Nitrite isotopes as tracers of marine N cycle processes

Particle-associated denitrification is the primary source of N2O in oxic coastal waters

The heavily human-perturbed coastal oceans are hotspots of nitrous oxide (N2O) emission to the atmosphere. The processes underpinning the N2O flux, however, remain poorly understood, leading to large uncertainties in assessing global N2O budgets. Using a suite of nitrogen isotope labeling experiments, we show that multiple processes contribute to N2O production throughout the estuarine-coastal gradient, sustaining intensive N2O flux to the atmosphere. Unexpectedly, denitrification, rather than ammonia oxidation as previously assumed, constitutes the major source of N2O in well-oxygenated coastal waters. Size-fractionated manipulation experiments with gene analysis further reveal niche partitioning of ammonia oxidizers and denitrifiers across the particle size spectrum; denitrification dominated on large particles and ammonia oxidizers on small particles. Total N2O production rate increases with substrate and particle concentrations, suggesting a crucial interplay between nutrients and particles in controlling N2O production. The controlling factors identified here may help understand climate feedback mechanisms between human activity and coastal oceans.

Nitrogen Kinetic Isotope Effects of Nitrification by the Complete Ammonia Oxidizer Nitrospira inopinata

Analysis of nitrogen isotope fractionation effects is useful for tracing biogeochemical nitrogen cycle processes. Nitrification can cause large nitrogen isotope effects through the enzymatic oxidation of ammonia (NH₃) via nitrite (NO₂⁻) to nitrate (NO₃⁻) (¹⁵ε_NH4+→NO2- and ¹⁵ε_NO2-→NO3-). The isotope effects of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and of nitrite-oxidizing bacteria (NOB) have been analyzed previously. Here, we studied the nitrogen isotope effects of the complete ammonia oxidizer (comammox) Nitrospira inopinata that oxidizes NH₃ to NO₃⁻. At high ammonium (NH₄⁺) availability (1 mM) and pH between 6.5 and 8.5, its ¹⁵ε_NH4+→NO2- ranged from −33.1 to −27.1‰ based on substrate consumption (residual substrate isotopic composition) and −35.5 to −31.2‰ based on product formation (cumulative product isotopic composition), while the ¹⁵ε_NO2-→NO3- ranged from 6.5 to 11.1‰ based on substrate consumption. These values resemble isotope effects of AOB and AOA and of NOB in the genus Nitrospira, suggesting the absence of fundamental mechanistic differences between key enzymes for ammonia and nitrite oxidation in comammox and canonical nitrifiers. However, ambient pH and initial NH₄⁺ concentrations influenced the isotope effects in N. inopinata. The ¹⁵ε_NH4+→NO2- based on product formation was smaller at pH 6.5 (−31.2‰) compared to pH 7.5 (−35.5‰) and pH 8.5 (−34.9‰), while ¹⁵ε_NO2-→NO3- was smaller at pH 8.5 (6.5‰) compared to pH 7.5 (8.8‰) and pH 6.5 (11.1‰). Isotopic fractionation via ¹⁵ε_NH4+→NO2- and ¹⁵ε_NO2-→NO3- was smaller at 0.1 mM NH₄⁺ compared to 0.5 to 1.0 mM NH₄⁺. Environmental factors, such as pH and NH₄⁺ availability, therefore need to be considered when using isotope effects in ¹⁵N isotope fractionation models of nitrification.

IMPORTANCE Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification. However, the contribution of comammox to nitrification in environmental and technical systems is far from being completely understood. This study revealed that, despite a phylogenetically distinct enzymatic repertoire for ammonia oxidation, nitrogen isotope effects of ¹⁵ε_NH4+→NO2- and ¹⁵ε_NO2-→NO3- in comammox do not differ significantly from those of canonical nitrifiers. Thus, nitrogen isotope effects are not suitable indicators to decipher the contribution of comammox to nitrification in environmental samples. Moreover, this is the first systematic study showing that the ambient pH and NH₄⁺ concentration influence the isotope effects of nitrifiers. Hence, these key parameters should be considered in comparative analyses of isotope effects of nitrifiers across different growth conditions and environmental samples.

Multiple isotopic compositions reveal complex nitrogen cycling in a subtropical estuary

Nitrogen (N) pollution and the resulting eutrophication can have deleterious consequences on estuaries, such as hypoxia, fish kills, and loss of biotic diversity. An understanding of N sources and cycling in estuaries is fundamental to determining how to effectively manage these ecologically and commercially important areas. We applied a multiple-isotopic approach to examine the transformations and sources of the N pools in the Pearl River Estuary (PRE) during winter. The surface water in the West PRE was characterized by low salinity and high NO₃^-, while that in the east had high salinity and low NO₃^-. The NO₃^- in the West PRE was largely regulated by a conservative mixing process. In contrast, assimilation and nitrification dominated in the East PRE, which was attributed to the long water-residence time. For the first time, the source contributions of NO₃^- and NH₄⁺ were estimated by isotope mixing models. Our results suggest that river discharge and nitrification contributed 81% and 12% to the NO₃^- pool, respectively. A major portion (68%) of the NH₄⁺ was from river discharge, with the remainder likely from sewage and the aquitard-aquifer system. Our study demonstrates that internal nitrification can potentially be of pivotal importance in determining the NO₃^- level in an estuary and its export to coastal waters.

Influence of δ18 O of water on measurements of δ18 O of nitrite and nitrate

RATIONALE

Oxygen isotope ratio measurements of NO₂ ^- and NO₃ ^- by the azide method and denitrifier method are sensitive to the δ¹⁸ O value of the sample water. However, the influence of δ¹⁸ O_H2O on those measurements has not been quantitatively evaluated and documented so far. Therefore, we investigated the influence of δ¹⁸ O_H2O of a sample on the δ¹⁸ O analysis of NO₂ ^- and NO₃ ^- .

METHODS

We prepared NO₂ ^- and NO₃ ^- standards (with known δ¹⁸ O_NO2- and δ¹⁸ O_NO3- values) dissolved in waters having different δ¹⁸ O_H2O values (δ¹⁸ O_H2O  = -12.6, 25.9, 56.7, and 110.1‰). Nitrite and nitrate were converted into N₂ O using the azide method and the denitrifier method, respectively. The isotope ratios of the generated N₂ O were measured with a Sercon purge-and-trap gas chromatography/isotope ratio mass spectrometry (PT-GC/IRMS) system. The measured δ¹⁸ O values of the produced N₂ O were plotted against known δ¹⁸ O_NO2- and δ¹⁸ O_NO3- values to evaluate the influence of exchange of an oxygen atom with H₂ O during the conversion of NO₂ ^- into N₂ O and NO₃ ^- into N₂ O, respectively.

RESULTS

The degree of oxygen isotope exchange was 10.8 ± 0.3% in the azide method and 5.5 ± 1.0% in the denitrifier method, indicating that the azide method is more susceptible to artifacts arising from differences in the δ¹⁸ O_H2O value of water than the denitrifier method. Thus, the intercept of the standard calibration curve must be corrected to account for differences in δ¹⁸ O_H2O . Abiotic NO₂ -H₂ O equilibrium isotope effect experiments yielded a rate constant of (1.13 ± 007) × 10^-2 (h^-1 ) and an equilibrium isotope effect of 11.9 ± 0.1‰ under the condition of pH = 7.5, 30°C, and 2.5% salinity.

CONCLUSIONS

Oxygen isotope ratio measurements of NO₂ ^- by the azide method are highly sensitive to δ¹⁸ O_H2O as a result of significant oxygen isotope exchange between NO₂ ^- and H₂ O. Therefore, to obtain the most accurate measurements water with the same δ¹⁸ O_H2O value as that of the sample must be used to make the NO₂ ^- and NO₃ ^- standards.

Nitrogen and Oxygen Isotope Signatures of Nitrogen Compounds during Anammox in the Laboratory and a Wastewater Treatment Plant

Isotopic fractionation factors against ¹⁵N and ¹⁸O during anammox (anaerobic ammonia oxidization by nitrite) are critical for evaluating the importance of this process in natural environments. We performed batch incubation experiments with an anammox-dominated biomass to investigate nitrogen (N) and oxygen (O) isotopic fractionation factors during anammox and also examined apparent isotope fractionation factors during anammox in an actual wastewater treatment plant. We conducted one incubation experiment with high δ¹⁸O of water to investigate the effects of water δ¹⁸O. The N isotopic fractionation factors estimated from incubation experiments and the wastewater treatment plant were similar to previous values. We also found that the N isotopic effect (¹⁵ε_NXR of -77.8 to -65.9‰ and ¹⁵Δ_NXR of -31.3 to -30.4‰) and possibly O isotopic effect (¹⁸ε_NXR of -20.6‰) for anaerobic nitrite oxidation to nitrate were inverse. We applied the estimated isotopic fractionation factors to the ordinary differential equation model to clarify whether anammox induces deviations in the δ¹⁸O vs δ¹⁵N of nitrate from a linear trajectory of 1, similar to heterotrophic denitrification. Although this deviation has been attributed to nitrite oxidation, the O isotopic fractionation factor for anammox is crucial for obtaining a more detailed understanding of the mechanisms controlling this deviation. In our model, anammox induced the trajectory of the δ¹⁸O vs δ¹⁵N of nitrate during denitrification to less than one, which strongly indicates that this deviation is evidence of nitrite oxidation by anammox under denitrifying conditions.

Dual nitrogen and oxygen isotope fractionation during anaerobic ammonium oxidation by anammox bacteria

Natural abundance of stable nitrogen (N) and oxygen (O) isotopes are invaluable biogeochemical tracers for assessing the N transformations in the environment. To fully exploit these tracers, the N and O isotope effects (¹⁵ε and ¹⁸ε) associated with the respective nitrogen transformation processes must be known. However, the N and O isotope effects of anaerobic ammonium oxidation (anammox), one of the major fixed N sinks and NO₃^- producers, are not well known. Here, we report the dual N and O isotope effects associated with anammox by three different anammox bacteria including "Ca. Scalindua japonica", a putative marine species, which were measured in continuous enrichment culture experiments. All three anammox species yielded similar N isotope effects of NH₄⁺ oxidation to N₂ (¹⁵ε_NH4→N2) ranging from 30.9‰ to 32.7‰ and inverse kinetic isotope effects of NO₂^- oxidation to NO₃^- (¹⁵ε_NO2→NO3 = -45.3‰ to -30.1‰). In contrast, ¹⁵ε_NO2→N2 (NO₂^- reduction to N₂) were significantly different among three species, which is probably because individual anammox bacteria species might possess different types of nitrite reductase. We also report the combined O isotope effects for NO₂^- oxidation (¹⁸E_NO2→NO3) by anammox bacteria. These obtained dual N and O isotopic effects could provide significant insights into the contribution of anammox bacteria to the fixed N loss and NO₂^- reoxidation (N recycling) in various natural environments.

Constraining the Oxygen Isotopic Composition of Nitrate Produced by Nitrification

Measurements of the stable isotope ratios of nitrogen (¹⁵N/¹⁴N) and oxygen (¹⁸O/¹⁶O) in nitrate (NO₃^-) enable identification of sources, dispersal, and fate of natural and contaminant NO₃^- in aquatic environments. The ¹⁸O/¹⁶O of NO₃^- produced by nitrification is often assumed to reflect the proportional contribution of oxygen atom sources, water, and molecular oxygen, in a 2:1 ratio. Culture and seawater incubations, however, indicate oxygen isotopic equilibration between nitrite (NO₂^-) and water, and kinetic isotope effects for oxygen atom incorporation, which modulate the NO₃^{- 18}O/¹⁶O produced during nitrification. To investigate the influence of kinetic and equilibrium effects on the isotopic composition of NO₃^- produced from the nitrification of ammonia (NH₃), we incubated streamwater supplemented with ammonium (NH₄⁺) and increments of ¹⁸O-enriched water. Resulting NO₃^{- 18}O/¹⁶O ratios showed (1) a disproportionate sensitivity to the ¹⁸O/¹⁶O ratio of water, mediated by isotopic equilibration between water and NO₂^-, as well as (2) kinetic isotope discrimination during O atom incorporation from molecular oxygen and water. Empirically, the NO₃^{- 18}O/¹⁶O ratios thus produced fortuitously converge near the ¹⁸O/¹⁶O ratio of water. More elevated NO₃^{- 18}O/¹⁶O values commonly reported in soils and oxic groundwater may thus derive from processes additional to nitrification, including NO₃^- reduction.