In this section, you will explore the following questions:

  • What is the need for nitrogen fixation and how is it accomplished?
  • What are examples of foods for which prokaryotes are used in processing?
  • What is bioremediation and how do prokaryotes play a role in this process?

Connection for AP® Courses

We commonly think of pathogens when we think of prokaryotes, focusing on their relationship with disease. However, most prokaryotes do not cause disease and they play a wide range of other roles in ecosystems. Nitrogen needed to synthesize proteins and nucleic acids is often the most limiting element in ecosystems and bacteria are able to “fix” nitrogen into forms that can be used by eukaryotes. Microbes also are used to remove pollutants from environments, a process called bioremediation. Microbes that call us home are necessary for our survival. They help us digest our food, produce crucial nutrients, protect us from pathogenic microbes, and help train our immune system to function correctly. In addition, without prokaryotes we wouldn’t have cheese, bread, wine, beer, and yogurt.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 4 of the AP® Biology Curriculum Framework. The AP® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP®Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties.
Enduring Understanding 4.B Competition and cooperation are important aspects of biological systems.
Essential Knowledge 4.B.2 Interactions among prokaryotes and between prokaryotes and other organisms lead to increased efficiency and utilization of energy and matter.
Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively.
Learning Objective 4.18 The student is able to use representations and models to analyze how cooperative interactions within organisms promote efficiency in the use of energy and matter.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 2.6][APLO 2.28][APLO 2.42][APLO 4.9][APLO 4.1]

Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the diversity of the microbial world. In fact, our life would not be possible without prokaryotes. Just think about the role of prokaryotes in biogeochemical cycles.

Cooperation between Bacteria and Eukaryotes: Nitrogen Fixation

Nitrogen is a very important element to living things, because it is part of nucleotides and amino acids that are the building blocks of nucleic acids and proteins, respectively. Nitrogen is usually the most limiting element in terrestrial ecosystems, with atmospheric nitrogen, N2, providing the largest pool of available nitrogen. However, eukaryotes cannot use atmospheric, gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can be “fixed,” meaning it is converted into ammonia (NH3) either biologically or abiotically. Abiotic nitrogen fixation occurs as a result of lightning or by industrial processes.

Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes: soil bacteria, cyanobacteria, and Frankia spp. (filamentous bacteria interacting with actinorhizal plants such as alder, bayberry, and sweet fern). After photosynthesis, BNF is the second most important biological process on Earth. The equation representing the process is as follows" display="block">N2 + 16ATP + 8e− + 8H+ → 2NH3 + 16ADP + 16Pi + H2N2 + 16ATP + 8e− + 8H+ → 2NH3 + 16ADP + 16Pi + H2" role="presentation" style="box-sizing: border-box; display: inline; font-style: normal; font-weight: normal; line-height: normal; font-size: 14px; text-indent: 0px; text-align: center; text-transform: none; letter-spacing: normal; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative;">N2 + 16ATP + 8e + 8H+ 2NH3 + 16ADP + 16Pi + H2N2 + 16ATP + 8e− + 8H+ → 2NH3 + 16ADP + 16Pi + H2

where Pi stands for inorganic phosphate. The total fixed nitrogen through BNF is about 100 to 180 million metric tons per year. Biological processes contribute 65 percent of the nitrogen used in agriculture.

Cyanobacteria are the most important nitrogen fixers in aquatic environments. In soil, members of the genus Clostridium are examples of free-living, nitrogen-fixing bacteria. Other bacteria live symbiotically with legume plants, providing the most important source of BNF. Symbionts may fix more nitrogen in soils than free-living organisms by a factor of 10. Soil bacteria, collectively called rhizobia, are able to symbiotically interact with legumes to form nodules, specialized structures where nitrogen fixation occurs (// email address is being protected from spambots. You need JavaScript enabled to view it.:a9-_ZmEY@12/22-5-Beneficial-Prokaryotes#fig-ch22_05_01">Figure 22.27). Nitrogenase, the enzyme that fixes nitrogen, is inactivated by oxygen, so the nodule provides an oxygen-free area for nitrogen fixation to take place. This process provides a natural and inexpensive plant fertilizer, as it reduces atmospheric nitrogen to ammonia, which is easily usable by plants. The use of legumes is an excellent alternative to chemical fertilization and is of special interest to sustainable agriculture, which seeks to minimize the use of chemicals and conserve natural resources. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen: the atmosphere. Bacteria benefit from using photosynthates (carbohydrates produced during photosynthesis) from the plant and having a protected niche. Additionally, the soil benefits from being naturally fertilized. Therefore, the use of rhizobia as biofertilizers is a sustainable practice.

Why are legumes so important? Some, like soybeans, are key sources of agricultural protein. Some of the most important grain legumes are soybean, peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are used to feed cattle.

This photo shows a legume root, which is thin and yellow with nodules sticking out of it.
Figure 22.27Soybean (Glycine max) is a legume that interacts symbiotically with the soil bacterium Bradyrhizobium japonicum to form specialized structures on the roots called nodules where nitrogen fixation occurs. (credit: USDA)

Early Biotechnology: Cheese, Bread, and Yogurt

According to the United Nations Convention on Biological Diversity, biotechnology is “any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use."// email address is being protected from spambots. You need JavaScript enabled to view it.:a9-_ZmEY@12/22-5-Beneficial-Prokaryotes#footnote1">5 The concept of “specific use” involves some sort of commercial application. Genetic engineering, artificial selection, antibiotic production, and cell culture are current topics of study in biotechnology. However, humans have used prokaryotes before the term biotechnology was even coined. In addition, some of the goods and services are as simple as cheese, bread, and yogurt, which employ both bacteria and other microbes, such as yeast, a fungus.

Cheese production began around 4,000–7,000 years ago when humans began to breed animals and process their milk. Fermentation in this case preserves nutrients: Milk will spoil relatively quickly, but when processed as cheese, it is more stable Evidence suggests that cultured milk products, like yogurt, have existed for at least 4,000 years.

Using Prokaryotes to Clean up Our Planet: Bioremediation

Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation has been used to remove agricultural chemicals (pesticides, fertilizers) that leach from soil into groundwater and the subsurface. Certain toxic metals and oxides, such as selenium and arsenic compounds, can also be removed from water by bioremediation. The reduction of SeO4-2 to SeO3-2 and to Se0 (metallic selenium) is a method used to remove selenium ions from water. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. As an active ingredient of some pesticides, mercury is used in industry and is also a by-product of certain processes, such as battery production. Methyl mercury is usually present in very low concentrations in natural environments, but it is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa, can convert Hg+2 into Hg0, which is nontoxic to humans.

One of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills. The importance of prokaryotes to petroleum bioremediation has been demonstrated in several oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989) (// email address is being protected from spambots. You need JavaScript enabled to view it.:a9-_ZmEY@12/22-5-Beneficial-Prokaryotes#fig-ch22_05_03">Figure 22.28), the Prestige oil spill in Spain (2002), the spill into the Mediterranean from a Lebanon power plant (2006), and more recently, the Deepwater Horizon oil spill in the Gulf of Mexico (2010). To clean up these spills, bioremediation is promoted by the addition of inorganic nutrients that help bacteria to grow. Hydrocarbon-degrading bacteria feed on hydrocarbons in the oil droplet, breaking down the hydrocarbons. Some species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil, whereas other bacteria degrade the oil into carbon dioxide. In the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur, inasmuch as there are oil-consuming bacteria in the ocean prior to the spill. In addition to naturally occurring oil-degrading bacteria, humans select and engineer bacteria that possess the same capability with increased efficacy and spectrum of hydrocarbon compounds that can be processed. Under ideal conditions, it has been reported that up to 80 percent of the nonvolatile components in oil can be degraded within one year of the spill. Other oil fractions containing aromatic and highly branched hydrocarbon chains are more difficult to remove and remain in the environment for longer periods of time.

Part a: This photo shows two men in yellow raingear hosing off oil-drenched rocks on a sea-shore. Part b: This photo shows an oil-drenched bird sitting in oily water.
Figure 22.28(a) Cleaning up oil after the Valdez spill in Alaska, workers hosed oil from beaches and then used a floating boom to corral the oil, which was finally skimmed from the water surface. Some species of bacteria are able to solubilize and degrade the oil. (b) One of the most catastrophic consequences of oil spills is the damage to fauna. (credit a: modification of work by NOAA; credit b: modification of work by GOLUBENKOV, NGO: Saving Taman)


A particularly fascinating example of our normal flora relates to our digestive systems. People who take high doses of antibiotics tend to lose many of their normal gut bacteria, allowing a naturally antibiotic-resistant species called Clostridium difficile to overgrow and cause severe gastric problems, especially chronic diarrhea. Obviously, trying to treat this problem with antibiotics only makes it worse. However, it has been successfully treated by giving the patients fecal transplants from healthy donors to reestablish the normal intestinal microbial community. Scientists are also discovering that the absence of certain key microbes from our intestinal tract may set us up for a variety of problems including obesity, insulin resistance, and autoimmune disorders. Pictured here is a scanning electron micrograph of Clostridium difficile, a Gram-positive, rod-shaped bacterium that causes severe diarrhea. Infection commonly occurs after the normal gut fauna is eradicated by antibiotics.

Micrograph shows small clusters of white rod-shaped bacteria against a dark background.
Figure 22.29(credit: modification of work by CDC, HHS; scale-bar data from Matt Russell)
What treatment is possible for people who have too much C. difficile in their digestive system?
  1. By taking antibiotics like metronidazole as treatment.
  2. They can have a fecal transplant from a healthy donor.
  3. They can have urine transplant from a healthy donor.
  4. By taking probiotic supplements to restore microbial intestinal community.



One of your classmates claims that prokaryotes are always detrimental and pathogenic. How would you explain to him that his claim is incorrect?