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Prokaryotes III - Evolution and Early Metabolism

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You should have a working knowledge of the following terms:

  • anaerobic
  • bioremediation
  • Cyanobacteria
  • facultative anaerobe
  • legume
  • nitrogen cycle
  • nitrogen fixation
  • nodule
  • obligate aerobe
  • obligate anaerobe
  • rhizobia
  • saprobe

Introduction and Goals

 The last two tutorials discussed the diversity of prokaryotes and their various relationships with life in the biosphere. Much of this diversity is reflected in their diverse metabolic activities. More specifically, prokaryotes can use a variety of nitrogen and carbon sources, and in doing so they are important members of the biosphere. Humanity has exploited this evolved diversity by utilizing various bacteria for the cleansing of toxins in the environment, in a process known as bioremediation. By the end of this tutorial you should be familiar with:

  • The diversity of prokaryotic carbon sources
  • Bioremediation
  • Nitrogen use and the prokaryote
  • Oxygen and metabolic relationships
  • Origins of metabolic processes

Diversity of Carbon Sources

Prokaryotes can use carbon in a variety of forms, both as an energy source and as a precursor for anabolic reactions. As you've learned, carbon dioxide is the simplest form of carbon used. Organisms that use this simple form of carbon are often called "carbon fixers." (You will learn more about this process in the photosynthesis tutorial.)

Most prokaryotes use sugars (monosaccharides and disaccharides) and complex carbohydrates (e.g., starch). However, very unusual forms of carbon can also be used by some prokaryotes. Some prokaryotes can feed on oil. Although a bane to the oil fields, these oil-eating bacteria have been used to help clean oil spills.

Some bacteria are capable of using exotic carbon compounds such as TNT and polychlorinated biphenols (PCBs). These bacteria render such compounds nontoxic. There is an emerging field of civil engineering that utilizes bacteria for the purpose of cleaning contaminated soils, wells, and river sediments.

Prokaryotes and the Nitrogen Cycle

 Figure 1. Overview of Nitrogen Fixation. (Click to enlarge)

Nitrogen is found in all proteins and nucleic acids, hence it is essential to all forms of life. This atom is abundant in the air around us in the form of atmospheric nitrogen. However, nitrogen availability is a problem because nitrogen, in its elemental form (N2 gas), is not usable by most organisms. Nitrogen can only be transformed into a biologically usable state (i.e., "fixed") by certain nitrogen-fixing bacteria, in a process termed nitrogen fixation. "Nitrogen-fixers" live in the aquatic environment, the soil, and in or around the roots and stems of certain species of plants.

Nitrogen gas (also known as dinitrogen or N2) is converted to ammonia (NH3) by nitrogen-fixing bacteria. The fixed nitrogen is then used by plants (and other soil- and aquatic-dwelling microorganisms) in various anabolic pathways leading to the synthesis of proteins, nucleic acids, and other nitrogenous molecules.

Plants, the primary energy producers in the terrestrial environment, are a major repository for fixed nitrogen in the terrestrial biosphere. When a plant is eaten, the herbivore obtains nitrogen in the form of proteins and nucleic acids (which are broken down during digestion and used by the herbivore for the production of its own nitrogen products). When a plant dies, a variety of saprobes (those organisms that live on dead and decaying matter) also obtain nitrogen from the nitrogenous compounds previously made by the plant. Finally, fixed nitrogen can be reconverted by soil bacteria back into atmospheric nitrogen. The nitrogen cycle is essential for all life on the planet. The previous tutorial briefly introduced the symbiosis that leads to nitrogen fixation. We will now examine this symbiosis in more detail.

The Nitrogen Fixers


Figure 2. Root Nodules of a Soybean Plant.  The nodules contain nitrogen-fixing bacteria.

Figure 3.  A Rhizobium. A bacterium capable of nitrogen-fixation.

Almost all legumes (e.g., peas, alfalfa, and soybeans) are capable of housing nitrogen-fixing bacteria. The plant-prokaryote mutualism (the plant gets fixed nitrogen from the bacteria, while the bacteria get carbon from the plant) that results is determined by a complex series of events that begins with chemical communication between the participating organisms. Plants that participate in these symbioses secrete molecules (e.g., flavonoids) that act as chemical signals to a select species of bacteria. The term rhizobia is applied to several species of bacteria that participate in these symbioses. The targeted rhizobia are induced to respond when the specific chemical signal stimulates specific genes to "turn on." Bacteria then migrate toward the plant's root. Once bacteria reach the root, a developmental change is induced in the root, which results in nodule formation. The bacteria take up residence inside the nodule. Thus, the events of nodule formation involve chemical cross-signaling between the two participants. The environment of the plant-derived nodule is favorable for the fixation of nitrogen by the bacteria that live inside.

Figure 4. A Cyanobacterium. (Click to enlarge)

In addition to rhizobia/legume symbioses, several other symbiotic nitrogen-fixing symbioses are known. For example, various species of Cyanobacteria (often referred to as blue-green algae) are capable of nitrogen fixation. One symbiosis is particularly important to humanity. Anabaena is a Cyanobacterium genus that colonizes on the leaves of an aquatic fern that grows in rice paddies; the symbiosis supplies nitrogen to the pond, where it subsequently is taken up and used by rice plants. About 75% of all rice is cultivated in flooded fields, and this symbiosis has allowed rice farmers to maintain high levels of productivity without the need for expensive chemical fertilizers.

Prokaryotes and Oxygen

It may be hard to envision life without oxygen, but the first prokaryotes (the first creatures on Earth) evolved in an environment with essentially no molecular oxygen (oxygen gas, or O2). Consequently, the first prokaryotes, which originated between 3.5 and 4 billion years ago, were anaerobic. Anaerobic is a general term that refers to any organism, environment, or cellular process that lacks or does not require oxygen, and can even be poisoned by oxygen.

The original anaerobic organisms thrived in an environment devoid of oxygen. Many scientists think that the early prokaryotes were chemoautotrophs, obtaining energy from inorganic chemicals, possibly using the then-abundant hydrogen sulfide (H2S). Evidence to support this hypothesis can be observed in some hot springs, which contain members of the Archaea. They obtain energy from the combining of ferrous sulfide (FeS) and hydrogen sulfide (H2S) in a redox reaction, which releases energy.

  • FeS + H2S --> FeS2 + H2

The cyanobacteria, originating between 2.5 and 3.4 billion years ago, were the first photosynthetic bacteria to use water (H2O) as an electron source. They released oxygen as a waste product. These photosynthetic organisms thrived wherever there was sufficient light and a body of water. However, this created a problem on a global scale. After several hundred million years, free oxygen began to accumulate in the atmosphere, which marks the change from a reducing to an oxidizing atmosphere. Initially the high levels of free oxygen were toxic to life. Several mechanisms evolved to take care of this problem; including the use of oxygen in metabolism. Because we need oxygen for our survival, it is hard to believe that oxygen is toxic to many life forms.

Today prokaryotes (and other life forms) exhibit various metabolic relationships with oxygen. Obligate aerobes require oxygen, whereas obligate anaerobes have no need for oxygen and may even be poisoned by oxygen. Facultative anaerobes can alternate their oxygen requirement. They can use oxygen if it is present, but they can also function in an anaerobic environment. In the upcoming tutorials on energy and cellular respiration, the role of oxygen in cellular processes and how anaerobic organisms get by without oxygen will be addressed.


This tutorial presented the diversity of prokaryotic carbon sources. Bacteria can use simple sugars, as well as complex sources of carbon. Some bacteria can live off oil, and some can decompose cellulose. The ability to breakdown complex carbon sources has been utilized for a variety of purposes. The field of bioremediation is based, to a large extent, on the use of bacteria that can breakdown harmful compounds that have been introduced into the environment from various industrial and agricultural sources. For example, bacteria are capable of breaking down TNT and PCBs.

A great deal of life on the planet depends on prokaryotes, either directly or indirectly. The saprophytes degrade material from dead organic matter, and in doing so make nitrogen and carbon available to other life forms. Without them, nutrients would quickly be tied up in the carcasses of dead organisms and unavailable for other organisms in the ecosystem.

Nitrogen is necessary for the synthesis of amino acids. As with carbon, bacteria obtain their nitrogen from various sources. Some bacteria can convert ammonia into a more useful form of nitrogen (like nitrates and nitrites). Saprophytic bacteria obtain their nitrogen from decaying organic matter, whereas nitrogen-fixing bacteria obtain their nitrogen from molecular nitrogen (N2) found in the atmosphere.

Cyanobacteria not only fix their own nitrogen from the air, but they also synthesize their own sugars from carbon dioxide, using sunlight as an energy source. They may be the most efficient form of life on the planet. Indeed, the ancestors of blue-green algae played an important role in the history of the planet because their photosynthetic activity converted our planet's early anaerobic environment into one that is oxygen rich.

We also examined the relationships between oxygen and metabolism, and in the next few tutorials we will explore, in more detail, the relationship between energy and metabolic processes.