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Regulation of denitrification at the cellular level: a clue to the understanding of N2O emissions from soils.

Bakken LR, Bergaust L, Liu B, Frostegård A - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2012)

Bottom Line: The process emits a mixture of NO, N(2)O and N(2), depending on the relative activity of the enzymes catalysing the stepwise reduction of NO(3)(-) to N(2)O and finally to N(2).Liming could be a way to reduce N(2)O emissions, but needs verification by field experiments.More sophisticated ways to reduce emissions may emerge in the future as we learn more about the regulation of denitrification at the cellular level.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Aas, Norway. lars.bakken@umb.no

ABSTRACT
Denitrifying prokaryotes use NO(x) as terminal electron acceptors in response to oxygen depletion. The process emits a mixture of NO, N(2)O and N(2), depending on the relative activity of the enzymes catalysing the stepwise reduction of NO(3)(-) to N(2)O and finally to N(2). Cultured denitrifying prokaryotes show characteristic transient accumulation of NO(2)(-), NO and N(2)O during transition from oxic to anoxic respiration, when tested under standardized conditions, but this character appears unrelated to phylogeny. Thus, although the denitrifying community of soils may differ in their propensity to emit N(2)O, it may be difficult to predict such characteristics by analysis of the community composition. A common feature of strains tested in our laboratory is that the relative amounts of N(2)O produced (N(2)O/(N(2)+N(2)O) product ratio) is correlated with acidity, apparently owing to interference with the assembly of the enzyme N(2)O reductase. The same phenomenon was demonstrated for soils and microbial communities extracted from soils. Liming could be a way to reduce N(2)O emissions, but needs verification by field experiments. More sophisticated ways to reduce emissions may emerge in the future as we learn more about the regulation of denitrification at the cellular level.

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Relationship between phylogeny and the transient accumulation of NO2−, NO and N2O for different strains of Thauera; experimental conditions were similar to that used for P. denitrificans (figure 2). The phylogenetic tree was constructed using UPGMA method (for details see Liu et al. [40]), and the table shows the maximum amounts of the three intermediates transiently accumulated: NO2− (µmol flask−1), NO and N2O-N (nmol flask−1) during batch incubations of 50 ml culture (2 mM NO3−) in 120 ml reaction vessels. 100 µmol NO2− implies that all NO3− accumulated as NO2− during the first phase of denitrification. To convert nmol NO to nM in the liquid: 1 nmol flask−1 is equivalent to 0.7 nM in the liquid. Thauera Phenylacetica lacked nosZ, and converted all nitrate to N2O. Data assembled from Liu et al. [40].
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RSTB20110321F4: Relationship between phylogeny and the transient accumulation of NO2−, NO and N2O for different strains of Thauera; experimental conditions were similar to that used for P. denitrificans (figure 2). The phylogenetic tree was constructed using UPGMA method (for details see Liu et al. [40]), and the table shows the maximum amounts of the three intermediates transiently accumulated: NO2− (µmol flask−1), NO and N2O-N (nmol flask−1) during batch incubations of 50 ml culture (2 mM NO3−) in 120 ml reaction vessels. 100 µmol NO2− implies that all NO3− accumulated as NO2− during the first phase of denitrification. To convert nmol NO to nM in the liquid: 1 nmol flask−1 is equivalent to 0.7 nM in the liquid. Thauera Phenylacetica lacked nosZ, and converted all nitrate to N2O. Data assembled from Liu et al. [40].

Mentions: We have also analysed the denitrification regulatory phenotype (DRP) of a number of reference strains and recently isolated strains within the genus Thauera under nearly identical experimental conditions as that for P. denitrificans shown in figure 2 [40]. One of the strains lacked nosZ and produced 100 per cent N2O, while the seven other strains had all the necessary genes to make a complete denitrification from NO3− to N2. A common feature of all the Thauera strains was robust control of NO at nanomolar levels, very similar to P. denitrificans (5–35 nM in the liquid phase). They deviated grossly, however, regarding the transient accumulation of both NO2− and N2O. Some of the strains reduced all NO3− to NO2− before expressing NIR and NOR, wheras others accumulated negligible amounts of NO2−. The strains were also different regarding the transient accumulation of N2O, ranging from 0.06 to 5 per cent of all NO3−-N finally reduced to N2. The results are summarized in figure 4, together with their phylogenetic relationship based on 16S rDNA.Figure 4.


Regulation of denitrification at the cellular level: a clue to the understanding of N2O emissions from soils.

Bakken LR, Bergaust L, Liu B, Frostegård A - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2012)

Relationship between phylogeny and the transient accumulation of NO2−, NO and N2O for different strains of Thauera; experimental conditions were similar to that used for P. denitrificans (figure 2). The phylogenetic tree was constructed using UPGMA method (for details see Liu et al. [40]), and the table shows the maximum amounts of the three intermediates transiently accumulated: NO2− (µmol flask−1), NO and N2O-N (nmol flask−1) during batch incubations of 50 ml culture (2 mM NO3−) in 120 ml reaction vessels. 100 µmol NO2− implies that all NO3− accumulated as NO2− during the first phase of denitrification. To convert nmol NO to nM in the liquid: 1 nmol flask−1 is equivalent to 0.7 nM in the liquid. Thauera Phenylacetica lacked nosZ, and converted all nitrate to N2O. Data assembled from Liu et al. [40].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3306626&req=5

RSTB20110321F4: Relationship between phylogeny and the transient accumulation of NO2−, NO and N2O for different strains of Thauera; experimental conditions were similar to that used for P. denitrificans (figure 2). The phylogenetic tree was constructed using UPGMA method (for details see Liu et al. [40]), and the table shows the maximum amounts of the three intermediates transiently accumulated: NO2− (µmol flask−1), NO and N2O-N (nmol flask−1) during batch incubations of 50 ml culture (2 mM NO3−) in 120 ml reaction vessels. 100 µmol NO2− implies that all NO3− accumulated as NO2− during the first phase of denitrification. To convert nmol NO to nM in the liquid: 1 nmol flask−1 is equivalent to 0.7 nM in the liquid. Thauera Phenylacetica lacked nosZ, and converted all nitrate to N2O. Data assembled from Liu et al. [40].
Mentions: We have also analysed the denitrification regulatory phenotype (DRP) of a number of reference strains and recently isolated strains within the genus Thauera under nearly identical experimental conditions as that for P. denitrificans shown in figure 2 [40]. One of the strains lacked nosZ and produced 100 per cent N2O, while the seven other strains had all the necessary genes to make a complete denitrification from NO3− to N2. A common feature of all the Thauera strains was robust control of NO at nanomolar levels, very similar to P. denitrificans (5–35 nM in the liquid phase). They deviated grossly, however, regarding the transient accumulation of both NO2− and N2O. Some of the strains reduced all NO3− to NO2− before expressing NIR and NOR, wheras others accumulated negligible amounts of NO2−. The strains were also different regarding the transient accumulation of N2O, ranging from 0.06 to 5 per cent of all NO3−-N finally reduced to N2. The results are summarized in figure 4, together with their phylogenetic relationship based on 16S rDNA.Figure 4.

Bottom Line: The process emits a mixture of NO, N(2)O and N(2), depending on the relative activity of the enzymes catalysing the stepwise reduction of NO(3)(-) to N(2)O and finally to N(2).Liming could be a way to reduce N(2)O emissions, but needs verification by field experiments.More sophisticated ways to reduce emissions may emerge in the future as we learn more about the regulation of denitrification at the cellular level.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Aas, Norway. lars.bakken@umb.no

ABSTRACT
Denitrifying prokaryotes use NO(x) as terminal electron acceptors in response to oxygen depletion. The process emits a mixture of NO, N(2)O and N(2), depending on the relative activity of the enzymes catalysing the stepwise reduction of NO(3)(-) to N(2)O and finally to N(2). Cultured denitrifying prokaryotes show characteristic transient accumulation of NO(2)(-), NO and N(2)O during transition from oxic to anoxic respiration, when tested under standardized conditions, but this character appears unrelated to phylogeny. Thus, although the denitrifying community of soils may differ in their propensity to emit N(2)O, it may be difficult to predict such characteristics by analysis of the community composition. A common feature of strains tested in our laboratory is that the relative amounts of N(2)O produced (N(2)O/(N(2)+N(2)O) product ratio) is correlated with acidity, apparently owing to interference with the assembly of the enzyme N(2)O reductase. The same phenomenon was demonstrated for soils and microbial communities extracted from soils. Liming could be a way to reduce N(2)O emissions, but needs verification by field experiments. More sophisticated ways to reduce emissions may emerge in the future as we learn more about the regulation of denitrification at the cellular level.

Show MeSH
Related in: MedlinePlus