15N/14N ratio of dissolved N2O in the eastern tropical Pacific Ocean

Pyisotopomer: A Python package for obtaining intramolecular isotope ratio differences from mass spectrometric analysis of nitrous oxide isotopocules

RATIONALE

Obtaining nitrous oxide isotopocule measurements with isotope ratio mass spectrometry (IRMS) involves analyzing the ion current ratios of the nitrous oxide parent ion (N₂ O⁺ ) as well as those of the NO⁺ fragment ion. The data analysis requires correcting for "scrambling" in the ion source, whereby the NO⁺ fragment ion obtains the outer N atom from the N₂ O molecule. While descriptions exist for this correction, and interlaboratory intercalibration efforts have been made, there has yet to be published a package of code for implementing isotopomer calibrations.

METHODS

We developed a user-friendly Python package (pyisotopomer) to determine two coefficients (γ and κ) that describe scrambling in the IRMS ion source, and then used this calibration to obtain intramolecular isotope deltas in N₂ O samples.

RESULTS

With two appropriate reference materials, γ and κ can be determined robustly and accurately for a given IRMS system. An additional third reference material is needed to define the zero-point of the delta scale. We show that IRMS scrambling behavior can vary with time, necessitating regular calibrations. Finally, we present an intercalibration between two IRMS laboratories, using pyisotopomer to calculate γ and κ, and to obtain intramolecular N₂ O isotope deltas in lake water unknowns.

CONCLUSIONS

Given these considerations, we discuss how to use pyisotopomer to obtain high-quality N₂ O isotopocule data from IRMS systems, including the use of appropriate reference materials and frequency of calibration.

Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems

Anaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (¹⁵N/¹⁴N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor ¹⁵ε for the reduction of nitrite to N₂ is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of ¹⁵ε for the oxidation of nitrite to nitrate (inverse isotope effect, - 16 to - 43‰) and for the reduction of ammonium to N₂ (normal isotope effect, 19-32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.

Mechanisms responsible for N2O emissions from intertidal soils of the Yangtze Estuary

Estuarine and coastal wetland ecosystems are important sources of atmospheric nitrous oxide (N₂O). However, the underlying driver of emitted N₂O from estuarine and coastal wetlands remains poorly understood. Here, natural-abundance isotope technique was applied to characterize the processes responsible for N₂O emission from the intertidal soils of the Yangtze Estuary. Measured N₂O emission rates ranged from 0.70 to 2.15 μmol m^-2 h^-1, with relatively high values at the upper estuarine sites. The δ¹⁵N, δ¹⁸O and SP (intramolecular ¹⁵N site preference) of emitted N₂O varied from -4.5 to 6.7‰, 42.4 to 53.2‰, and 6.7 to 15.4‰, respectively. Gross N₂O production and consumption rates were within the ranges of 3.16-14.34 μmol m^-2 h^-1 and 2.22-12.54 μmol m^-2 h^-1, respectively, showing a similar spatial pattern to N₂O emission. N₂O consumption proportion varied from 69.56 to 90.31%, which was generally lower at the upper estuarine sites. The gross production rates and consumption degree of N₂O simultaneously controlled the variations in N₂O emission. Bacterial denitrification was the dominant production pathway (78.22-97.36%), while hydroxylamine (NH₂OH) oxidation contributed 2.64-21.78% to N₂O production. Soil pH, Fe²⁺/Fe³⁺, sulfide and substrate availability were probably the main factors governing the N₂O emission dynamics. Overall, these results highlight the substantial role of NH₂OH oxidation and N₂O consumption in N₂O release in redox-dynamic soils of estuarine intertidal wetlands.

Isotopocule analysis of biologically produced nitrous oxide in various environments

Natural abundance ratios of isotopocules, molecules that have the same chemical constitution and configuration, but that only differ in isotope substitution, retain a record of a compound's origin and reactions. A method to measure isotopocule ratios of nitrous oxide (N₂ O) has been established by using mass analysis of molecular ions and fragment ions. The method has been applied widely to environmental samples from the atmosphere, ocean, fresh water, soils, and laboratory-simulation experiments. Results show that isotopocule ratios, particularly the ¹⁵ N-site preference (difference between isotopocule ratios ¹⁴ N¹⁵ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O and ¹⁵ N¹⁴ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O), have a wide range that depends on their production and consumption processes. Observational and laboratory studies of N₂ O related to biological processes are reviewed and discussed to elucidate complex material cycles of this trace gas, which causes global warming and stratospheric ozone depletion. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:135-160, 2017.

Assessment of nitrogen and oxygen isotopic fractionation during nitrification and its expression in the marine environment

Nitrification is a microbially-catalyzed process whereby ammonia (NH(3)) is oxidized to nitrite (NO(2)(-)) and subsequently to nitrate (NO(3)(-)). It is also responsible for production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Because the microbes responsible for nitrification are primarily autotrophic, nitrification provides a unique link between the carbon and nitrogen cycles. Nitrogen and oxygen stable isotope ratios have provided insights into where nitrification contributes to the availability of NO(2)(-) and NO(3)(-), and where it constitutes a significant source of N(2)O. This chapter describes methods for determining kinetic isotope effects involved with ammonia oxidation and nitrite oxidation, the two independent steps in the nitrification process, and their expression in the marine environment. It also outlines some remaining questions and issues related to isotopic fractionation during nitrification.

Nylon production: an unknown source of atmospheric nitrous oxide

Nitrous oxide in the earth's atmosphere contributes to catalytic stratospheric ozone destruction and is also a greenhouse gas component. A precise budgetary accounting of N(2)O sources has remained elusive, and there is an apparent lack of source identification. One source of N(2)O is as a by-product in the manufacture of nylon, specifically in the preparation of adipic acid. Characterization of the reaction N(2)O stoichiometry and its isotopic composition with a simulated industrial adipic acid synthesis indicates that because of high rates of global adipic acid production, this N(2)O may account for approximately 10 percent of the increase observed for atmospheric N(2)O.

Isotopologue fractionation during N(2)O production by fungal denitrification

Identifying the importance of fungi to nitrous oxide (N2O) production requires a non-intrusive method for differentiating between fungal and bacterial N2O production such as natural abundance stable isotopes. We compare the isotopologue composition of N2O produced during nitrite reduction by the fungal denitrifiers Fusarium oxysporum and Cylindrocarpon tonkinense with published data for N2O production during bacterial nitrification and denitrification. The fractionation factors for bulk nitrogen isotope values for fungal denitrification were in the range -74.7 to -6.6 per thousand. There was an inverse relationship between the absolute value of the fractionation factors and the reaction rate constant. We interpret this in terms of variation in the relative importance of the rate constants for diffusion and enzymatic reduction in controlling the net isotope effect for N2O production during fungal denitrification. Over the course of nitrite reduction, the delta(18)O values for N2O remained constant and did not exhibit a relationship with the concentration characteristic of an isotope effect. This probably reflects isotopic exchange with water. Similar to the delta(18)O data, the site preference (SP; the difference in delta(15)N between the central and outer N atoms in N2O) was unrelated to concentration during nitrite reduction and, therefore, has the potential to act as a conservative tracer of production from fungal denitrification. The SP values of N2O produced by F. oxysporum and C. tonkinense were 37.1 +/- 2.5 per thousand and 36.9 +/- 2.8 per thousand, respectively. These SP values are similar to those obtained in pure culture studies of bacterial nitrification but quite distinct from SP values for bacterial denitrification. The large magnitude of the bulk nitrogen isotope fractionation and the delta(18)O values associated with fungal denitrification are distinct from bacterial production pathways; thus multiple isotopologue data holds much promise for resolving bacterial and fungal production. Our work further provides insight into the role that fungal and bacterial nitric oxide reductases have in determining site preference during N2O production.

Estimation of pathways of the production of greenhouse gases in the tropical swamp forest in Thailand by stable isotope investigation

Dynamics of greenhouse gases (N(2)O and CH(4)) with the dry-wet cycle along with the variation of oxidation-reduction boundaries were investigated in the tropical wetland in monsoon Asia. It was clarified that the production of N(2)O and CH(4) was closely related to the development of a redox boundary in the Bang Nara River systems. An intermittent increase in N(2)O was observed at the beginning of the rainy season, when a large amount of easily decomposable organic matter was introduced into the river. After 10 days, when dissolved oxygen was consumed completely at the middle reaches, the emission of CH(4) became maximal due to the possible occurrence of denitrification. The distribution of stable isotope ratios in N(2)O clearly demonstrated that nitrification is the major process for its production. Furthermore, the production of N(2)O in this study area was found to vary in time and space with changes in the redox boundary along the water flow.

Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria

Nitric oxide (NO) and nitrous oxide (N2O) are climatically important trace gases that are produced by both nitrifying and denitrifying bacteria. In the denitrification pathway, N2O is produced from nitric oxide (NO) by the enzyme nitric oxide reductase (NOR). The ammonia-oxidizing bacterium Nitrosomonas europaea also possesses a functional nitric oxide reductase, which was shown recently to serve a unique function. In this study, sequences homologous to the large subunit of nitric oxide reductase (norB) were obtained from eight additional strains of ammonia-oxidizing bacteria, including Nitrosomonas and Nitrosococcus species (i.e., both beta- and gamma-Proteobacterial ammonia oxidizers), showing widespread occurrence of a norB homologue in ammonia-oxidizing bacteria. However, despite efforts to detect norB homologues from Nitrosospira strains, sequences have not yet been obtained. Phylogenetic analysis placed nitrifier norB homologues in a subcluster, distinct from denitrifier sequences. The similarities and differences of these sequences highlight the need to understand the variety of metabolisms represented within a "functional group" defined by the presence of a single homologous gene. These results expand the database of norB homologue sequences in nitrifying bacteria.

Site-selective nitrogen isotopic ratio measurement of nitrous oxide using 2 microm diode lasers

We demonstrate a high-precision measurement of the isotopomer abundance ratio 14N(15)N(16)O/15N(14)N(16)O/14N(14)N(16)O (approximately 0.37/0.37/100) using three wavelength-modulated 2 microm diode lasers combined with a multipass cell which provides different optical pathlengths of 100 and 1 m to compensate the large abundance difference. A set of absorption lines for which the absorbances have almost the same temperature dependence are selected so that the effect of a change in gas temperature is minimized. The test experiment using pure nearly natural-abundance N(2)O samples showed that the site-selective 15N/14N ratios can be measured relative to a reference material with a precision of +/-3 x 10(-4) (+/-0.3 per thousand) in approximately 2 h.

Gas chromatography/isotope-ratio mass spectrometry method for high-precision position-dependent 15N and 18O measurements of atmospheric nitrous oxide

We describe an automated gas chromatography/isotope-ratio mass spectrometry (GC/IRMS) method for the determination of the (18)O and position-resolved (15)N content of nitrous oxide at natural isotope abundance. The position information is obtained from successive measurement of the isotopic composition of the N(2)O(+) ion at m/z 44, 45, 46 and the NO(+) fragment ion at m/z 30, 31. The fragment ion analysis is complicated by a non-linearity in the mass spectrometer that has to be taken into account. Evaluation of the absolute peak areas allows for a simultaneous determination of the N(2)O mixing ratio for atmospheric samples. Samples with mixing ratios ranging from a few nmol/mol up to the percent level can be analyzed using different sample inlet systems. The high concentration inlet system provides an easy and quick method to carry out various diagnostic tests, in particular to perform realistic linearity tests. A gas chromatographic set-up with a split column and a backflush possibility improves analytical precision and excludes interferences by substances with long retention times from preceding runs. We also describe a new open split interface that uses only a single transfer capillary to the mass spectrometer for sample and reference gas.

Constraining the atmospheric N2O budget from intramolecular site preference in N2O isotopomers

Nitrous oxide (N2O) is an important trace gas in the atmosphere. It is an active greenhouse gas in the troposphere and it also controls ozone concentration in the stratosphere through nitric oxide production. One way to trace the geochemical cycle of N2O is by measuring the natural abundance of stable isotopes, namely 15N and 18O (refs 2-15). Here we report the intramolecular distribution of 15N within the linear NNO molecule, determined by measuring molecular and fragment ions of N2O on a modified mass spectrometer. This revealed a preference for 15N at the central N position, or alpha-site, within N2O isotopomers (isotope-containing molecules). Moreover, this preference varied significantly throughout the atmosphere. In the troposphere, low alpha-site preference indicates local emission of N2O from soils and fossil-fuel combustion, each with distinct isotopomer signatures, which then mixes with background N2O. In the stratosphere, on the other hand, loss of N2O is observed as enhanced alpha-site preference for 15N, due to fractionation during ultraviolet photolysis of N2O. We have constructed an atmospheric mass balance of N2O, incorporating isotopomer abundance, which shows that the intramolecular distribution of 15N is a parameter that has the potential to increase significantly the resolution with which sources and sinks of N2O can be identified and quantified in the atmosphere.

Nitrogen cycling in coastal marine ecosystems

It is generally considered that nitrogen availability is one of the major factors regulating primary production in temperate coastal marine environments. Coastal regions often receive large anthropogenic inputs of nitrogen that cause eutrophication. The impact of these nitrogen additions has a profound effect in estuaries and coastal lagoons where water exchange is limited. Such increased nutrient loading promotes the growth of phytoplankton and fast growing pelagic macroalgae while rooted plants (sea-grasses) and benthic are suppressed due to reduced light availability. This shift from benthic to pelagic primary production introduces large diurnal variations in oxygen concentrations in the water column. In addition oxygen consumption in the surface sediments increases due to the deposition of readily degradable biomass. In this review the physico-chemical and biological factors regulating nitrogen cycling in coastal marine ecosystems are considered in relation to developing effective management programmes to rehabilitate seagrass communities in lagoons currently dominated by pelagic macroalgae and/or cyanobacteria.

Steady-state nitrogen isotope effects of N2 and N2O production in Paracoccus denitrificans

Nitrogen stable-isotope compositions (delta15N) can help track denitrification and N2O production in the environment, as can knowledge of the isotopic discrimination, or isotope effect, inherent to denitrification. However, the isotope effects associated with denitrification as a function of dissolved-oxygen concentration and their influence on the isotopic composition of N2O are not known. We developed a simple steady-state reactor to allow the measurement of denitrification isotope effects in Paracoccus denitrificans. With [dO2] between 0 and 1.2 microM, the N stable-isotope effects of NO3- and N2O reduction were constant at 28.6 per thousand +/- 1.9 per thousand and 12.9 per thousand +/- 2.6 per thousand, respectively (mean +/- standard error, n = 5). This estimate of the isotope effect of N2O reduction is the first in an axenic denitrifying culture and places the delta15N of denitrification-produced N2O midway between those of the nitrogenous oxide substrates and the product N2 in steady-state systems. Application of both isotope effects to N2O cycling studies is discussed.