scholarly journals Distinguishing Nitrous Oxide Production from Nitrification and Denitrification on the Basis of Isotopomer Abundances

2006 ◽  
Vol 72 (1) ◽  
pp. 638-644 ◽  
Author(s):  
R. L. Sutka ◽  
N. E. Ostrom ◽  
P. H. Ostrom ◽  
J. A. Breznak ◽  
H. Gandhi ◽  
...  
Keyword(s):  
Nitrogen Isotopes ◽  
Ammonia Oxidation ◽  
Nitrite Reduction ◽  
Site Preference ◽  
Ammonia Oxidizers ◽  
Site Preferences ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production ◽  
Nitrification And Denitrification ◽  
Nitrate And Nitrite

ABSTRACT The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 ± 1.2‰, 32.5 ± 0.6‰, and 35.6 ± 1.4‰ for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 ± 4.2‰) was similar to that produced during hydroxylamine oxidation (33.5 ± 1.2‰) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 ± 1.7‰), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (−0.6 ± 1.9‰ and −0.5 ± 1.9‰, respectively) were similar to those during nitrate reduction (−0.5 ± 1.9‰ and −0.5 ± 0.6‰, respectively), indicating no influence of either substrate on site preference. Site preferences of ∼33‰ and ∼0‰ are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.

scholarly journals Isotopic evidence for alteration of nitrous oxide emissions and producing pathways contribution under nitrifying conditions

2019 ◽  
Author(s):  
Guillaume Humbert ◽  
Mathieu Sébilo ◽  
Justine Fiat ◽  
Longqi Lang ◽  
Ahlem Filali ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Biofilm Reactor ◽  
Nitrite Reduction ◽  
Nitrous Oxide Emissions ◽  
Site Preference ◽  
N2o Emissions ◽  
Ammonium Oxidation ◽  
N2o Production ◽  
Oxidation Rates ◽  
Nitrifier Denitrification

Abstract. Nitrous oxide (N2O) emissions by a nitrifying biofilm reactor were investigated with N2O isotopocules. The site preference of N2O (15N-SP) indicated the contribution of producing and consuming pathways in response to changes in oxygenation level (from 0 to 21 % O2 in the gas mix), temperature (from 13.5 to 22.3 °C), and ammonium concentrations (from 6.2 to 62.1 mg N L−1). Nitrite reduction, either nitrifier-denitrification or heterotrophic denitrification, was the main N2O producing pathway under the tested conditions. Nitrite oxidation rates decreased as compared to ammonium oxidation rates at temperatures above 20 °C and sub-optimal oxygen levels, increasing N2O production by the nitrite reduction pathway. Below 20 °C, a difference in temperature sensitivity between hydroxylamine and ammonium oxidation rates is most likely responsible for an increase in the N2O production via the hydroxylamine oxidation pathway (nitrification). A negative correlation between the reaction kinetics and the apparent isotope fractionation was additionally shown from the variations of δ15N and δ18O values of N2O produced from ammonium.

scholarly journals Isotopic evidence for alteration of nitrous oxide emissions and producing pathways' contribution under nitrifying conditions

2020 ◽  
Vol 17 (4) ◽  
pp. 979-993
Author(s):  
Guillaume Humbert ◽  
Mathieu Sébilo ◽  
Justine Fiat ◽  
Longqi Lang ◽  
Ahlem Filali ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Biofilm Reactor ◽  
Nitrite Reduction ◽  
Nitrous Oxide Emissions ◽  
Site Preference ◽  
N2o Emissions ◽  
Ammonium Oxidation ◽  
N2o Production ◽  
Oxidation Rates ◽  
Nitrifier Denitrification

Abstract. Nitrous oxide (N2O) emissions from a nitrifying biofilm reactor were investigated with N2O isotopocules. The nitrogen isotopomer site preference of N2O (15N-SP) indicated the contribution of producing and consuming pathways in response to changes in oxygenation level (from 0 % to 21 % O2 in the gas mix), temperature (from 13.5 to 22.3 ∘C) and ammonium concentrations (from 6.2 to 62.1 mg N L−1). Nitrite reduction, either nitrifier denitrification or heterotrophic denitrification, was the main N2O-producing pathway under the tested conditions. Difference between oxidative and reductive rates of nitrite consumption was discussed in relation to NO2- concentrations and N2O emissions. Hence, nitrite oxidation rates seem to decrease as compared to ammonium oxidation rates at temperatures above 20 ∘C and under oxygen-depleted atmosphere, increasing N2O production by the nitrite reduction pathway. Below 20 ∘C, a difference in temperature sensitivity between hydroxylamine and ammonium oxidation rates is most likely responsible for an increase in N2O production via the hydroxylamine oxidation pathway (nitrification). A negative correlation between the reaction kinetics and the apparent isotope fractionation was additionally shown from the variations of δ15N and δ18O values of N2O produced from ammonium. The approach and results obtained here, for a nitrifying biofilm reactor under variable environmental conditions, should allow for application and extrapolation of N2O emissions from other systems such as lakes, soils and sediments.

scholarly journals Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Paula B. Matheus Carnevali ◽  
Adi Lavy ◽  
Alex D. Thomas ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Nitrogen Compound ◽  
Nitrite Reduction ◽  
Soil Microbiome ◽  
Metabolic Potential ◽  
Floodplain Soil ◽  
Core Microbiome ◽  
East River ◽  
Floodplain Soils ◽  
Nitrate And Nitrite

Abstract Background Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor. Results We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor. Conclusions The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

scholarly journals Nitrous oxide distribution and its origin in the central and eastern South Pacific Subtropical Gyre

2007 ◽  
Vol 4 (3) ◽  
pp. 1673-1702 ◽  
Author(s):  
J. Charpentier ◽  
L. Farias ◽  
N. Yoshida ◽  
N. Boontanon ◽  
P. Raimbault
Keyword(s):  
Nitrous Oxide ◽  
Coastal Upwelling ◽  
South Pacific ◽  
Site Preference ◽  
Intermediate Water ◽  
Low Oxygen ◽  
N2o Production ◽  
Oxide Production ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production

Abstract. The biogeochemical mechanism of bacterial N2O production in the ocean has been the subject of many discussions in recent years. New isotopomeric tools can help further knowledge on N2O sources in natural environments. This research shows and compares hydrographic, nitrous oxide concentration, and N2O isotopic and isotopomeric data from three stations across the South Pacific Ocean, from the center of the subtropical oligotrophic gyre (~26° S; 114° W) to the upwelling zone along the central Chilean coast (~34° S). Althought AOU/N2O and NO3− trends support the idea that most of N2O source (mainly from intermediate water (200–1000 m)) come from nitrification, N2O isotopomeric composition (intramolecular distribution of 15N isotopes in N2O) reveals an abrupt change in the mechanism of nitrous oxide production, always observed through lower SP (site preference of 15N), at a high – stability layer, where particles could act as microsites and N2O would be produced by nitrifier denitrification (reduction of nitrite to nitrous oxide mediated by primary nitrifiers). There, nitrifier denitrification can account for 40% and 50% (center and east border of the gyre, respectively) of the nitrous oxide produced in this specific layer. This process could be associated with the deceleration of sinking organic particles in highly stable layers of the water column. In constrast, coastal upwelling system is characterized by oxygen deficient condition and some N deficit in a eutrophic system. Here, nitrous oxide accumulates up to 480% saturation, and isotopic and isotopomer signal show highly complex nitrous oxide production processes, which presumably reflect both the effect of nitrification and denitrification at low oxygen levels on N2O production, but non N2O consumption by denitrification was observed.

scholarly journals Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

2020 ◽  
Author(s):  
Paula B. Matheus Carnevali ◽  
Adi Lavy ◽  
Alex D. Thomas ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Nitrite Reduction ◽  
Soil Microbiome ◽  
Watershed Scale ◽  
Metabolic Potential ◽  
Floodplain Soil ◽  
East River ◽  
Floodplain Soils ◽  
Biogeochemical Transformations ◽  
Nitrate And Nitrite

AbstractBiogeochemical exports of C, N, S and H2 from watersheds are modulated by the activity of microorganisms that function over micron scales. This disparity of scales presents a substantial challenge for development of predictive models describing watershed function. Here, we tested the hypothesis that meander-bound regions exhibit patterns of microbial metabolic potential that are broadly predictive of biogeochemical processes in floodplain soils along a river corridor. We intensively sampled floodplain soils located in the upper, middle, and lower reaches of the East River in Colorado and reconstructed 248 draft quality genomes representative at a sub-species level. Approximately one third of the representative genomes were detected across all three locations with similar levels of abundance, and despite the very high microbial diversity and complexity of the soils, ~15% of species were detected in two consecutive years. A core floodplain microbiome was enriched in bacterial capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. We did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, at the watershed scale meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations in floodplain soils. Given this, we conducted a transcriptomic analysis of the middle site. Overall, the most highly transcribed genes were amoCAB and nxrAB (for nitrification) followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Thus, widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

scholarly journals Straw mulching and nitrogen application altered ammonia oxidizers communities and improved soil quality in the alkaline purple soil of southwest China

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Songhe Chen ◽  
Rencai Gao ◽  
Xiaoling Xiang ◽  
Hongkun Yang ◽  
Hongliang Ma ◽  
...  
Keyword(s):  
Soil Quality ◽  
Ammonia Oxidation ◽  
Management Strategies ◽  
Rflp Analysis ◽  
Available Phosphorus ◽  
Purple Soil ◽  
Ammonia Oxidizers ◽  
Nitrogen Application ◽  
Available Nitrogen ◽  
Straw Mulching

AbstractMicrobe-mediated ammonia oxidation is a key process in soil nitrogen cycle. However, the effect of maize straw mulching on the ammonia oxidizers in the alkaline purple soil remains largely unknown. A three-year positioning experiment was designed as follows: straw mulching measures as the main-plot treatment and three kinds of nitrogen application as the sub-plot treatment. We found the contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK), available nitrogen (AN), available phosphorus (AP), and NH4+-N were increased after straw mulching and nitrogen application in alkaline purple soil, so did the amoA genes abundance of ammonia-oxidizing archaeal (AOA) and bacterial (AOB). Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that Thaumarchaeote (448-bp T-RF) was dominated the AOA communities, whereas Nitrosospira sp (111-bp T-RF) dominated the AOB communities. The community compositions of both AOA and AOB were altered by straw mulching and nitrogen application in alkaline purple soil, however, the AOB communities was more responsive than AOA communities to the straw mulching and nitrogen application. Further analysis indicated that SOC and AP were the main factors affecting the abundance and community compositions of AOA and AOB in alkaline purple soil. The present study reported that straw mulching and nitrogen strategies differently shape the soil ammonia oxidizers community structure and abundance, which should be considered when evaluating agricultural management strategies regarding their sustainability and soil quality.

scholarly journals Low nitrous oxide production through nitrifier-denitrification in intermittent-feed high-rate nitritation reactors

2017 ◽  
Vol 123 ◽  
pp. 429-438 ◽  
Author(s):  
Qingxian Su ◽  
Chun Ma ◽  
Carlos Domingo-Félez ◽  
Anne Sofie Kiil ◽  
Bo Thamdrup ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
High Rate ◽  
Oxide Production ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production

Computational Studies of Magnesium and Strontium Substitution in Hydroxyapatite

2012 ◽  
Vol 529-530 ◽  
pp. 123-128 ◽  
Author(s):  
Flora E. Imrie ◽  
Marta Corno ◽  
Piero Ugliengo ◽  
Iain R. Gibson
Keyword(s):  
Density Functional ◽  
Structural Changes ◽  
Harmonic Approximation ◽  
Site Preference ◽  
Ionic Radii ◽  
Biologically Relevant ◽  
Site Preferences ◽  
Mechanical Approach ◽  
Quantum Mechanical Approach ◽  
Mg Substitution

The properties of hydroxyapatite can be improved by substitution of biologically relevant ions, such as magnesium (Mg) and strontium (Sr), into its structure. Previous work in the literature has not reached agreement as to site preferences in these substitutions, and there are suggestions that these may change with differing levels of substitution. The current work adopted a quantum mechanical approach based on density functional theory using the CRYSTAL09 code to investigate the structural changes relating to, and site preferences of, magnesium and strontium substitution (to 10 mol%) in hydroxyapatites and also to predict the corresponding vibrational spectra in the harmonic approximation. The structures underwent full geometrical optimisation within the P63 space group, indicating an energetic site preference for the Ca (2) site in the case of Mg substitution, and the Ca (1) site in the case of Sr. Shrinkage of the unit cell was observed in the case of Mg substitution, and expansion in the case of Sr substitution, in agreement with the corresponding ionic radii. Thermodynamic properties of the structures obtained from the harmonic vibrational frequency calculations confirmed that the structures were minima on the potential energy surface. Isotopic substitutions indicated that the main contribution of Sr and Mg to vibrational modes is at frequencies < 400 cm-1.

scholarly journals Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors

2012 ◽  
Vol 367 (1593) ◽  
pp. 1213-1225 ◽  
Author(s):  
Stephen Spiro
Keyword(s):  
Nitrous Oxide ◽  
Transcription Initiation ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Environmental Signals ◽  
Production And Consumption ◽  
Genes Encoding ◽  
Nitrous Oxide Production ◽  
Biochemical Mechanisms ◽  
Nitrate And Nitrite

Several biochemical mechanisms contribute to the biological generation of nitrous oxide (N 2 O). N 2 O generating enzymes include the respiratory nitric oxide (NO) reductase, an enzyme from the flavo-diiron family, and flavohaemoglobin. On the other hand, there is only one enzyme that is known to use N 2 O as a substrate, which is the respiratory N 2 O reductase typically found in bacteria capable of denitrification (the respiratory reduction of nitrate and nitrite to dinitrogen). This article will briefly review the properties of the enzymes that make and consume N 2 O, together with the accessory proteins that have roles in the assembly and maturation of those enzymes. The expression of the genes encoding the enzymes that produce and consume N 2 O is regulated by environmental signals (typically oxygen and NO) acting through regulatory proteins, which, either directly or indirectly, control the frequency of transcription initiation. The roles and mechanisms of these proteins, and the structures of the regulatory networks in which they participate will also be reviewed.

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