Anaerobic respiration Fermentation
(CH2O)n Organic compounds
Figure 30.9 Carbon Cycle consumed is employed to create biomass, however; some is used as an energy source, generating carbon dioxide as a product.
As plants lose their leaves, and members of the food web die, various decomposers degrade the resulting detritus, using it both as an energy source and to create biomass. The type of organic material helps dictate which species are involved in the degradation. For example, a wide variety of organisms utilize the more readily decomposable organic substances such as sugars, amino acids, and proteins. Bacteria, which usually multiply rapidly, generally play the dominant role in the decomposition of animal flesh. In contrast, only certain fungi can break down lignin, a major component of wood (figure 30.10). Aerobic conditions are required for this degradation, which is why water-saturated wood in anaerobic conditions such as a marsh resists decay.
The supply of oxygen has a profound influence on the carbon cycle. Not only does oxygen allow the degradation of certain compounds such as lignin, it also helps determine the types of carbon-containing gases produced. During the aerobic decomposition of organic matter, a great deal of carbon dioxide is formed through aerobic respiration:
Carbon Water dioxide
When the level of oxygen is low, however, as is the case in wet rice-paddy soil, marshes, swamps, and manure piles, the degradation is incomplete, generating some CO2 and a variety of other products. Some of the CO2 produced is used by the methanogens, anaerobic members of the Domain Archaea. These prokaryotes gain energy by oxidizing hydrogen gas, using carbon dioxide as a terminal electron acceptor, generating methane (CH4):
Methane that enters the atmosphere is oxidized by ultraviolet light and chemical ions to carbon monoxide (CO) and carbon dioxide. ■ methanogens, p. 271
Nitrogen is an important constituent of proteins and nucleic acids. As consumers ingest plants and animals to fill their carbon and energy needs, they also obtain their required nitrogen, using it soley to build biomass. Prokaryotes, as a group, are far more diverse in their use of nitrogen-containing compounds. Some use oxidized nitrogen compounds such as nitrate (NO3:) and nitrite (NO2 " ) as a terminal electron acceptor; others used reduced nitrogen compounds such as ammonium (NH4+) as an energy source. These metabolic activities represent essential steps in the nitrogen cycle (figure 30.11).
Nitrogen fixation is the process in which nitrogen gas (N2) is reduced to form ammonia (NH3), which can then be incorporated into cellular material. Although the atmosphere consists of approximately 79% N2, relatively few organisms, all of which are prokaryotes, can reduce this gaseous form of the element. Thus, just as animals, including humans, depend on other organisms to fix carbon, they rely on prokaryotes to convert atmospheric nitrogen to a form they can assimilate to create biomass.
Nitrogenase, the enzyme complex that mediates nitrogen fixation, is readily inactivated by O2. Therefore, nitrogen-fixing aerobes must have a mechanism to protect it from exposure to O2. In addition, nitrogen fixation requires a tremendous expenditure of energy, at least 16 molecules of ATP for every molecule of nitrogen fixed, because N2 has a very stable triple bond.
Nitrogen-fixing prokaryotes, or diazotrophs, may be free-living, or they may live in symbiotic association with higher
Hydrogen Carbon dioxide ch4 + 2 h2o
Animals eat plants
Organic N (animals)
Hydrogen Carbon dioxide
Organic N (plants, microorganisms)
Plants take up nitrogen Lightning
Nitrogen fixation (symbiotic and free-living)
N2 Chemical fixation
Denitrification (anaerobic bacteria)
Nitrification (NNrobaater, Nitrospira) NO2-
776 Chapter 30 Microbial Ecology organisms, particularly certain plants. Those that form symbiotic relationships will be discussed later. Among the free-living examples are members of the genus Azotobacter. These heterotrophic, aerobic, Gram-negative rods may be the chief suppliers of fixed nitrogen in grasslands and other similar ecosystems that lack plants with nitrogen-fixing symbionts. Azotobacter species have an exceedingly high respiratory rate, consuming O2 so rapidly that an anaerobic environment is produced inside the cell, thereby protecting the O2-sensitive nitrogenase. Certain cyanobacteria species are also diazotrophs, enabling these pho-tosynthetic organisms to use both nitrogen and carbon from the atmosphere. In order to prevent their nitrogenase from being inactivated by the O2 generated during photosynthesis, some dia-zotrophic cyanobacteria confine nitrogen fixation to specialized non-photosynthetic cells called heterocysts (see figure 11.9). The dominant free-living, anaerobic, nitrogen-fixing organisms of soil are certain members of the genus Clostridium, which are distributed widely in nature. Other free-living diazotrophs are found in a variety of genera including anoxygenic phototrophs, methanogens, sulfate-reducers and sulfur-oxidizers. ■ symbiotic nitrogen-fixers and plants, p. 779 ■ the genus Azotobacter, p. 283 ■ nitrogen-fixing cyanobacteria, p. 278 ■ the genus Clostridium, p. 275 ■ cyanobacteria, p. 278
Energy-expensive chemical processes developed to fix nitrogen are widely used to make fertilizers. These synthetic compounds are playing an increasingly larger role in the nitrogen cycle. In fact, fixed nitrogen sources associated with human intervention, including fertilizer production and planting crops that foster the growth of symbiotic nitrogen-fixers, now appear to surpass natural biological nitrogen fixation.
Ammonification is the decomposition process that converts organic nitrogen into ammonia (NH3). In neutral environments, ammonium (NH4+), a positively charged ion that adheres to negatively charged particles, is formed; in alkaline environments, such as heavily limed soil, the gaseous ammonia may enter the atmosphere.
A wide variety of organisms, including aerobic and anaerobic bacteria as well as fungi, can degrade protein, one of the most prevalent nitrogen-containing organic compounds. They do this initially through the action of extracellular proteolytic enzymes that break down proteins into short peptides or amino acids. After transport of the breakdown products into the cell, the amino groups are removed, releasing ammonium. The decomposer will assimilate much of this compound to create biomass. Some, however, will be released into the environment, where it can then be assimilated by other organisms such as plants. ■ deamination, p. 153
Nitrification is the process that oxidizes ammonium (NH4+) to nitrate (NO3:). A group of bacteria known collectively as nitri-fiers do this in a cooperative two-step process, using ammonium and an intermediate, nitrite (NO2), as energy sources. ■ nitrifiers, p. 280
The nitrifiers encompass two populations of chemo-lithotrophic bacteria—the ammonia oxidizers and the nitrite oxidizers. Nitrosomonas species are among the few ammonia oxidizers, converting ammonium to nitrite. Nitrobacter and Nitrospira species are among the few nitrite oxidizers, converting nitrite to nitrate:
Nitrifiers are obligate aerobes, using molecular oxygen as a terminal electron acceptor. Consequently, nitrification does not occur in waterlogged soils or in anaerobic regions of aquatic environments. ■ chemolithotroph, pp. 153,268
Nitrification has some important consequences with respect to agricultural practices and pollution. Farmers often apply ammonium-containing compounds to soils as a source of nitrogen for plants. The ammonium is retained by soils, because its positive charge enables it to adhere to negatively charged soil particles. Nitrification converts the ammonium to nitrate, a form of nitrogen more readily used by plants, but rapidly leached from soil by rainwater. To impede nitrification, certain chemicals may be added to ammonium-fertilized soils. Another negative aspect of ammonium oxidation is that nitrite can accumulate in soil if insufficient numbers of nitrite oxidizers are present. If the nitrite leaches into groundwater, it may contaminate wells used for drinking water. Nitrite is toxic because it combines with hemoglobin of the blood, reducing blood's O2-carrying capacity. Even nitrate, which in itself is not very toxic, can be dangerous if high levels contaminate groundwater. When ingested, it can be converted to nitrite by intestinal bacteria that use it as a terminal electron acceptor.
Denitrification is the process that converts nitrate (NO3:) to gaseous nitrogen. Nitrate (NO3:) represents fully oxidized nitrogen. Some Pseudomonas species and a variety of other bacteria can use nitrate as a terminal electron acceptor when molecular oxygen is not available; this is the process of anaerobic respiration. The nitrate is reduced to gaseous nitrogen compounds such as nitrous oxide (N2O) and molecular nitrogen (N2). Release of these gases to the atmosphere represents a loss of nitrogen from an ecosystem. In addition, nitrous oxide contributes to global warming. ■ anaerobic respiration, p. 149
Under anaerobic conditions in wet soils, denitrifying bacteria may use the oxidized nitrogen compounds of expensive fertilizers, resulting in the release of gaseous nitrogen to the atmosphere and consequent economic loss to the farmer. In some areas, this process may represent 80% of nitrogen lost from fertilized soil. Denitrification is not always undesirable, however. The process may be actively fostered in certain steps of waste-water treatment as a means to remove nitrate. This compound
Animals eat plants
Organic S (animals)
Organic S (plants, microorganisms)
Sulfate incorporated into plants
S oxidation (photosynthetic and non-photosynthetic sulfur bacteria)
Sulfate reduction (bacteria)
H2S oxidation (photosynthetic and non-photosynthetic sulfur bacteria)
Figure 30.12 Sulfur Cycle could otherwise act as a fertilizer in the waters to which the sewage is discharged, thereby promoting algal growth. ■ microbiology of sewage treatment, p. 786
Recently, an unusual bacterium, Brocadia anamoxidans, was characterized that oxidizes ammonium under anaerobic conditions, using nitrate as a terminal electron acceptor. This reaction, called anammox (for anoxic ammonia oxidation), forms N2 and might provide an economical means of removing nitrogen compounds during sewage treatment.
Sulfur occurs in all living matter, chiefly as a component of the amino acids methionine and cysteine. It is also a component of certain coenzymes such as biotin. Like the nitrogen cycle, key steps of the sulfur cycle depend on the activities of prokaryotes (figure 30.12). Some prokaryotes use the reduced form of sulfur, H2S and elemental sulfur (S0), as energy sources or electron donors; others use oxidized sulfur compounds such sulfate (SO4:2) as terminal electron acceptors.
Most plants and microorganisms assimilate sulfur as sulfate (SO4:2), reducing it to form biomass. Like nitrogen, organic sulfur is present chiefly as a part of proteins. These organic compounds are first degraded into their constituent amino acids by proteolytic enzymes secreted by a wide variety of microorganisms. Decomposition of the sulfur-containing amino acids releases hydrogen sulfide, a gas.
Hydrogen sulfide and elemental sulfur (S0) can both serve as an energy source for certain chemolithotrophs. Sulfur-
oxidizing prokaryotes, including Beggiatoa, Thiothrix, and Thiobacillus species, oxidize these molecules to sulfate (SO42:). Certain bacteria in anaerobic marine environments can oxidize elemental sulfur, using nitrate as a terminal electron acceptor. As discussed in chapter 11, these organisms, including Thioploca species and the largest known bacterium, Thiomargarita nami-biensis, have unusual mechanisms to cope with the fact that their energy source and terminal electron acceptor are found in two different environments. ■ sulfur-oxidizing bacteria, p. 279 ■ sulfur-oxidizing, nitrate-reducing marine bacteria, p. 290
Hydrogen sulfide and elemental sulfur are oxidized anaer-obically by photosynthetic green and purple sulfur bacteria. These bacteria use sunlight for energy, but require reduced molecules as a source of electrons to generate reducing power. Like the chemolithotrophs that use hydrogen sulfide and elemental sulfur, the photosynthetic sulfur oxidizers produce sulfate. ■ green sulfur bacteria, p. 277 ■ purple sulfur bacteria, p. 276
Under anaerobic conditions, sulfate generated by the sulfur-oxidizers can then be used as a terminal electron acceptor by certain organisms. The sulfur- and sulfate-reducing bacteria and archaea use sulfate in the process of anaerobic respiration, reducing it to hydrogen sulfide (H2S). In addition to its unpleasant odor, the H2S is a problem because it reacts with metals, resulting in corrosion. ■ sulfur- and sulfate-reducing bacteria, p. 274
Phosphorus is a component of several critical biological compounds including nucleic acids, phospholipids, and ATP. Most plants and microorganisms readily take up phosphorus as orthophosphate (PO43:), assimilating it into biomass. From there, the phosphorus is passed along the food web. When plants and animals die, decomposers convert organic phosphate back to inorganic phosphate.
In many aquatic habitats, growth of algae and cyanobac-teria, the primary producers, is often limited by low concentrations of phosphorus. Addition of phosphates from sources such as agricultural runoff, phosphate-containing detergent, and wastewater can result in eutrophication.
Other important elements, including iron, calcium, zinc, manganese, cobalt, and mercury, are also recycled by microorganisms. Many prokaryotes contain plasmids coding for enzymes that carry out oxidation of metallic ions.
All chemotrophs, including animals, harvest the energy trapped in chemical bonds to generate ATP. This energy cannot be totally recycled, however, since a portion is always lost as heat when bonds are broken. Thus, energy is continually lost from biological systems. To compensate for this outflow, energy must be added to ecosystems.
Photosynthesis, carried out by chlorophyll-containing plants and microorganisms, converts solar energy to chemical bond energy in the form of organic compounds, which can be
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