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Chapter 14 : Soil Nitrifiers and Nitrification

Author: James I. Prosser1
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Affiliations: 1: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, United Kingdom
Content Type: Monograph
Publication Year: 2011

Category: Environmental Microbiology

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Abstract:

This chapter provides an overview of soil nitrification, paying particular attention to these recent advances. The focus is on the specific factors associated with soil that influence the nitrification process and nitrifier communities. Thus, the chapter considers how soil nitrification differs from nitrification in pure cultures growing in liquid medium or in oceans, estuaries, and wastewater treatment plants. The links between phylogenetic diversity and physiological or functional diversity are discussed in relation to soil characteristics and environmental factors. Three important aspects of surface growth are discussed: effects on growth and inhibition, survival and recovery from starvation, and protection from effects of low pH. Cell activities, and other kinetic parameters, are being reassessed using cultivation-independent quantitative PCR (qPCR) techniques to assess cell abundance used this approach to determine the influence of ammonia concentration on growth characteristics of soil communities in microcosms and in the field. Although low pH inhibits ammonia oxidizers in laboratory culture, a metastudy of nitrification in almost 300 soils provided no evidence for a significant effect of soil pH on nitrification. The chapter deals with more general aspects of the impact of heterogeneity. The focus is on a single process within the nitrogen cycle, but soil nitrification is intimately linked to mineralization, soil organic matter decomposition, and denitrification.

Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
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Soil Nitrifiers and Nitrification
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Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
/content/10.1128/9781555817145.ch14.ch14fig01
FIGURE 1
Ammonia oxidizer community structure influences nitrification kinetics following addition of synthetic sheep urine. Microcosms containing grassland soil were amended with synthetic sheep urine containing 1 mg of urea-N kg of soil. Ammonium (filled and open triangles) and nitrite + nitrate (filled and open squares) concentrations and ammonia oxidizer sequence types were determined in control (open square and triangle) and in amended (filled square and triangle) microcosms. Ammonia oxidizer sequences were analyzed by DGGE. Soil was initially dominated by cluster 3a (a) or cluster 3b (b). (From ], with permission.)
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Image of FIGURE 1
FIGURE 1

Ammonia oxidizer community structure influences nitrification kinetics following addition of synthetic sheep urine. Microcosms containing grassland soil were amended with synthetic sheep urine containing 1 mg of urea-N kg of soil. Ammonium (filled and open triangles) and nitrite + nitrate (filled and open squares) concentrations and ammonia oxidizer sequence types were determined in control (open square and triangle) and in amended (filled square and triangle) microcosms. Ammonia oxidizer sequences were analyzed by DGGE. Soil was initially dominated by cluster 3a (a) or cluster 3b (b). (From ], with permission.)

Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
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FIGURE 2
Bacterial ammonia oxidizer abundances in long-term ecological research plots subjected to different management regimes. Viable cell abundance was determined using the MPN method with mineral salts medium containing 5, 50, or 1,000 mg of NH -N ml. Total bacterial ammonia oxidizer abundance was determined by competitive PCR amplification of 16S rRNA genes using primers targeting betaproteobacterial ammonia oxidizers. Treatments were as follows: Tr1, conventional tilling; Tr2, no tilling; Tr5, perennial cover crop; Tr7, historically tilled. Suffixes T and F indicate tillage and fertilization, respectively, and NDF represents native deciduous forest. Error bars represent standard errors. (From Phillips et al. [2000], with permission.)
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10.1128/9781555817145/f0359-01.gif
Image of FIGURE 2
FIGURE 2

Bacterial ammonia oxidizer abundances in long-term ecological research plots subjected to different management regimes. Viable cell abundance was determined using the MPN method with mineral salts medium containing 5, 50, or 1,000 mg of NH -N ml. Total bacterial ammonia oxidizer abundance was determined by competitive PCR amplification of 16S rRNA genes using primers targeting betaproteobacterial ammonia oxidizers. Treatments were as follows: Tr1, conventional tilling; Tr2, no tilling; Tr5, perennial cover crop; Tr7, historically tilled. Suffixes T and F indicate tillage and fertilization, respectively, and NDF represents native deciduous forest. Error bars represent standard errors. (From Phillips et al. [2000], with permission.)

Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
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FIGURE 3
Growth of NpAV, a ureolytic ammonia oxidizer, on urea in liquid batch culture at initial pH values of 4 (a), 5 (b), 7 (c), and 7.5 (d). Growth on ammonia was inhibited at pH <7. Growth was followed by measuring changes in urea, ammonium, and nitrite concentrations and pH. (From ], with permission.)
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10.1128/9781555817145/f0361-01.gif
Image of FIGURE 3
FIGURE 3

Growth of NpAV, a ureolytic ammonia oxidizer, on urea in liquid batch culture at initial pH values of 4 (a), 5 (b), 7 (c), and 7.5 (d). Growth on ammonia was inhibited at pH <7. Growth was followed by measuring changes in urea, ammonium, and nitrite concentrations and pH. (From ], with permission.)

Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
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FIGURE 4
Relationships between soil pH and gross nitrification rate in mineral and organic soil layers from agricultural and woodland ecosystems. (Data kindly provided by J. M. Stark. Adapted from ].)
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10.1128/9781555817145/f0363-01.gif
Image of FIGURE 4
FIGURE 4

Relationships between soil pH and gross nitrification rate in mineral and organic soil layers from agricultural and woodland ecosystems. (Data kindly provided by J. M. Stark. Adapted from ].)

Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
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FIGURE 5
Abundance and transcriptional activity of crenarchaeal and bacterial ammonia oxidizers in long-term pH plots, maintained at pH values in the range 4.5 to 7.5, determined by quantification of gene and gene transcripts (a) and by ratios of gene transcript:gene abundance (b). Error bars represent standard errors of replicate field samples at each soil pH. (From ], with permission.)
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10.1128/9781555817145/f0365-01.gif
Image of FIGURE 5
FIGURE 5

Abundance and transcriptional activity of crenarchaeal and bacterial ammonia oxidizers in long-term pH plots, maintained at pH values in the range 4.5 to 7.5, determined by quantification of gene and gene transcripts (a) and by ratios of gene transcript:gene abundance (b). Error bars represent standard errors of replicate field samples at each soil pH. (From ], with permission.)

Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
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FIGURE 6
Influence of temperature and incubation time on relative abundance of crenarchaeal gene transcripts of different phylotypes in soil microcosms incubated at temperatures in the range 10 to 30°C and sampled at 2, 12, 26, and 40 days. gene transcript sequences were analyzed by DGGE, and histograms represent relative intensity of bands within individual lanes from triplicate microcosms. Data are presented as means of triplicate values and standard errors. (From ], with permission.)
10.1128/9781555817145/f0371-01_thmb.gif
10.1128/9781555817145/f0371-01.gif
Image of FIGURE 6
FIGURE 6

Influence of temperature and incubation time on relative abundance of crenarchaeal gene transcripts of different phylotypes in soil microcosms incubated at temperatures in the range 10 to 30°C and sampled at 2, 12, 26, and 40 days. gene transcript sequences were analyzed by DGGE, and histograms represent relative intensity of bands within individual lanes from triplicate microcosms. Data are presented as means of triplicate values and standard errors. (From ], with permission.)

Citation: Prosser J. 2011. Soil Nitrifiers and Nitrification, p 347-383. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch14
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References

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