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Web Review of Todar's Online Textbook of Bacteriology. "The Good, the Bad, and the Deadly"

Tag words: carbon cycle, primary production, nitrogen cycle, sulfur cycle, biodgradation, methanogen, methanogenesis, nitrogen fixation, denitrification, nitrification, anoxygenic photosynthesis, anaerobic respiration, lithotroph, lithotrophy.









Kenneth Todar currently teaches Microbiology 100 at the University of Wisconsin-Madison.  His main teaching interest include general microbiology, bacterial diversity, microbial ecology and pathogenic bacteriology.

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Bacteria and Archaea and the Cycles of Elements in the Environment (page 3)

(This chapter has 4 pages)

© Kenneth Todar, PhD

The Nitrogen Cycle

The nitrogen cycle is the most complex of the cycles of elements that make up biological systems. This is due to the importance and prevalence of N in cellular metabolism, the diversity of types of nitrogen metabolism, and the existence of the element in so many forms. Procaryotes are essentially involved in the biological nitrogen cycle in three unique processes.

Nitrogen Fixation: this process converts N2 in the atmosphere into NH3 (ammonia), which is assimilated into amino acids and proteins. Nitrogen fixation occurs in many free-living bacteria such as clostridia, azotobacters and cyanobacteria, and in symbiotic bacteria such as Rhizobium and Frankia, which associate with plant roots to form characteristic nodules. Biological nitrogen fixation is the most important way that N2 from the air enters into biological systems.

N2 ----------------> 2 NH nitrogen fixation

Anaerobic Respiration: this relates to the use of oxidized forms of nitrogen (NO3 and NO2) as final electron acceptors for respiration. Anaerobic respirers such as Bacillus and Pseudomonads are common soil inhabitants that will use nitrate (NO3) as an electron acceptor. NO3 is reduced to NO2 (nitrite) and then to a gaseous form of nitrogen such as N2 or N2O (nitrous oxide). The process is called denitrification. (A related process conducted by some Bacillus species, called dissimilatory nitrate reduction reduces NO3 to ammonia (NH3), but this is not considered denitrification.) Denitrifying bacteria are typically facultative microbes that respire whenever oxygen is available by aerobic respiration. If O2 is unavailable for respiration, they will turn to the alternative anaerobic respiration which uses NO3. Since NO3 is a common and expensive form of fertilizer in soils, denitrification may not be so good for agriculture, and one rationale for tilling the soil is to keep it aerobic, thereby preserving nitrate fertilizer in the soil.

NO3 ----------------> NO2 ----------------> N2 denitrification


The overall reactions of denitrification shown above proceed through the formation of nitrous oxide (N2O). A recent article by Wunsch an Zumft in Journal of Bacteriology, vol. 187 (2005), sheds new light on the process of denitrification. N2O is a bacterial metabolite in the REVERSAL of Nitrogen fixation. The anthropogenic atmospheric increase of N2O is a cause for concern, as noted above (as a greenhouse gas, N2O  has 300 times the heat absorbing capacity as CO2). Denitrifying bacteria respire using N2O  as an electron acceptor yielding N2  and the thereby provide a sink for N2O. This article provides new insight into this process by identifying a membrane-bound protein in denitrifying bacteria called NosR, that is necessary for the expression of N2O reductase from the nosZ gene. The NosR protein has redox centers positioned on opposite sides of the cytoplasmic membrane, which allows it to sustain whole-cell N2O respiration by acting on N2O reductase.

Nitrification is a form of lithotrophic metabolism that is chemically the opposite of denitrification. Nitrifying bacteria such as Nitrosomonas utilize NH3 as an energy source, oxidizing it to NO2, while Nitrobacter will oxidize NO2 to NO3. Nitrifying bacteria generally occur in aquatic environments and their significance in soil fertility and the global nitrogen cycle is not well understood.

The Overall process of Nitrification

NH3 ----------------> NO2 (Nitrosomonas)

NO2 ----------------> NO3 (Nitrobacter)

A final important aspect of the nitrogen cycle that involves procaryotes, though not exclusively, is decomposition of nitrogen-containing compounds. Most organic nitrogen (in protein, for example) yields ammonia (NH3) during the process of deamination. Fungi are involved in decomposition, as well.

Plants, animals and protista, as well as the procaryotes, complete the nitrogen cycle during the uptake of the element for their own nutrition. Nitrogen assimilation is usually in the form of nitrate, an amino group, or ammonia.
 


Figure 2. The Nitrogen Cycle




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Kenneth Todar has taught microbiology to undergraduate students at The University of Texas, University of Alaska and University of Wisconsin since 1969.

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