Derived copy of Bis2A 08.0 Metabolism from a microbes perspective *

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1 OpenStax-CNX module: m Derived copy of Bis2A 08.0 Metabolism from a microbes perspective * Erin Easlon Based on Bis2A 08.0 Metabolism from a microbes perspective by OpenStax Mitch Singer This work is produced by OpenStax-CNX and licensed under the Creative Commons Attribution License 4.0 By the end of this section, you will be able to: Abstract 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 and nitrogen cycles 1 METABOLISM: Putting it into perspective How organisms interact and change with their environment is in essence biology. For simplicity we can start by looking at how the simplest single cell organisms interact and alter their environment and the consequences of those interactions. WE are discussing of course, bacteria and archaea, and we can throw in a simple eukaryote as well. During your reading, think about how cellular activity can change the environment. What does that mean to the environment and the organism. Bacterial and Archeal metabolism Bacteria and Archaea are metabolically diverse organisms. There are many dierent environments on Earth with various energy and carbon sources, and variable conditions. They have been able to live in every environment by using whatever energy and carbon sources are available. Bacteria and Archaea ll 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 bacteria and archaea occupy is possible because they have diverse metabolic processes. * Version 1.1: Jul 17, :01 pm

2 OpenStax-CNX module: m Needs of single cell microbes 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. 2.1 Macronutrients 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 macronutrientscarbon, 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 (N 2 ) or another inorganic form. Diatomic (N 2 ) nitrogen, however, can be converted into an organic form only by certain organisms, called nitrogen-xing 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. 2.2 Micronutrients In addition to these macronutrients, bacteria and archaea 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 elementssuch as boron (B), chromium (Cr), and manganese (Mn)primarily as enzyme cofactors. 2.3 The Ways in Which Bacteria and Archaea Obtain Energy Bacteria and Archaea can use dierent sources of energy to assemble macromolecules from smaller molecules. Phototrophs (or phototrophic organisms) obtain their energy from sunlight. Chemotrophs (or chemosynthetic organisms) obtain their energy from chemical compounds. Chemotrophs that can use organic compounds as energy sources are called chemoorganotrophs. Those that can also use inorganic compounds as energy sources are called chemolitotrophs. 2.4 The Ways in Which Bacteria and Archaea Obtain Carbon Bacteria and Archaea not only can use dierent sources of energy but also dierent sources of carbon compounds. Recall that organisms that are able to x inorganic carbon are called autotrophs. Autotrophic organisms synthesize organic molecules from carbon dioxide. In contrast, heterotrophic organisms obtain carbon from organic compounds. To make the picture more complex, the terms that describe how organisms obtain energy and carbon can be combined. Thus, photoautotrophs use energy from sunlight, and carbon from carbon dioxide and water, whereas chemoheterotrophs obtain energy and carbon from an organic

3 OpenStax-CNX module: m chemical source. Chemolitoautotrophs obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide. The table below (Table 1) summarizes carbon and energy sources. Carbon and Energy Sources in Prokaryotes Energy Sources Carbon Sources Light Chemicals Carbon dioxide Organic compounds Phototrophs Chemotrophs Autotrophs Heterotrophs Organic chemicals Chemo-organotrophs Inorganic chemicals Table 1 Chemolithotrophs 3 Role of Microbes in Ecosystems Bacteria and archaea are ubiquitous: There is no niche or ecosystem in which they are not present. They play many roles in the environments they occupy. The roles they play in the carbon and nitrogen cycles are vital to life on Earth. 3.1 Microbes and the Carbon Cycle Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle (Figure 1). 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 bacteria, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including bacteria, 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 signicant 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, archaea, produce methane (CH 4 ). 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.

OpenStax-CNX module: m56799 4 Figure 1: Prokaryotes play a signicant role in continuously moving carbon through the biosphere. (credit: modication of work by John M. Evans and Howard Perlman, USGS) 3.

4 OpenStax-CNX module: m Figure 1: Prokaryotes play a signicant role in continuously moving carbon through the biosphere. (credit: modication of work by John M. Evans and Howard Perlman, USGS) 3.2 Bacteria 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 2, 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 xed into more readily available forms such as ammonia through the process of nitrogen xation. Ammonia can be used by plants or converted to other forms. Another source of ammonia is ammonication, 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 N 2 and N 2 O. Ammonia is catabolized anaerobically by some prokaryotes, yielding N 2 as the nal product. Nitrication is the conversion of ammonium to nitrite and nitrate. Nitrication 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 N 2 O, NO, and N 2, a process called denitrication.

OpenStax-CNX module: m56799 5 : Figure 2: Prokaryotes play a key role in the nitrogen cycle.

5 OpenStax-CNX module: m : Figure 2: Prokaryotes play a key role in the nitrogen cycle. (credit: Environmental Protection Agency) Which of the following statements about the nitrogen cycle is false? a.nitrogen xing bacteria exist on the root nodules of legumes and in the soil. b.denitrifying bacteria convert nitrates (NO 3- ) into nitrogen gas (N 2 ). c.ammonication is the process by which ammonium ion (NH 4+ ) is released from decomposing organic compounds. d.nitrication is the process by which nitrites (NO 2- ) are converted to ammonium ion (NH 4+ ). 4 Section Summary Prokaryotes are the most metabolically diverse organisms; they ourish in many dierent environments with various carbon energy and carbon sources, variable temperature, ph, pressure, and water availability. Nutrients required in large amounts are called macronutrients, whereas those required in trace amounts are called micronutrients or trace elements. Macronutrients include C, H, O, N, P, S, K, Mg, Ca, and Na. In addition to these macronutrients, prokaryotes require various metallic elements for growth and enzyme function. Prokaryotes use dierent sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain energy from chemical compounds. Prokaryotes play roles in the carbon and nitrogen cycles. Carbon is returned to the atmosphere by the respiration of animals and other chemoorganotrophic organisms. Consumers use organic compounds

6 OpenStax-CNX module: m generated by producers and release carbon dioxide into the atmosphere. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material. Nitrogen is recycled in nature from organic compounds to ammonia, ammonium ions, nitrite, nitrate, and nitrogen gas. Gaseous nitrogen is transformed into ammonia through nitrogen xation. Ammonia is anaerobically catabolized by some prokaryotes, yielding N 2 as the nal product. Nitrication is the conversion of ammonium into nitrite. Nitrication in soils is carried out by bacteria. Denitrication is also performed by bacteria and transforms nitrate from soils into gaseous nitrogen compounds, such as N 2 O, NO, and N 2. 5 Art Connections Exercise 1 (Solution on p. 8.) Figure 2 Which of the following statements about the nitrogen cycle is false? a. Nitrogen xing bacteria exist on the root nodules of legumes and in the soil. b. Denitrifying bacteria convert nitrates (NO 3- ) into nitrogen gas (N 2 ). c. Ammonication is the process by which ammonium ion (NH 4+ ) is released from decomposing organic compounds. d. Nitrication is the process by which nitrites (NO 2- ) are converted to ammonium ion (NH 4+ ). 6 Review Questions Exercise 2 (Solution on p. 8.) Which of the following elements is not a micronutrient? a. boron b. calcium c. chromium d. manganese Exercise 3 (Solution on p. 8.) Prokaryotes that obtain their energy from chemical compounds are called. a. phototrophs b. auxotrophs c. chemotrophs d. lithotrophs Exercise 4 (Solution on p. 8.) Ammonication is the process by which. a. ammonia is released during the decomposition of nitrogen-containing organic compounds b. ammonium is converted to nitrite and nitrate in soils c. nitrate from soil is transformed to gaseous nitrogen compounds such as NO, N 2 O, and N 2 d. gaseous nitrogen is xed to yield ammonia Exercise 5 (Solution on p. 8.) Plants use carbon dioxide from the air and are therefore called. a. consumers b. producers c. decomposer d. carbon xers

7 OpenStax-CNX module: m Free Response Exercise 6 (Solution on p. 8.) Think about the conditions (temperature, light, pressure, and organic and inorganic materials) that you may nd in a deep-sea hydrothermal vent. What type of prokaryotes, in terms of their metabolic needs (autotrophs, phototrophs, chemotrophs, etc.), would you expect to nd there?

8 OpenStax-CNX module: m Solutions to Exercises in this Module Figure 2 D B C A B to Exercise (p. 7) Responses will vary. In a deep-sea hydrothermal vent, there is no light, so prokaryotes would be chemotrophs instead of phototrophs. The source of carbon would be carbon dioxide dissolved in the ocean, so they would be autotrophs. There is not a lot of organic material in the ocean, so prokaryotes would probably use inorganic sources, thus they would be chemolitotrophs. The temperatures are very high in the hydrothermal vent, so the prokaryotes would be thermophilic. Glossary Denition 2: ammonication process by which ammonia is released during the decomposition of nitrogen-containing organic compounds Denition 2: chemotroph organism that obtains energy from chemical compounds Denition 2: decomposer organism that carries out the decomposition of dead organisms Denition 2: denitrication transformation of nitrate from soil to gaseous nitrogen compounds such as N 2 O, NO and N 2 Denition 2: nitrication conversion of ammonium into nitrite and nitrate in soils Denition 2: nitrogen xation process by which gaseous nitrogen is transformed, or xed into more readily available forms such as ammonia

Prokaryotic Metabolism *

OpenStax-CNX module: m44606 1 Prokaryotic Metabolism * OpenStax This work is produced by OpenStax-CNX and licensed under the Creative Commons Attribution License 3.0 By the end of this section, you will