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Chapter 56 : Quantification of Nitrogen Transformations

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Abstract:

This chapter describes some of the most useful methods for measuring the most important soil nitrogen transformations (N fixation, nitrogen mineralization, nitrification, and denitrification) and includes briefer descriptions of less important soil nitrogen transformations (NO immobilization, heterotrophic nitrification, dissimilatory NO reduction to NH , and anammox) and newer functional gene detection methods. The most recently developed method for estimating N fixation is the use of acetylene as a surrogate substrate for the nitrogenase enzyme. In most soils, autotrophic nitrification is the dominant NO producing transformation; however, NO production directly from organic N by heterotrophic microorganisms can be important in some soils. The simplest and least expensive is the so-called acetylene block method, which takes advantage of the fact that acetylene inhibits the last step in the denitrification process, the reduction of NO to N. Two applications of denitrification method are presented here, namely, an assay for denitrifier enzyme activity and field measurements using soil cores. Most commonly, the composition or diversity of a given functional gene has been assayed either by using fingerprinting techniques, such as denaturing gradient gel electrophoresis (DGGE) or terminal restriction fragment length polymorphism analysis, or by cloning and sequencing. More recently, functional gene copy numbers have been quantified by the use of approaches such as competitive or quantitative PCR, which should serve as indexes of the population size of the organisms harboring specific genes.

Citation: Myrold D. 2007. Quantification of Nitrogen Transformations, p 687-696. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch56

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Microbial Ecology
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Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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Figures

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FIGURE 1

N cycle, showing pools of N and N transformations that potentially occur in soil. Dark gray shapes represent N in insoluble forms; light gray shapes represent dissolved, ionic forms of N; and white shapes represent N gases. ANR, assimilatory NO reduction, also known as NO immobilization; HN, heterotrophic nitrification; DNRA, dissimilatory NO reduction to NH , also known as NO ammonification.

Citation: Myrold D. 2007. Quantification of Nitrogen Transformations, p 687-696. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch56
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References

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Tables

Generic image for table
TABLE 1

Calculation of gross N mineralization and NH consumption rates, using an equation initially developed by Kirkham and Bartholomew ( )

Citation: Myrold D. 2007. Quantification of Nitrogen Transformations, p 687-696. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch56
Generic image for table
TABLE 2

Use of Bunsen absorption coefficient to calculate total amount of NO in a system

Citation: Myrold D. 2007. Quantification of Nitrogen Transformations, p 687-696. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch56
Generic image for table
TABLE 3

Example calculations for denitrification, using the principle of isotope distribution ( )

Citation: Myrold D. 2007. Quantification of Nitrogen Transformations, p 687-696. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch56
Generic image for table
TABLE 4

Functional genes associated with key N cycle processes

Citation: Myrold D. 2007. Quantification of Nitrogen Transformations, p 687-696. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch56

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