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This chapter considers nutrient cycling and the roles of microorganisms in global element relationships. The chapter also includes discussions of the carbon, nitrogen, sulfur, and other biogeochemical cycles. A discussion of global climate change and its consequences concludes the chapter.
After reading this chapter you should be able to:
• describe the roles microbes play in nutrient cycles
• describe redox reactions important in carbon, nitrogen, and sulfur cycling in the environment
• describe nutrient cycles that do not involve redox chemistry
• discuss global climate change and its consequences
I.
Biogeochemical Cycling
A.
Biogeochemical cycling (nutrient cycling) involves both biological and chemical processes
1.
Oxidation-reduction (redox) reactions change the chemical and physical properties of nutrients
2.
Environments with high redox potentials are more likely to accept electrons, while those with low redox potentials are more likely to donate electrons; reduction and oxidation reactions are always coupled
B.
Carbon cycle
1.
Carbon can be interconverted among methane, complex organic matter, and carbon dioxide; conversions involve reductants (sources of electrons) and oxidants (sinks for electrons) a.
Organic compounds are produced primarily by carbon fixation carried out by the activities of plants, cyanobacteria, green algae, photosynthetic bacteria, and chemolithoautotrophs b.
Organic carbon is returned to the atmosphere by oxidation to carbon dioxide (inorganic carbon) through respiration and fermentation c.
Inorganic and organic carbon can be reduced anaerobically to methane by archaea in anoxic zones (e.g., marshes, rice paddies, ruminant guts, and termite guts); the methane produced moves into aerobic areas where it is oxidized by methylotrophic bacteria, although methane oxidation is also seen in anoxic environments
2.
Carbon dioxide is produced by the degradation of organic matter through the process of mineralization a.
Organic matter varies in terms of elemental composition, structure of basic repeating units, linkages between repeating units, and physical and chemical characteristics b.
Degradation of organic matter is influenced by redox potential, nutrients availability, abiotic conditions (pH, O
2
, osmotic conditions), and the microbial community present c.
Microbial degradation of complex organic material occurs when microbes use these molecules for growth
1) Chitin, protein, and nucleic acids contain large amounts of nitrogen; when these are degraded, any excess nitrogen is released by mineralization
2) Molecules containing only hydrogen, carbon, and oxygen cannot support the growth of microbes; the inability to assimilate sufficient levels of nutrients limits growth
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3) Immobilization occurs when nutrients held in biomass are unavailable for nutrient cycling d.
Most organic substrates can be degraded in the presence or absence of oxygen; however, degradation of hydrocarbons and lignin usually occurs aerobically
1) Hydrocarbon degradation usually requires oxygen because the first step adds molecular oxygen to the molecule; slow anaerobic digestion in the presence of sulfate or nitrate has been observed
2) Filamentous fungi are major lignin degraders and they require oxygen; anaerobic degradation is slower and thus lignified materials accumulate in peat bogs e.
The presence or absence of oxygen affects the final products that accumulate when organic substances are degraded
1) Aerobic conditions—oxidized products are made (carbon dioxide, nitrate, sulfate)
2) Anaerobic conditions—reduced end products are formed (ammonium, sulfide, methane)
C.
Nitrogen cycle
1.
Nitrogen is cycled among organic nitrogen, ammonia, nitrogen gas, nitrite, nitrous oxide, and nitrate
2.
Nitrogen fixation a.
Sequential reduction of gaseous nitrogen to ammonia; it requires an expenditure of energy; the ammonia is immediately incorporated into organic matter as an amine b.
Can be carried out by prokaryotic aerobes or anaerobes; the actual reduction process must be done anaerobically, even by aerobic microorganisms; physical barriers, O
2
scavenging molecules, and high rates of metabolic activity are used to maintain the anaerobic conditions required for nitrogen fixation; cyanobacteria form specialized cells
(heterocysts) for nitrogen fixation
3.
Nitrification—aerobic oxidation of ammonium ion to nitrite and ultimately to nitrate; it is carried out by chemolithoautotrophs and by some heterotrophs (heterotrophic nitrification)
4.
Nitrogen assimilation a.
Assimilatory reduction—reduction of nitrate and incorporation into new microbial biomass b.
Dissimilatory reduction—reduction of nitrate to nitrite, nitrous oxide, and gaseous N
2
; the sequence of reactions is known as denitrification
5.
Anoxic ammonia oxidation (anammox reaction)—oxidation of ammonia is coupled with the reduction of nitrite to nitrogen gas by chemolithotrophs
D.
Phosphorus cycle
1.
This cycle has no gaseous component; found in soils in inorganic and organic forms as phosphates or polyphosphates; it is always in valence state +5 (not redox active)
2.
Inorganic phosphorus compounds are relatively insoluble and not bioavailable, often limiting microbial growth in the environment
E.
Sulfur cycle
1.
Sulfur can be interconverted among elemental sulfur, sulfide, and sulfate by the actions of various microorganisms; under certain conditions, transformations of the sulfur cycle can occur in the absence of microorganisms
2.
Dissimilatory sulfate reduction (anaerobic respiration) produces sulfide, which accumulates in the environment; assimilatory sulfate reduction results in the reduction of sulfate for use in amino acid biosynthesis
3.
Dissimilatory elemental sulfur reduction is known and sulfite reduction is seen in a variety of microbes
F.
Iron cycle
1.
Iron can be interconverted among ferric iron, ferrous iron, and magnetite; iron in aerobic environments above pH 4 is mainly insoluble, so microbes use siderophore molecules to capture Fe +3 (ferric) which is reduced to Fe +2 (ferrous) for assimilation
2.
Iron reduction from Fe +3 to Fe +2 occurs under anaerobic conditions and is carried out by bacteria that use Fe +3 as a final electron acceptor, often in a crystalline form outside of the cell;
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this metabolism is widespread and may have ancient origins as evidenced by banded iron formations
3.
Magnetotactic bacteria reduce iron to magnetite, which is used to construct intracellular magnetic compasses to migrate toward oxygen
4.
Iron oxidation from Fe +2 to Fe +3 is carried out by a number of genera under aerobic conditions; can occur under anaerobic conditions using nitrate as the electron acceptor
G.
Manganese and mercury cycles
1.
Microbial transformation of manganous ion (Mn +2 ) to MnO
2
(with Mn +4 ); occurs in hydrothermal vents and bogs
2.
Mercury and other metals can be methylated in anaerobic sediments becoming volatile and lipid soluble; methylated metals can be concentrated in the food chain (a process known as biomagnification) and have severe health consequences
H.
Interaction between elemental cycles—numerous links exist between biogeochemical cycles through such processes as carbon fixation using electrons from ammonium or iron and anaerobic respiration oxidizing organic carbon compounds using inorganic electron acceptors
II.
Global Climate Change
A.
Over the last century, the rate at which greenhouse gases (CO
2
, CH
4
, nitrogen oxides) have entered the atmosphere has outpaced the rate at which biogeochemical cycles can recycle them
B.
The burning of fossil fuels, deforestation, and agricultural practices have led to the accumulation of greenhouse gases and the upset of global nitrogen cycles
C.
Global warming has been attributed to the accumulation of greenhouse gases; ecological ramifications of climate change include infectious disease outbreaks and animal extinctions
Place the letter of each term in the space next to the definition or description that best matches it.
____ 1. Reduction of sulfate for use in amino acid biosynthesis
____ 2. The incorporation of simple, soluble substances into the body of an organism, making it unavailable for use by other organisms
____ 3. The decomposition of organic matter that results in the production of inorganic nutrients
____ 4. The increase in concentration of a substance (e.g., toxic metals) in higher-level consumer organisms
____ 5. Produces an accumulation of sulfide in the environment
____ 6. The process by which atmospheric nitrogen gas is converted into ammonia
____ 7. The aerobic process by which ammonia is converted into nitrite and nitrate
____ 8. The process by which nitrate is converted into nitrogen gas
____ 9. The anaerobic process by which ammonia is oxidized
____ 10. Common pool of organic matter found in aquatic systems
____ 11. Components that retain heat in the atmosphere such as CO
2
and CH
4
____ 12. The tendency of a compound to accept electrons a. anammox b. assimilatory sulfate reduction c. biomagnification d. denitrification e. dissimilatory sulfate reduction f. dissolved organic matter g. greenhouse gases h. immobilization i. mineralization j. nitrification k. nitrogen fixation l. redox potential
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1. Bacteria such as Nitrosococcus are chemolithoautotrophs that carry out environments, certain bacteria and fungi oxidize ammonia in a process called
. In acidic
Still other microorganisms are capable of coupling the oxidation of ammonia with the reduction of nitrite to nitrogen gas. This is called the (anoxic ammonia oxidation) process.
2. Microbial communities play major roles in ____________ cycling, in which both biological and chemical processes are involved in the cycling of nutrients. These cycles often involve and reactions, and change the concentrations of gaseous components (e.g., carbon, nitrogen, and sulfur).
3. Sulfate, when used as an external electron acceptor, is reduced to sulfide and accumulates in the environment. This is an example of ____________ reduction. In contrast, if sulfate is reduced for use in the synthesis of proteins and other molecules, it is referred to as ____________ reduction.
4. The reduction of nitrate to nitrite, nitrous oxide, and gaseous molecular nitrogen is referred to as
____________. The reduction of nitrogen gas to ammonia is called
5. Bacteria called
.
bacteria transform extracellular iron to magnetite and use it to construct intracellular compasses that are used to orient the bacteria in bogs or swamps at the appropriate oxygen level.
6. In the natural carbon cycle, the most reduced form of carbon is , while the most oxidized
7. form of carbon is .
Greenhouse gases are added to the atmosphere through the burning of from the guts of animals such as and , and from the submerged fields of
.
,
For each of the questions below select the one best answer.
1. Which of the following metals can be methylated and thereby rendered capable of crossing the vertebrate blood-brain barrier and causing central nervous system damage? a. silver b. mercury c. zinc d. platinum
2. What is the term that describes the process in which toxic compounds accumulate in organisms of a food chain such that the toplevel consumers ingest concentrations higher than those that are normally found in the environment? a. bioconcentration b. biomagnification c. bioamplification d. bioaccumulation
3. Which of the following organic compounds cannot be degraded in the absence of oxygen? a. lignin b. hemicellulose c. chitin d. lipids
4. Which of the following is used by aerobic nitrogen-fixing bacteria to maintain the
245 anaerobic conditions needed for the reduction of nitrogen? a. physical barriers to keep oxygen out of certain compartments b. O
2
-scavenging molecules to remove oxygen c. high metabolic rates to utilize oxygen as quickly as it becomes available d. All of the above are correct.
5. Which group of metals is harmful to humans and other homeothermic animals? a. noble metals (e.g., silver) b. metals that can be transformed to organometals (e.g., mercury) c. metals that occur in ionic forms (e.g., copper) d. None of the above are harmful to homeothermic animals.
6. In which cycle are there inorganic and organic forms that are not redox active and no gaseous component? a. iron b. phosphorus c. manganese d. sulfur
.

____ 1. Mineralization is the process of obtaining various minerals from ores by the action of microorganisms.
____ 2. Denitrification generally occurs in aerobic locations.
____ 3. Only carbon compounds can act as greenhouse gases and contribute to global warming.
____ 4. Dissimilatory reduction of iron uses ferric iron as an electron acceptor.
____ 5. Nitrogen fixation can be carried out by organisms growing aerobically or anaerobically, but the process itself must take place in an anaerobic microenvironment—even in aerobic microorganisms.
____ 6. Metals such as copper are toxic at extremely low levels and serve no useful purpose for microorganisms.
____ 7. Biogeochemical cycles should be considered separately as they rarely interact with each other.
____ 8. Degradation of organic material by microorganisms is influenced by several factors, including the composition and structure of the organic material and the microbial community present.
1. Explain why wood structures can exist for longer periods of time in swamps and bogs with little or no structural degradation. What would happen if the water table fell or the swamp was drained?
2. The release of greenhouse gases and the production of fixed nitrogen compounds has increased over the last century. What are the consequences of disrupting the carbon and nitrogen cycles? What measures might you suggest to limit negative consequences and how might this affect modern life?
Terms and Definitions
1. b, 2. h, 3. i, 4. c, 5. e, 6. k, 7. j, 8. d, 9. a, 10. f, 11. g, 12. l
Fill in the Blank
1. nitrification; heterotrophic nitrification; anammox 2. biogeochemical; oxidation; reduction 3. dissimilatory; assimilatory 4. denitrification; nitrogen fixation 5. magnetotactic 6. methane; carbon dioxide 7. fossil fuels; ruminants; termites; rice paddies
Multiple Choice
1. b, 2. b, 3. a, 4. d, 5. b, 6. b
True/False
1. F, 2. F, 3. F, 4. T, 5. T, 6. F, 7. F, 8. T
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