Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants

Schmidt, Ingo; Spanning, Rob J.M. van; Jetten, Mike S. M.

doi:10.1099/mic.0.27382-0

Cited by 168 publications

(136 citation statements)

References 35 publications

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“…For oxidizing NH 3 , dinitrogen tetroxide (N 2 O 4 ), rather than O 2 , has been proposed to be the primary oxidant, as described in the NO x cycle hypothesis (Schmidt et al, 2001;Kampschreur et al, 2006;Schmidt, 2008) in which NO is an important intermediate: NO produced by NO 2 À reduction can feed into the NO x cycle and the nitrite reductase is thereby indirectly involved in ammonia oxidation. This is supported by lower growth yield and growth defects (Schmidt et al, 2004) and slower ammonia oxidation rate (Cantera and Stein, 2007a) in Nitrosomonas europaea nirK mutants. Furthermore, when NO is scavenged from the growth media, N. eutropha is unable to oxidize ammonia (Zart et al, 2000), whereas ammonia oxidation activity increases when NO is added to the media (Zart and Bock, 1998).…”

Section: Introductionmentioning

confidence: 67%

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

2012

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Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (nirK), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal nirK genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the nirK variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the nirK from Candidatus Nitrosopumilus maritimus and Candidatus Nitrosoarchaeum limnia. The two nirK variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal amoA, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used amoA primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal nirK was expressed 10–100-fold more than amoA in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.

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Section: Introductionmentioning

confidence: 67%

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

2012

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“…The ratios of a lab-scale column biofilm reactor (Okabe et al, 2011) and a full scale floc based sequential PN reactor (Desloover et al, 2011) were higher than the other reactors. The variation in N 2 O emission in previous studies (Figure 1) is attributed to a complicated pathway of biological and chemical N 2 O production, for example, NH 2 OH oxidation by AOB, NO reduction by heterotrophic bacteria and AOB, and chemodenitrification (Poughon et al, 2001;Lu and Chandran, 2010;Wrage et al, 2001;van Cleemput, 1998) and consumption (N 2 O reduction by heterotrophic bacteria and AOB (Pan et al, 2012;Schmidt et al, 2004)). Therefore, it was obvious that difference in operational parameters (DO concentration, NH 4 + and NO 2 -concentration, COD/N ratio, NH 4 + loading rate, and pH) 13 of the PN reactors could strongly affect them (Kampschreur et al, 2009a;Law et al, 2011;Burgess et al, 2002).…”

Section: Fluorescence In Situ Hybridization (Fish)mentioning

confidence: 99%

“…During nitrification, it is produced from hydroxylamine (NH 2 OH) as a side product of the oxidation of ammonium (NH 4 + ) to nitrite (NO 2 -) (Poughon et al, 2001;Hooper and Terry, 1979). During denitrification, N 2 O is produced as an intermediate during reduction of nitrate to N 2 by heterotrophic denitrifiers (Lu and Chandran, 2010;Schmidt et al, 2004). Some ammonia-oxidizing bacteria (AOB) reduce NO 2 -to N 2 O or N 2 through a process called nitrifier denitrification (Tallect et al, 2006;Wrage et al, 2001;Colliver and Stephenson, 2000).…”

Section: Introductionmentioning

confidence: 99%

Source identification of nitrous oxide on autotrophic partial nitrification in a granular sludge reactor

et al. 2013

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Emission of nitrous oxide (N 2 O) during biological wastewater treatment is of growing concern since N 2 O is a major stratospheric ozone-depleting substance and an important greenhouse gas. The emission of N 2 O from a lab-scale granular sequencing batch reactor (SBR) for partial nitrification (PN) treating synthetic wastewater without organic carbon was therefore determined in this study, because PN process is known to produce more N 2 O than conventional nitrification processes. The average N 2 O emission rate from the SBR was 0.32 ± 0.17 mg-N L -1 h -1 , corresponding to the average emission of N 2 O of 0.8 ± 0.4% of the incoming nitrogen load (1.5 ± 0.8% of the converted NH 4 + ). Analysis of dynamic concentration profiles during one cycle of the SBR operation demonstrated that N 2 O concentration in off-gas was the highest just after starting aeration whereas N 2 O concentration in effluent was gradually increased in the initial 40 min of the aeration period and was decreased thereafter. Isotopomer analysis was conducted to identify the main N 2 O production pathway in the reactor during one cycle. The hydroxylamine (NH 2 OH) oxidation pathway accounted for 65% of the total N 2 O production in the initial phase during one cycle, whereas contribution of the NO 2 -reduction pathway to N 2 O production was comparable with that of the NH 2 OH oxidation pathway in the latter phase. In addition, 3 spatial distributions of bacteria and their activities in single microbial granules taken from the reactor were determined with microsensors and by in situ hybridization. Partial nitrification occurred mainly in the oxic surface layer of the granules and ammonia-oxidizing bacteria were abundant in this layer. N 2 O production was also found mainly in the oxic surface layer. Based on these results, although N 2 O was produced mainly via NH 2 OH oxidation pathway in the autotrophic partial nitrification reactor, N 2 O production mechanisms were complex and could involve multiple N 2 O production pathways.

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“…Nitrous oxide, as an important component of the N cycle, is produced by biological processes such as denitrification and nitrification in terrestrial and aquatic systems (Schmidt et al, 2004;Smith and Arah, 1990;Wrage et al, 2001). In order to accurately estimate preindustrial N 2 O emissions using the processbased Dynamic Land Ecosystem Model (DLEM; Tian et al, 2010), uncertainties associated with key parameters, such as maximum nitrification and denitrification rates, biological N fixation (BNF) rates, and the adsorption coefficient for soil ammonium (NH + 4 ) and nitrate (NO − 3 ), were required to be considered in model simulation.…”

Section: Introductionmentioning

confidence: 99%

Preindustrial nitrous oxide emissions from the land biosphere estimated by using a global biogeochemistry model

Tian

Lü

et al. 2017

Clim. Past

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Abstract. To accurately assess how increased global nitrous oxide (N 2 O) emission has affected the climate system requires a robust estimation of the preindustrial N 2 O emissions since only the difference between current and preindustrial emissions represents net drivers of anthropogenic climate change. However, large uncertainty exists in previous estimates of preindustrial N 2 O emissions from the land biosphere, while preindustrial N 2 O emissions on the finer scales, such as regional, biome, or sector scales, have not been well quantified yet. In this study, we applied a processbased Dynamic Land Ecosystem Model (DLEM) to estimate the magnitude and spatial patterns of preindustrial N 2 O fluxes at the biome, continental, and global level as driven by multiple environmental factors. Uncertainties associated with key parameters were also evaluated. Our study indicates that the mean of the preindustrial N 2 O emission was approximately 6.20 Tg N yr −1 , with an uncertainty range of 4.76 to 8.13 Tg N yr −1 . The estimated N 2 O emission varied significantly at spatial and biome levels. South America, Africa, and Southern Asia accounted for 34.12, 23.85, and 18.93 %, respectively, together contributing 76.90 % of global total emission. The tropics were identified as the major source of N 2 O released into the atmosphere, accounting for 64.66 % of the total emission. Our multi-scale estimates provide a robust reference for assessing the climate forcing of anthropogenic N 2 O emission from the land biosphere

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Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants

Cited by 168 publications

References 35 publications

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

Source identification of nitrous oxide on autotrophic partial nitrification in a granular sludge reactor

Preindustrial nitrous oxide emissions from the land biosphere estimated by using a global biogeochemistry model

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