromes involved in electron-transport reactions. Some prokaryotes require other elements—such as boron (B), chromium (Cr), and manganese (Mn)—primarily as enzyme cofactors.

Practice Question

The substances needed to sustain life are _____.

  1. trace elements
  2. DNA and proteins
  3. nutrients
  4. building blocks

How Prokaryotes Get Energy

Like all living things, prokaryotes need energy and carbon. They meet these needs in a variety of ways. In fact, prokaryotes have just about every possible type of metabolism. They may get energy from light (photo) or chemical compounds (chemo). They may get carbon from carbon dioxide (autotroph) or other living things (heterotroph). Most prokaryotes are chemoheterotrophs. They depend on other organisms for both energy and carbon. Many break down organic wastes and the remains of dead organisms. They play vital roles as decomposers and help recycle carbon and nitrogen. Photoautotrophs are important producers. They are especially important in aquatic ecosystems.

Classification of Prokaryotes Based on Metabolism

Two major nutritional needs can be used to group prokaryotes. These are (1) carbon metabolism, their source of carbon for building organic molecules within the cells, and (2) energy metabolism, their source of energy used for growth.

In terms of carbon metabolism, prokaryotes are classified as either heterotrophic or autotrophic:

  • Heterotrophic organisms use organic compounds, usually from other organisms, as carbon sources.
  • Autotrophic organisms use carbon dioxide (CO2) as their only source or their main source of carbon. Many autotrophic bacteria are photosynthetic, and get their carbon from the carbon dioxide in the atmosphere. This process of capturing inorganic carbon and converting it to organic sugar molecules is known as carbon fixation.

Energy metabolism in prokaryotes is classified as one of the following:

  • Phototrophic organisms capture light energy from the sun and convert it into chemical energy inside their cells.
  • Chemotrophic organisms break down either organic or inorganic molecules to supply energy for the cell. Some chemotrophic organisms can also use their organic energy-supplying molecules as a carbon supply, which would make them chemoheterotrophs.

Organisms are then classified as follows:

  • Photoheterotrophs are organisms that capture light energy to convert to chemical energy in the cells, but they get carbon from organic sources (other organisms). Examples are purple non-sulfur bacteria, green non-sulfur bacteria and heliobacteria.
  • Chemoheterotrophs are organisms that get their energy source and carbon source from organic sources. Chemoheterotrophs must consume organic building blocks that they are unable to make themselves. Most get their energy from organic molecules such as sugars. This nutritional mode is very common among eukaryotes, including humans.
  • Photoautotrophs are cells that capture light energy, and use carbon dioxide as their carbon source. There are many photoautotrophic prokaryotes, which include cyanobacteria. Photoautotrophic prokaryotes use similar compounds to those of plants to trap light energy.
  • Chemoautotrophs are cells that break down inorganic molecules to supply energy for the cell, and use carbon dioxide as a carbon source. Chemoautotrophs include prokaryotes that break down hydrogen sulfide (H2S the “rotten egg” smelling gas), and ammonia (NH4). Nitrosomonas, a species of soil bacterium, oxidizes NH4+ to nitrite (NO2). This reaction releases energy that the bacteria use. Many chemoautotrophs also live in extreme environments such as deep sea vents (extremophiles).
This flowchart helps to determine if a species is an autotroph or a heterotroph, a phototroph or a chemotroph

Figure 1. This flowchart helps to determine if a species is an autotroph or a heterotroph, a phototroph or a chemotroph. For example, “Obtain carbon elsewhere?” asks if the source of carbon is another organism. If the answer is “yes”, the organism is heterotrophic. If the answer is “no,” the organisms is autotrophic.

In Summary: How Prokaryotes Get Energy

Prokaryotes fulfill their carbon and energy needs in various ways. They may be photoautotrophs, chemoautotrophs, photoheterotrophs, or chemoheterotrophs.

Nutritional mode Energy source Carbon source
Photoautotroph Light Carbon dioxide (or related compounds)
Photoheterotroph Light Organic compounds
Chemoautotroph Chemical compounds Carbon dioxide (or related compounds)
Chemoheterotroph Chemical compounds Organic compounds

Role of Prokaryotes in Ecosystems

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.

Prokaryotes and the Carbon Cycle

Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle (Figure 2). Carbon is cycled through Earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. The movement of carbon is via carbon dioxide, which 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.

A large amount of available carbon is found in land plants. Plants, which are producers, use carbon dioxide from the air to synthesize carbon compounds. Related to this, one very significant source of carbon compounds is humus, which is a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. Consumers such as animals use organic compounds generated by producers and release carbon dioxide to the atmosphere. Then, bacteria and fungi, collectively called decomposers, carry out the breakdown (decomposition) of plants and animals and their organic compounds. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material (dead animals, plants, and humus) that undergo respiration.

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.

This illustration shows the role of bacteria in the carbon cycle. Bacteria break down organic carbon, which is released as carbon dioxide into the atmosphere.

Figure 2. 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 part 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 myriad processes, many of which are carried out only by prokaryotes. As illustrated in Figure 3, prokaryotes are key to the nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen 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 through the process of nitrogen fixation. Ammonia can be used by plants or converted to other forms.

Another source of ammonia is ammonification, the process by which ammonia is released during the decomposition of nitrogen-containing organic compounds. Ammonia released to the atmosphere, however, represents only 15 percent of the total nitrogen released; the rest is as N2 and N2O. Ammonia is catabolized anaerobically by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium to nitrite and nitrate. Nitrification in soils is carried out by bacteria belonging to the genera Nitrosomas, Nitrobacter, and Nitrospira. The bacteria performs the reverse process, the reduction of nitrate from the soils to gaseous compounds such as N2O, NO, and N2, a process called denitrification.

This illustration shows the role of bacteria in the nitrogen cycle. Nitrogen-fixing bacteria in root nodules of legumes convert nitrogen gas, or N2, into organic nitrogen found in plants. Nitrogen-fixing soil bacteria produce ammonium ion, or NH4+. Decomposers, including bacteria and fungi, decompose organic matter, also releasing NH4+. Nitrification is the process by which nitrifying bacteria produce nitrites (NO2-) and nitrates (NO3-). Nitrates are assimilated by plants, then animals, then decomposers. Denitrifying bacteria convert nitrates to nitrogen gas, completing the cycle.

Figure 3. Prokaryotes play a key role in the nitrogen cycle. (credit: Environmental Protection Agency)

Practice Questions

Which of the following statements about the nitrogen cycle is false?

  1. Nitrogen fixing bacteria exist on the root nodules of legumes and in the soil.
  2. Denitrifying bacteria convert nitrates (NO3) into nitrogen gas (N2).
  3. Ammonification is the process by which ammonium ion (NH4+) is released from decomposing organic compounds.
  4. Nitrification is the process by which nitrites (NO2) are converted to ammonium ion (NH4+).

Think about the conditions (temperature, light, pressure, and organic and inorganic materials) that you may find in a deep-sea hydrothermal vent. What type of prokaryotes, in terms of their metabolic needs (autotrophs, phototrophs, chemotrophs, etc.), would you expect to find there?

Check Your Understanding

Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times.

Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.