Controls on the Isotopic Composition of Nitrite (δ¹⁵N and δ¹⁸O) during Denitrification in Freshwater Sediments

Abstract

The microbial reduction of nitrate, via nitrite into gaseous di-nitrogen (denitrification) plays a major role in nitrogen removal from aquatic ecosystems. Natural abundance stable isotope measurements can reveal insights into the dynamics of production and consumption of nitrite during denitrification. In this study, batch experiments with environmental bacterial communities were used to investigate variations of concentrations and isotope compositions of both nitrite and nitrate under anoxic conditions. To this end, denitrification experiments were carried out with nitrite or nitrate as sole electron acceptors at two substrate levels respectively. For experiments with nitrate as substrate, where the intermediate compound nitrite is both substrate and product of denitrification, calculations of the extent of isotope fractionation were conducted using a non-steady state model capable of tracing chemical and isotope kinetics during denitrification. This study showed that nitrogen isotope fractionation was lower during the use of nitrite as substrate (ε = −4.2 and −4.5‰ for both treatments) as compared to experiments where nitrite was produced as an intermediate during nitrate reduction (ε = −10 and −15‰ for both treatments). This discrepancy might be due to isotopic fractionation within the membrane of denitrifiers. Moreover, our results confirmed previously observed rapid biotic oxygen isotope exchange between nitrite and water.

Introduction

The growing world population requires an increased food production, necessitating the intensive use of nitrogen-containing synthetic fertilizers, which has led to nitrate pollution in many surface water and groundwater bodies^1–5. Even though essential for plants, dissolved nitrate can be responsible for contamination of drinking water supplies from surface and groundwaters, posing a potential threat to human health^6–10. Fortunately, it has been shown that denitrification plays a significant role in the mitigation of nitrate pollution^11–13. Denitrification is the microbial dissimilatory reduction of NO₃⁻ to N₂ via several steps, governed by different enzymes^14–16. During this beneficial removal of NO₃⁻, the intermediates nitrite (NO₂⁻), a toxic component at low concentrations¹⁷, and nitrous oxide (N₂O), which participates in ozone layer destruction¹⁸, are formed. Whereas the production of N₂O has received considerable attention due to its role as a potent greenhouse gas, the intermediate compound nitrite (NO₂⁻) has received much less attention since it is often assumed to be thermodynamically unstable, short-lived, and therefore not accumulating in the environment. However, nitrite has been detected at concentrations exceeding the European Water Framework Directive (EU WFD) of 0.009 mg N L⁻¹ in urbanized rivers^19–23. Therefore, a better understanding of its dynamics in aquatic systems is highly desirable.

During denitrification, nitrite is both the product of nitrate reduction and the substrate of its own reduction into NO, N₂O and N₂ (Fig. 1):

$${\mathrm{NO}}_3^{-}+2{\mathrm{e}}^{-}+2{\mathrm{H}}^{+}\to {\mathrm{NO}}_2^{-}+{\mathrm{H}}_2\mathrm{O}$$ 1

$${\mathrm{NO}}_2^{-}+{\mathrm{e}}^{-}+2{\mathrm{H}}^{+}\to \mathrm{NO}+{\mathrm{H}}_2\mathrm{O}$$ 2

$$2\mathrm{NO}+2{\mathrm{e}}^{-}+2{\mathrm{H}}^{+}\to {\mathrm{N}}_2\mathrm{O}+{\mathrm{H}}_2\mathrm{O}$$ 3

$${\mathrm{N}}_2\mathrm{O}+2{\mathrm{e}}^{-}+2{\mathrm{H}}^{+}\to {\mathrm{N}}_2+{\mathrm{H}}_2\mathrm{O}$$ 4

Figure 1.

Theoretical trends of NO₃⁻ and NO₂⁻ concentrations during denitrification.

Nitrate reduction initially results in nitrite production. During phase 1, the “net nitrite production” phase, the NO₂⁻ concentration rises and reaches a maximum; then, in phase 2, the concentration of nitrite decreases until nitrite is completely consumed. It is noted that during phase 1 production as well as reduction of NO₂⁻ can take place simultaneously. The same holds for phase 2, where nitrite is mostly reduced but also still being produced. In addition of being an intermediate during denitrification, nitrite is also an important intermediate at the crossroads of other nitrogen transformation processes, such as codenitrification^24,25, dissimilatory nitrate reduction to ammonium (DNRA)^26–28, anaerobic ammonium oxidation (Anammox)²⁹, nitrifier denitrification³⁰ and nitrification^31,32.

Stable isotope techniques can provide unique insights into sources and processes regulating the N cycle in ecosystems. The nitrogen and oxygen isotope ratios of NO₃⁻ (δ¹⁵N and δ¹⁸O) have been used since several decades to better distinguish the origin of NO₃^{− 33–36}. In addition, it provides information regarding the processes involved in its transformation, e.g. denitrification and nitrification in lakes, groundwater, riparian zones, rivers, soils, and marine environments^37–43. Denitrification is accompanied by significant N and O isotope fractionation affecting the remaining NO₃⁻ due to reaction kinetics differences between the lighter and the heavier isotopes of N and O (¹⁴N vs. ¹⁵N and ¹⁶O vs. ¹⁸O). Enrichment in heavy isotopes of N and O in the remaining nitrate is caused by the fact that ¹⁴N and ¹⁶O react faster than ¹⁵N and ¹⁸O during denitrification^33,44.

Denitrification is a unidirectional reaction in which nitrate is reduced to gaseous nitrogen (N₂) via different intermediates (NO₂⁻, NO, and N₂O). The N and O isotope enrichment factors ε¹⁵N and ε¹⁸O during denitrification are usually determined by measuring variations in concentrations and isotope ratios of the remaining nitrate, while the isotopic compositions of the final product N₂ or of the intermediate compounds such as NO₂⁻ and N₂O are rarely analyzed. In past studies, the concentrations and isotopic compositions of nitrate and nitrite have not always been separately determined due to analytical limitations for the latter. Therefore, the “net ε¹⁵N” and “net ε¹⁸O” determined for the entire denitrification process assessed solely based on measurements of the progressively disappearing nitrate may not always be accurate.

Only a few studies used nitrite (NO₂⁻) rather than nitrate as source of nitrogen for the determination of ε¹⁵N for nitrite reduction. Two of these studies were carried out in soil experiments^45,46 another with a microbial culture⁴³. Due to new chemical reduction analytical methods, it is now possible to determine the isotopic composition of NO₂⁻ alone, separating the isotopic analyses of NO₃⁻ from those of coexisting NO₂^{− 47–50}. Recent studies of the isotopic composition of nitrite focused mainly on nitrification^51–56. A few studies mention ε¹⁵N values for nitrite reduction during denitrification. These studies were conducted using pure cultures of denitrifiers^41–43, marine incubations⁴², in-situ marine environments⁵⁵ or more recently abiotic denitrification⁵⁷. In order to improve our knowledge on the isotope effects affecting nitrite, we investigated isotope fractionation during denitrification in laboratory experiments with environmental bacterial communities. Nitrite was either applied as a substrate or analyzed as intermediate during nitrate reduction.

Since during denitrification and nitrate consumption nitrite is both substrate and product, it is not possible to use the Rayleigh equation to calculate concentrations and isotope compositions of the intermediate compound nitrite. For this reason, we developed the Isonitrite numerical model that simulates the evolution of oxygen and nitrogen isotope compositions of NO₃⁻ and NO₂⁻ during simultaneous nitrite production and consumption. The model, constrained by our experimental data, is used to estimate isotope fractionation factors of oxygen and nitrogen (ε¹⁵N and ε¹⁸O) associated to denitrification. To our knowledge, this study is the first focusing on freshwater benthic denitrifying communities with two distinct sources of dissolved inorganic nitrogen, i.e, nitrite or nitrate.

Results

Isotopic enrichment factors associated with nitrite reduction

In the low nitrite experiment (101 µM), concentrations decreased with time reaching 9.7 µM after 240 min (Fig. 2a). In the high nitrite experiment (614 µM), concentrations decreased continuously to 0 µM after 390 min (Fig. 2b). Nitrite reduction rates of 119 nmol min⁻¹ g⁻¹ were observed at high initial nitrite concentrations whereas the low initial nitrite concentration resulted in lower nitrite reduction rates of 35 nmol min⁻¹ g⁻¹ under the experimental conditions.

Figure 2.

Kinetics of nitrite concentrations (a,b), variations of δ¹⁵N (c,d) and calculation of ε¹⁵N (e,f) for low and high nitrite treatments respectively.

The decrease in nitrite concentrations was associated with a change in δ¹⁵N-NO₂⁻ of the remaining NO₂⁻ increasing from −18.1‰ to −8.4‰ and from −19.6‰ to −17.6‰ for low and high treatments respectively (Fig. 2c,d). The N isotope enrichment factors associated with the reduction of NO₂⁻ was −4.2 and −4.7‰ for low and high nitrite treatments respectively (Fig. 2e,f).

The reduction of nitrite generated constant and low oxygen isotope values in the remaining nitrite (Fig. 3a,b). The oxygen isotope ratios of nitrite remained constant throughout the experiment with mean δ¹⁸O-NO₂⁻ of −0.6 ± 1.1‰ and −0.9 ± 0.6‰ for low and high nitrite treatments respectively.

Figure 3.

Variations of δ¹⁸O-NO₂⁻ with the decrease of nitrite concentration for low (a) and high (b) nitrite treatments.

Isotopic enrichment factor associated with nitrate reduction

Similar to the experiments carried out with nitrite only, the kinetics of denitrification were investigated with solutions with low (97 µM) and high (508 µM) initial nitrate concentrations (Fig. 4b). Nitrate concentrations decreased from 97 to 1.8 µM and from 508 to 1.2 µM over the 180 and 420 minutes of the experiments. The rates of nitrate reduction were 50 nmol g⁻¹ min⁻¹ and 137 nmol g⁻¹ min⁻¹ for low and high nitrate treatments respectively. The nitrate reduction rates are in the same range as the nitrite reduction rates (35 and 119 nmol g⁻¹ min⁻¹, see previous section).

Figure 4.

Variations of nitrite (open symbol) and nitrate (filled symbol) concentrations (a,b), variations of δ¹⁵N-NO₃⁻ (c,d) and of δ¹⁸O-NO₃⁻ (e,f) for low and high nitrate treatments respectively.

In both nitrate experiments (low and high), initial NO₂⁻ concentrations were less than 1 µM. In the low nitrate treatment, NO₂⁻ concentrations increased to 23 µM at 90 minutes and then decreased to 0.2 µM at 105 minutes (Fig. 4a, open symbols). For the high nitrate treatment, NO₂⁻ concentrations increased to 105 µM at 300 minutes and subsequently decreased to 0.4 µM at 420 minutes (Fig. 4b, open symbols). As expected, the trends in NO₂⁻ concentrations reveal two phases; an increase due to nitrate reduction to nitrite leading to an initial net production of nitrite, followed by a decrease of nitrite concentrations as the newly formed nitrite is further reduced to N₂ (see Fig. 1).

In the two experiments with NO₃⁻, the decrease in NO₃⁻ concentrations was accompanied by a corresponding enrichment of ¹⁵N in the remaining NO₃⁻. The δ¹⁵N-NO₃⁻ of the remaining nitrate increased from 5.5 to 33.7‰ within 90 minutes and from 7.5 to 47.4‰ within 300 minutes in low and high nitrate treatments (Fig. 4c,d). The decrease in NO₃⁻ concentrations due to denitrification was also accompanied by a corresponding enrichment of ¹⁸O in the remaining NO₃⁻. δ¹⁸O-NO₃⁻ increased from 19.8 to 45.6‰ within 90 minutes and from 22.9 to 57.0‰ within 300 minutes in low and high nitrate treatments respectively (Fig. 4e,f). The increase in δ¹⁸O-NO₃⁻ was initially very slow as long as nitrite was net produced, in all likelihood due to the rapid oxygen isotope exchange between nitrite and water.

The N isotope enrichment factor associated with the reduction of nitrate varied between −21.1 and −24.4‰ (Fig. 5a,b) and the O isotope enrichment factors ranged between −19.6 and −21.9‰ (Fig. 5c,d) for low and high nitrate treatments respectively. Despite different nitrate reduction rates between the two experimental treatments with amended nitrate concentrations, the observed N and O isotopic enrichment factors did not vary by more than 3.3‰.

Figure 5.

Calculation of ε¹⁵N-NO₃⁻ (a,b) and ε¹⁸O-NO₃⁻ (c,d) for low and high nitrate treatments respectively.

Modeling kinetics and isotopic composition of nitrite and nitrate during denitrification

The Isonitrite model provides the kinetic parameters of the multi-step process of NO₃⁻ reduction to N₂ via the intermediate NO₂⁻. The model was applied to simulate concentrations and isotope compositions of nitrite and nitrate observed in the batch experiments for the low and high concentration treatments. Overall, the model achieved good simulations of the temporal evolution of NO₃⁻ and NO₂⁻ concentrations (Fig. 6) and N and O isotope ratios of nitrate and nitrite (Fig. 7).

Figure 6.

Measured (red dots) and modeled (blue lines) nitrate (a,b) and nitrite concentrations (c,d) for low and high nitrate treatments respectively.

Figure 7.

Measured (red dots) and modeled (blue lines) δ¹⁵N-NO₃⁻ (a,b) and δ¹⁸O-NO₃⁻ (c,d) for low and high nitrate treatments respectively.

When simulating the low-nitrate treatment, the model fit of the experimental NO₃⁻ and NO₂⁻ concentrations was obtained by using kinetic constants of 4.2 × 10⁻⁵ min⁻¹ for NO₃⁻ reduction (equation 11 in Methods) and 7.2 × 10⁻⁵ min⁻¹ for NO₂⁻ reduction (Eq. 8), and a reaction order (n in Eqs. 7 and 8) of 0.4. In these experiments, the model constrains N and O isotope enrichment factors (ε¹⁵N = −19‰, ε¹⁸O = −18‰ for NO₃⁻ reduction) that are very close to the values obtained by applying the Rayleigh model to the data (Fig. 5). This indicates that the model is able to correctly reproduce the N and O isotope fractionation of the reduction of NO₃⁻ to NO₂⁻. However, in order to obtain a good fit of the model to the concentration and isotope data obtained in the multi-step (NO₃⁻ → NO₂⁻ → N₂) experiment (Fig. 8a), it was necessary to impose a higher ε¹⁵Ν for NO₂⁻ reduction (−10‰) than the value determined in batch experiments where only NO₂⁻ reduction occurred (−4.2‰; Fig. 2).

Figure 8.

Determination of ε¹⁵N of nitrite during the reduction of nitrate for low (a) and high (b) nitrate treatment.

Similar results were obtained with the model applied to the experiment with high nitrate treatment. However, to obtain a good fit of the NO₃⁻ and NO₂⁻ concentration trends, a slightly different approach was implemented to simulate the kinetics of NO₃⁻ and NO₂⁻ reduction. To reproduce the increase in NO₃⁻ consumption at 170 minutes observed in this experiment (Fig. 5c), a change in the kinetic constant of NO₃ reduction from 1.8 × 10⁻⁵ min⁻¹ to 6.9 × 10⁻⁵ min⁻¹ at 170 minutes was necessary. Also, the NO₂⁻ reduction rate was set to 6 × 10⁻¹ µM min⁻¹ for the first 170 minutes, and to 1.8 × 10⁻² µM min⁻¹ for the remaining part of the experimental high nitrate treatment to achieve a satisfactory fit of the observed nitrite concentrations (Fig. 6d). A very good fit of the experimental trends in δ¹⁵N-NO₃⁻ and δ¹⁸O-NO₃⁻ was obtained by imposing model N and O isotope enrichment factors (ε¹⁵Ν = −19.1‰, ε¹⁸O = −19.2‰ for NO₃⁻ reduction) that were very close to the values measured in the batch experiments where only NO₃⁻ was reduced (Fig. 7). Similar to the low nitrate experiment, it was necessary to use a higher model ε¹⁵Ν for NO₂⁻ reduction (ε varied between −10 and −15‰) than that determined in batch experiments where only NO₂⁻ reduction took place (ε = −4.7‰) to obtain a good model fit for the data of the multi-step NO₃⁻ → NO₂⁻ → N₂ experiment (Fig. 8b). This confirms that the Isonitrite model is capable of accurately predicting the concentrations of nitrate and nitrite, and the isotope composition of the remaining nitrate during denitrification.

Discussion

N isotope fractionation during denitrification and transformation of nitrite and nitrate

Even though initial nitrite concentrations affected the nitrite reduction rates, a similar isotope enrichment factor (ε¹⁵N) for nitrite reduction to N₂ of −4.5 ± 0.3‰ was determined. This ε¹⁵N value for nitrite reduction is on the low end of previously reported values. Chien et al.⁴⁵ reported ε¹⁵N values between −33.2 and −2.9‰ in soil experiments. Martin and Casciotti (2016) calculated ε¹⁵N between −22 to −8‰ for reduction of nitrite associated with different marine strains.

During denitrification, a gradual decrease in NO₃⁻ concentration is usually accompanied by a significant enrichment of ¹⁵N in the remaining nitrate³³. The nitrogen isotope fractionation factors calculated in the current study for denitrification of nitrate (low and high nitrate treatments) of −21.1 and −24.4‰ are in good agreement with those found in the literature under similar conditions where denitrification occurs⁵⁸. During nitrate reduction, the observed ¹⁵N enrichment of the remaining nitrate is caused by the preferential reduction of ¹⁴N-NO₃⁻ and a consequent enrichment of ¹⁴N of the product and intermediate compound NO₂⁻ during phase 1 of “net NO₂⁻ production” as shown in Fig. 1. As a result, NO₂⁻ concentrations increase and reach a maximum value during this phase 1 of denitrification (see Fig. 4a,b). During phase 2 or “net NO₂⁻ reduction” (Fig. 1), the NO₂⁻ concentration progressively decreases, leading to ¹⁵N enrichment of remaining NO₂⁻ due to preferential reaction of ¹⁴N-NO₂⁻. During phase 1, production and reduction of NO₂⁻ take place simultaneously, however production occurs at a higher rate leading to an increase in nitrite concentrations. In phase 2, production and reduction of NO₂⁻ also take place simultaneously, but since NO₂⁻ reduction rates are higher than production rates, nitrite concentrations decrease.

Based on the N isotope enrichment factor (ε¹⁵Ν) measured for nitrite reduction alone (ε = −4.2‰) in the experiment with the low nitrite treatment, and combined with the ε¹⁵N of nitrate reduction (ε = −21‰), the model did not accurately predict the measured δ¹⁵N-NO₂⁻ and constantly underestimated the measured δ¹⁵N-NO₂⁻ value (Fig. 8). When the apparent N isotope enrichment factor (ε¹⁵Ν) of NO₂⁻ reduction was changed to −10‰ in the model, an almost perfect fit between simulated and observed δ¹⁵N-NO₂⁻ was achieved (Fig. 8a). A similar approach was used for the experiment with the high nitrate treatment with an N isotope enrichment factor varying between −10 and −15‰ to fit simulated and observed δ¹⁵N-NO₂⁻ (Fig. 8b). For both low and high nitrate treatments, the apparent N isotopic enrichment factor of nitrite reduction required by the model to achieve a good fit with the observed data (ε¹⁵N = −10 and −15‰ respectively) is higher than the ε¹⁵N obtained from the experiments with nitrite as sole source of nitrogen (ε¹⁵N = −4.2 and −4.7‰ for low and high nitrite treatment respectively).

It is also interesting to note that the calculated rates in the model revealed that the nitrite production rate varies during nitrate reduction, as shown especially for the high nitrate treatment. The nitrogen isotope enrichment factor determined for experiments with nitrite as the sole electron acceptor was lower for both treatments (ε¹⁵N varied between −4.7 and −4.2‰) than suggested by the Isonitrite model, independent of the nitrite reduction rates or nitrite concentrations. The apparent nitrogen isotope fractionation of nitrite during nitrate reduction seemed to increase with increasing availability of nitrite. The amount of nitrite available for nitrite reductase during denitrification is variable and lower than in the experiments with nitrite addition. Hence, either the variable or the lower nitrite concentrations may explain the difference in nitrogen isotope enrichment factors compared with those calculated in the nitrite reduction experiment.

Nitrite reduction is mediated by two different types of periplasmic enzymes, the copper containing nitrite reductase (nirK or Cu-NIR) or the cytochrome cd1-containing nitrite reductase (nirS or Fe-NIR)¹⁶. During denitrification with nitrite as a sole electron acceptor, nitrite is directly used by one of these enzymes at the outer side of the cell wall. During the experiment with nitrate as electron acceptor, nitrite is produced in the cytoplasm and consumed within the periplasm. Nitrite concentrations as substrate are low compared to those in the case of nitrite addition. When nitrite is produced from the reduction of nitrate, the comparatively low amount of nitrite-nitrogen could be limiting and generate low N isotope fractionation. In addition to lower net concentrations of nitrite, nitrite is subject to transport upon reduction of nitrate, which may affect the extent of isotope fractionation⁵⁹. Nitrate reduction can occur in the periplasm (via the enzyme Nap), but in most cases nitrate is reduced by the membrane bound nitrate reductase Nar. The membrane bound Nar reduces nitrate to nitrite in the cytoplasm, nitrite is then transported over the cell membrane via a transporter (nark or nasH) back to the periplasm where it is reduced further by either nirS or nirK¹⁶. The affinity with the transporter might thus generate nitrogen isotope fractionation. Combined transport and limiting nitrite concentrations could thus be responsible for higher nitrogen isotope fractionation during nitrate reduction as opposed to experiments were nitrite was the sole electron acceptor.

O isotope fractionation during nitrate and nitrite reduction

During denitrification, a gradual decrease in NO₃⁻ concentrations is usually accompanied by a significant enrichment of ¹⁸O in the remaining nitrate⁴⁴. The oxygen isotope fractionation factors of −19.6 and −21.9‰ calculated in the current study are on the high end of what has been previously reported in the literature^42,44.

In our study, the nitrogen and oxygen isotope fractionation during denitrification were in the same range (ε¹⁵N −21.1 to −24.4‰ and ε¹⁸O −19.6 to −21.9‰) for low and high nitrate treatments with a ratio of N and O isotope enrichment factors (¹⁸ε/¹⁵ε) observed in this study of 0.9 for low and high nitrate treatments. This is in agreement with results from a number of recent isotopic denitrification studies where the observed ¹⁸ε/¹⁵ε ratio was close to 1.0^50,60–62. The role of the different nitrate reductases from various bacterial strains has recently been discussed potentially explaining the large range of ε¹⁵N values observed during denitrification in marine sediments⁴². Moreover, Frey et al.⁶³ showed with pure cultures that the extent of N isotope fractionation during denitrification may depend on the different nitrate reduction enzymes (periplasmic Nap versus membrane bound Nar).

In the experiments with nitrite as sole source of nitrogen, δ¹⁸O-NO₂⁻ remained constant during the nitrite reduction experiments. This is clear evidence for rapid oxygen isotope exchange between H₂O and NO₂⁻ under experimental conditions keeping the δ¹⁸O-NO₂⁻ constant. Therefore, the observed oxygen isotope enrichment for denitrification of −21‰, as revealed in experimental low and high nitrate treatments, appears to be entirely associated with reduction of nitrate to nitrite.

The Isonitrite model was used to obtain a lower limit for the kinetics of oxygen isotope exchange between NO₂⁻ and H₂O. Kinetics of this exchange were estimated by ensuring that the oxygen isotope fractionation associated with the reduction of NO₃⁻ and NO₂⁻ was not able to deviate the δ¹⁸O-NO₂⁻ from its equilibrium value with water having a δ¹⁸O-H₂O value of −10‰. Repeated model runs varying the kinetic constant of the oxygen isotope exchange between NO₂⁻ and H₂O (Eq. 21 in Methods) suggest that this kinetic constant must be greater than 5 * 10⁻¹⁰ µM s⁻¹ in order for δ¹⁸O-NO₂⁻ to not deviate from its equilibrium value with water near 0‰ (Fig. 8). The fact that the δ¹⁸O-NO₂⁻ remained constant despite that NO₂⁻ production and consumption probably fractionate oxygen isotope ratios considerably suggests that the kinetic isotope constant for O isotope exchange between nitrite and water represented in Eq. (21) is greater than 3 * 10⁻⁸ µM⁻¹ min⁻¹.

In the absence of published values of the kinetic constant of oxygen isotope exchange k⁺ (reaction 17), it was compared with the chemical kinetic constant of NO₃⁻ reduction k_NO3 (Eq. 7). In order to do this comparison, the units of k⁺ (µM⁻¹ min⁻¹) were converted into the units of k_NO3 (min⁻¹) by considering relation 18 and multiplying k⁺ (µM⁻¹ min⁻¹) by the concentration of H₂¹⁶O (55 × 10⁶ µM). A k⁺ constant of 1.65 min⁻¹ was obtained which is 5 orders of magnitude higher than the k_NO3 (4.2 × 10⁻⁵ min⁻¹). It appears thus that oxygen isotope exchange in our experiment is very rapid compared to the microbial mediated reduction of NO₃⁻. Previous studies hypothesized that isotopic exchange can occur between the oxygen of water and the oxygen of nitrite over long time periods^41,43,53. Our study confirms rapid oxygen isotope exchange between the intermediate nitrite and water. Due to the fast change of the δ¹⁸O-NO₂⁻, it appears that isotope variations are driven not by physical parameters but are caused by bacteria activity.

Conclusions

This study reports the N and O isotope enrichment factors associated with the multi-step biogeochemical process of denitrification. Isotope measurements and calculation of isotope fractionation based on the Isonitrite model provide insights into the apparent isotopic fractionation of nitrite during denitrification. Due to rapid isotopic exchange between the oxygen of nitrite and water, δ¹⁸O-NO₂⁻ changed immediately and remained stable during nitrate reduction. Model calculations also confirmed rapid oxygen isotope equilibrium exchange between water and nitrite with a kinetic isotope constant for O isotope exchange of >5 * 10⁻² kg mol⁻¹ s⁻¹.

Based on N and O isotope enrichment factors obtained from batch experiments, model simulations revealed an apparent nitrogen isotope enrichment factor for nitrite reduction (of −10‰ and −15‰) higher than those calculated for the experiments (−4.1‰ and −4.7‰) with nitrite as initial source of nitrogen with two different concentrations. The reduction of nitrate seems to drive the change of the nitrogen isotope fractionation factor affecting nitrite reduction. We hypothesize that this difference is due to variations of the amount of available nitrite. This suggests that the amount of available nitrite and transport determine the extent of nitrogen isotope fractionation during the process of denitrification.

Methods

Experimental setup and materials

In order to determine the variations in nitrogen and oxygen isotope ratios, N and O isotopic enrichment factors for nitrite reduction were determined under denitrifying conditions (in the absence of oxygen) with NO₂⁻ as the sole electron acceptor in a laboratory batch incubation experiment. Subsequently, the same experimental approach was used with NO₃⁻ as electron acceptor in order to determinate the N (ε¹⁵N) and O (ε¹⁸O) isotope enrichment during denitrification of NO₃⁻. For both experiments, two treatments at the low (101 µM for nitrite and 97 µM for nitrate) and high end (614 µM for nitrite and 508 µM for nitrate) of concentrations measured in surface waters were used. Subsequently, a non-steady state model was developed to simulate the changes in concentrations and N and O isotope ratios of nitrate and nitrite tracing kinetics and isotope variations during reduction of nitrate concentrations associated with initial net production of nitrite and subsequent net reduction of nitrite.

Batch experiments

Muddy organic sediments were collected from the Morbras Stream, La Queue en Brie, a tributary of the Marne River in the Seine watershed upstream of Paris (France). Sediments from this stream had been used in a preliminary test and showed significant nitrate reduction potential (data not shown). The land use in the upstream catchment is mainly crops. The sediment was homogenized in the laboratory prior to the experiments. Contents and isotopic compositions ot total organic carbon and total nitrogen were determined by EA-IRMS (C_org = 8.6%; N_org = 0.8%; C/N = 14.9; δ¹³C_org = −24.6‰; δ¹⁵N_total = 2.9‰). Thirty grams of sediment were weighed in 300 ml glass bottles and 280 mL of nitrite or nitrate in milliQ water was added to create a sediment slurry. The slurries were flushed with He for twenty minutes to achieve anoxic conditions prior to crimp capping the bottles with a septum and a ring. The solutions in the first set of experiments contained 101 and 614 µM of nitrite derived from KNO₂ (low and high nitrite treatments), and the second set of experiments contained 97 and 508 µM of nitrate derived from KNO₃ (low and high nitrate treatments). Prior to addition, the salts were dissolved in milliQ water with a δ¹⁸O-H₂O value of −10‰. Bottles were incubated under continuous agitation in order to maintain sediments in suspension and optimize denitrification (Sebilo et al. 2003) in the dark at 20 °C for 270 and 330 minutes for low and high nitrite treatments and for 180 and 420 minutes for low and high nitrate treatments, respectively. For each treatment, 14 similar slurries were prepared and considered homogeneous at the beginning of the experiment. Every 15 to 30 minutes for each treatment, a bottle was sacrificed and the slurry was centrifuged at 4000 rpm for 15 minutes. The supernatant was then filtered first through a 0.45μm glass microfiber filters (GFF-Whatman) and subsequently through a 0.2 µm nylon membrane (Whatman) to remove all sediment. Solutions were immediately preserved with mercuric chloride (0.3 ml at 5%) to avoid any residual transformation of the dissolved compounds in the solution. An aliquot of this solution was used to determine nitrite and nitrate concentrations. Ammonium concentrations were determined at the beginning and at the end of the experiments to check the ammonium budget. As ammonium consumption due to nitrification can be excluded under anoxic conditions, ammonium production should be only caused by ammonification (degradation of organic matter) or DNRA. Ammonium concentrations were below the limit of detection for all analyzed samples. Another aliquot of the solution was frozen and stored for subsequent N and O isotope analysis on nitrite and nitrate.

Nutrient concentration analyses

Nutrient concentrations were determined by colorimetry. Nitrate concentrations were determined using the colorimetric hydrazine method. Nitrate was converted to nitrite with hydrazine. Then nitrite reacted with sulphanilamide and N-1-naphthylethylenediamine dihydrochloride. Nitrite concentrations were directly measured by colorimetry by using the same reactants. Ammonium reacted with sodium nitroprussiate and sodium hydroxide. The absorbance of coloration was determined at 540 nm and 660 nm (Gallery Water ThermoFisher Scientific) to obtain nitrite or nitrate and ammonium concentrations respectively with a precision of the measurement ±0.3 µM.

Isotope ratio measurements

Nitrogen and oxygen isotope ratios of nitrate and nitrite were determined separately following a modified protocol of McIlvin and Altabet⁶⁴. Nitrate was reduced to nitrite in an activated column of cadmium. Yields of nitrate reduction were calculated using concentration measurements with a yield of reduction >95%.

When both nitrite and nitrate concentrations were not negligible, the liquid samples were diluted with a salted buffer to obtain a concentration of 20 µM of NO₂⁻ at the column outlet, which is composed of reduced NO₃⁻ and the initial NO₂⁻ (called later NO_x⁻). Subsequently, the NO₂⁻ (i.e. NO_x⁻ and NO₂⁻) was further reduced to nitrous oxide by sodium azide solution. To achieve this, each sample was diluted with a salt solution (NaCl = 35.5 g l⁻¹) to obtain 1 µM of NO₂⁻ concentration in 15 ml and transferred into a 20 ml glass vial. The vials were crimp-sealed with Teflon-backed silicone septa (IVA, 70220804) and aluminum caps. The sodium azide solution, which consists of a 40 ml mixture of 20 ml of azide (NaN₃, 2 M) and 20 ml of acetic acid (C₂H₄O₂, 20%), was flushed with He for 30 min to avoid any N₂O pollution from the buffer. In order to reduce the NO₂⁻ to N₂O, 0.8 ml of azide solution was injected in each vial, and vials were placed in a water bath at 30 °C for one hour. The yield of conversion was better than 95%.

The isotope compositions of all N₂O samples were measured with an isotope ratio mass spectrometer (IRMS, Delta Vplus, Thermo Scientific, Bremen, Germany) in continuous-flow mode with a purge-and-trap system coupled with a Finnigan GasBench II system (Thermo Scientific, Bremen, Germany). Results are reported in the internationally accepted delta notation in ‰ with respect to the standards air for δ¹⁵N and Vienna Standard Mean Ocean Water (V-SMOW) for δ¹⁸O, respectively. Nitrate and nitrite reference materials subject to the same analytical procedures were used to calibrate the isotopic composition of N₂O (USGS34, δ¹⁵N = −1.8‰, δ¹⁸O = −27.9‰, USGS35, δ¹⁵N = +2.7‰, δ¹⁸O = +57.5‰ and USGS32, δ¹⁵N = +180‰, δ¹⁸O = +25.7‰ for nitrate standards; lab nitrite standards Lb1, δ¹⁵N = −63‰ and Lb2, δ¹⁵N = +2.7‰ for nitrite standards). The precision was ±0.3‰ for δ¹⁵N-NO₂⁻ and ±0.5‰ for δ¹⁸O-NO₂⁻.

Finally, using the isotopic compositions of NO_x⁻ (NO₂⁻ + NO₃⁻) and NO₂⁻ alone, the δ¹⁵N-NO₃⁻ and δ¹⁸O-NO₃⁻ were calculated as follows:

$${\mathrm{\delta }}^{15}\mathrm{N}‐{\mathrm{NO}}_3^{-}=({\mathrm{\delta }}^{15}\mathrm{N}-{\mathrm{NOx}}^{-}\times [{\mathrm{NOx}}^{-}]-{\mathrm{\delta }}^{15}\mathrm{N}-{\mathrm{NO}}_2^{-}\times [{\mathrm{NO}}_2^{-}]/[{\mathrm{NO}}_3^{-}]$$ 5

$${\mathrm{\delta }}^{18}\mathrm{O}‐{\mathrm{NO}}_3^{-}=({\mathrm{\delta }}^{18}\mathrm{O}-{\mathrm{NOx}}^{-}\times [{\mathrm{NOx}}^{-}]-{\mathrm{\delta }}^{18}\mathrm{O}-{\mathrm{NO}}_2^{-}\times [{\mathrm{NO}}_2^{-}])/[{\mathrm{NO}}_3^{-}]$$ 6

where [NO₃⁻] and [NO₂⁻] are the concentrations of NO₃⁻ and NO₂⁻, respectively.

Based on this calculation, the precision for δ¹⁵N-NO₃⁻ was ±0.5‰ and ±0.8‰ for δ¹⁸O-NO₃⁻.

Determination of isotope enrichment factors

The nitrite experiment in a closed system without any renewal of substrate ensured Rayleigh conditions and therefore the N and O isotope enrichment factors (ε) were calculated using the following equations:

$${\mathrm{\delta }}^{15}\mathrm{N}‐{\mathrm{NO}}_2^{-}(\mathrm{t})={\mathrm{\delta }}^{15}\mathrm{N}-{\mathrm{NO}}_2^{-}(\mathrm{t}0)+\mathrm{\epsilon }\ln \mathrm{f}={\mathrm{\delta }}^{15}\mathrm{N}-{\mathrm{NO}}_2^{-}(\mathrm{t}0)+\mathrm{\epsilon }\ln C(t)/C(0)$$ 7

and

$${\mathrm{\delta }}^{18}\mathrm{O}‐{\mathrm{NO}}_2^{-}(\mathrm{t})={\mathrm{\delta }}^{18}\mathrm{O}-{\mathrm{NO}}_2^{-}(\mathrm{t}0)+\mathrm{\epsilon }\ln \mathrm{f}={\mathrm{\delta }}^{18}\mathrm{O}-{\mathrm{NO}}_2^{-}(\mathrm{t}0)+\mathrm{\epsilon }\ln C(t)/C(0)$$ 8

where δ¹⁵N and δ¹⁸O-NO₂⁻ (t0) are the N and O isotope ratios of the substrate at time zero, and C0 and Ct are the concentrations of nitrite at time zero and t, respectively. This relationship was used to determine the N and O isotope enrichment factor of nitrite reduction by plotting measured values of δ¹⁵N(t) and δ¹⁸O(t) against ln C_t/C₀. The same approach was used to determine the N and O isotope enrichment factor for denitrification for the experiments where nitrate was the sole source of nitrogen.

Isonitrite model

As nitrite is both a substrate and a product during denitrification of nitrate, Rayleigh conditions and equations are not applicable to determine the N and O isotope enrichment factor associated with the reduction of NO₂⁻ when these two processes occur concurrently in a batch reactor. Although our batch experiments alone are sufficient to derive enrichment factors (ε) for the separately tested NO₃⁻ = >NO₂⁻ and NO₂⁻ = >N₂ steps, a model was developed to calculate the isotope enrichment factors when these processes occur simultaneously in a batch reactor. The model simulates the multi-step denitrification process and considers the presence of the intermediate product (NO₂⁻) as well as the N and O isotopic compositions of nitrite and nitrate. The model is constrained with experimentally determined concentrations and N and O isotopic ratios of nitrite and nitrate. The model was used to estimate instantaneous isotopic enrichment factors associated with NO₃⁻ reduction to NO₂⁻ and NO₂⁻ reduction to N₂. Moreover, the model was used to investigate the kinetics of oxygen isotope exchange between water and NO₂⁻.

The model considers that denitrification is a two-stage process:

$${\mathrm{NO}}_3^{-}+2{\mathrm{e}}^{-}+2{\mathrm{H}}^{+}\to {\mathrm{NO}}_2^{-}+{\mathrm{H}}_2\mathrm{O}$$ 9

$${\mathrm{NO}}_2^{-}+3{\mathrm{e}}^{-}+4{\mathrm{H}}^{+}\to 1/2{\mathrm{N}}_2+2{\mathrm{H}}_2\mathrm{O}$$ 10

The rate of these processes is computed as:

$${\mathrm{R}}_{\mathrm{NO}3}={\mathrm{k}}_{\mathrm{NO}3}\times {\mathrm{NO}}_3^{\mathrm{nNO}3}$$ 11

and

$${\mathrm{R}}_{\mathrm{NO}2}={\mathrm{k}}_{\mathrm{NO}2}\times {\mathrm{NO}}_2^{\mathrm{nNO}2}$$ 12

where NO₃⁻ and NO₂⁻ concentrations are expressed in µM, R_x (x = NO₃⁻ or NO₂⁻) is the nitrite production or reduction (reaction) rate in µM min⁻¹, k_x is the kinetic constant in min⁻¹ and nx is the reaction order.

To simulate both N and O isotope ratios simultaneously, three isotopic species must be considered for each chemical species, with the total chemical concentration being equal to the sum of the isotopic species:

$${\mathrm{NO}}_3={}^{14}\mathrm{N}_{16}{\mathrm{O}}_3+{}^{15}\mathrm{N}^{16}{\mathrm{O}}_3+{}^{14}\mathrm{N}^{18}{\mathrm{O}}_3$$ 13

$${\mathrm{NO}}_2={}^{14}\mathrm{N}_{16}{\mathrm{O}}_2+{}^{16}\mathrm{N}^{15}{\mathrm{O}}_2+{}^{14}\mathrm{N}^{18}{\mathrm{O}}_2$$ 14

With ¹⁸O₃: ¹⁸O¹⁶O¹⁶O and ¹⁸O₂: ¹⁸O¹⁶O.

From these isotopic species, the δ¹⁵N and the δ¹⁸O values of NO₂⁻ and NO₃⁻ can be calculated as follows (equations shown for NO₃):

$${\delta }^{15}{N}_{N{O}_3}=\left(\frac{{}^{15}N{}^{16}O_3}{{}^{14}N{}^{16}O_3+{}^{14}N{}^{18}O_3}/N_{STD}-1\right)\times {10}^3$$ 15

$${\delta }^{18}{O}_{N{O}_3}=\left(\frac{{}^{14}N{}^{18}O_3}{3\cdot ({}^{14}N{}^{16}O_3+{}^{15}N{}^{16}O_3)+2\cdot ({}^{14}N{}^{18}O_3)}/SMOW-1\right)\times {10}^3$$ 16

where SMOW is the ¹⁸O/¹⁶O ratio in the SMOW standard and N_STD is the ¹⁵N/¹⁴N ratio of air.

The rate of reaction for NO₃⁻ and NO₂⁻ reduction for the different isotope species have to sum up to the rate of the total chemical species calculated with Eqs. 3 and 4. For example, for NO₃⁻ reduction:

$$R_{N{O}_3}=R_{{}^{14}N{}^{16}O_3}+R_{{}^{15}N{}^{16}O_3}+R_{{}^{14}N{}^{18}O_3}$$ 17

The expressions for the rates of the isotopic species are obtained by solving a system of three equations comprising equation 14 and equations 12 and 13 written in terms of rates rather than concentrations, and introducing isotopic enrichment factors for N and O isotopes (¹⁵ε_NO3 and ¹⁸ε_NO3, respectively):

$$R_{{}^{14}N{}^{16}O_3}=\frac{R_{N{O}_3}\cdot \left({10}^6-\left({10}^3+{\delta }^{18}{O}_{N{O}_3}+{}^{18}\epsilon _{N{O}_3}\right)\cdot \left(2\cdot {10}^3+3\cdot \left({10}^3+{\delta }^{15}{N}_{N{O}_3}+{}^{15}\epsilon _{N{O}_3}\right)\cdot N_{STD}\right)\cdot SMOW\right)}{\left({10}^3+\left({10}^3+{\delta }^{15}{N}_{N{O}_3}+{}^{15}\epsilon _{N{O}_3}\right)\cdot N_{STD}\right)\cdot \left({10}^3+\left({10}^3+{\delta }^{18}{O}_{N{O}_3}+{}^{18}\epsilon _{N{O}_3}\right)\cdot SMOW\right)}$$ 18

$$R_{{}^{15}N{}^{16}O_3}=\frac{R_{N{O}_3}\cdot \left({10}^3+{\delta }^{15}{N}_{N{O}_3}+{}^{15}\epsilon _{N{O}_3}\right)\cdot N_{STD}}{{10}^3+\left({10}^3+{\delta }^{15}{N}_{N{O}_3}+{}^{15}\epsilon _{N{O}_3}\right)\cdot N_{STD}}$$ 19

$$R_{{}^{14}N{}^{18}O_3}=\frac{3\cdot R_{N{O}_3}\cdot \left({10}^3+{\delta }^{18}{O}_{N{O}_3}+{}^{18}\epsilon _{N{O}_3}\right)\cdot SMOW}{{10}^3+\left({10}^3+{\delta }^{18}{O}_{N{O}_3}+{}^{18}\epsilon _{N{O}_3}\right)\cdot SMOW}$$ 20

Exchange of oxygen isotopes between NO₂⁻ and H₂O takes place according to the following isotopic exchange reaction:

$$N{}^{18}O_2+H_2{}^{16}O\underset{k^{-}}{\overset{k^{+}}{\leftrightarrow }}N{}^{16}O_2+H_2{}^{18}O$$ 21

The forward and backwards rates of this reaction are calculated as:

$$R_{+}^{N{O}_2\leftrightarrow H_{2}O}=k^{+}\cdot N{}^{18}O_2\cdot H_2{}^{16}O$$ 22

$$R_{-}^{N{O}_2\leftrightarrow H_{2}O}=k^{-}\cdot N{}^{16}O_2\cdot H_2{}^{18}O$$ 23

where N¹⁶O₂ = ¹⁴N¹⁶O₂ + ¹⁵N¹⁶O₂, the rates are in µM min⁻¹, and the forwards (k⁺) and backwards (k⁻) kinetic constants (in µM⁻¹ min⁻¹) are related to the equilibrium constant of the isotope exchange reaction a follows:

$$K_{EQ}^{N{O}_2\leftrightarrow H_{2}O}=\frac{k^{-}}{k^{+}}$$ 24

where the equilibrium constant for the isotope exchange reaction is obtained from the equilibrium concentrations of the species involved in the oxygen isotope exchange:

$$K_{EQ}^{N{O}_2\leftrightarrow H_{2}O}=\frac{({[{}^{14}N{}^{16}O_3]}_i+{[{}^{15}N{}^{16}O_3]}_i)\cdot {[H_2{}^{18}O]}_i}{{[{}^{14}N{}^{18}O_3]}_i\cdot {[H_2{}^{16}O]}_i}$$ 25

where the subscript i refers to the initial, equilibrium concentration of isotopic species.

The concentrations of the six isotopic model species in time are calculated by integrating the following system of six coupled differential equations starting from initial chemical and isotopic equilibrium conditions:

$$\frac{\partial ({}^{14}N{}^{16}O_3)}{\partial t}=-R_{{}^{14}N{}^{16}O_3}$$ 26

$$\frac{\partial ({}^{15}N{}^{16}O_3)}{\partial t}=-R_{{}^{15}N{}^{16}O_3}$$ 27

$$\frac{\partial ({}^{14}N{}^{18}O_3)}{\partial t}=-R_{{}^{14}N{}^{18}O_3}$$ 28

$$\begin{array}{lll}\hfill \frac{\partial ({}^{14}N{}^{16}O_2)}{\partial t}& \hfill =\hfill & +R_{{}^{14}N{}^{16}O_3}-R_{{}^{14}N{}^{16}O_2}+\frac{{}^{14}N{}^{16}O_2}{{}^{15}N{}^{16}O_2+{}^{14}N{}^{16}O_2}\cdot R_{+}^{N{O}_2\leftrightarrow H_{2}O}\hfill \\ \hfill & \hfill & -\frac{{}^{14}N{}^{16}O_2}{{}^{15}N{}^{16}O_2+{}^{14}N{}^{16}O_2}\cdot R_{-}^{N{O}_2\leftrightarrow H_{2}O}\hfill \end{array}$$ 29

$$\begin{array}{lll}\hfill \frac{\partial ({}^{15}N{}^{16}O_2)}{\partial t}& \hfill =\hfill & +R_{{}^{15}N{}^{16}O_3}-R_{{}^{15}N{}^{16}O_2}+\frac{{}^{15}N{}^{16}O_2}{{}^{15}N{}^{16}O_2+{}^{14}N{}^{16}O_2}\cdot R_{+}^{N{O}_2\leftrightarrow H_{2}O}\hfill \\ \hfill & \hfill & -\frac{{}^{15}N{}^{16}O_2}{{}^{15}N{}^{16}O_2+{}^{14}N{}^{16}O_2}\cdot R_{-}^{N{O}_2\leftrightarrow H_{2}O}\hfill \end{array}$$ 30

$$\frac{\partial ({}^{14}N{}^{18}O_2)}{\partial t}=+R_{{}^{14}N{}^{18}O_3}-R_{{}^{14}N{}^{18}O_2}-R_{+}^{N{O}_2\leftrightarrow H_{2}O}+R_{-}^{N{O}_2\leftrightarrow H_{2}O}$$ 31

To summarise, known model input parameters are: (1) the simulation time (that corresponds to the duration of the experiment), (2) the initial concentrations of NO₃⁻ and NO₂⁻, (3) the oxygen and nitrogen isotope compositions of NO₃⁻ and NO₂⁻, and (4) the δ¹⁸O of water. Unknown (fitting) parameters are: (1) the kinetic constants for NO₂⁻ production, for NO₂⁻ consumption and for isotope exchange between NO₂⁻ and H₂O, and (2) the oxygen and nitrogen isotope fractionation factors in NO₂⁻ production and NO₂⁻ consumption.

The model was implemented with the software Mathematica version 9 (Wolfram Research). Model outputs are changes of nitrite and nitrate concentrations and nitrogen and oxygen isotope compositions for both NO₂⁻ and NO₃⁻.

Author contributions

M.S. wrote the manuscript, M.S., A.M.L., E.P. and A.M. designed the study. E.P., A.M. and V.V. performed the analysis, G.A. and M.S. developed the model. M.S., A.M.L., B.M. and G.A. discussed the results and reviewed the manuscript.

Competing interests

The authors declare no competing interests.