Annie Bourbonnais

Simulating the global distribution of nitrogen isotopes in the ocean

9 isotopes, 14 N and 15 N, in the nitrate (NO3 ), phytoplankton, zooplankton, and detritus 10 variables of the marine ecosystem model. The isotope effects of algal NO3 uptake, 11 nitrogen fixation, water column denitrification, and zooplankton excretion are considered 12 as well as the removal of NO3 by sedimentary denitrification. A global database of 13 d 15 NO3 observations is compiled from previous studies and compared to the model 14 results on a regional basis where sufficient observations exist. The model is able to 15 qualitatively and quantitatively reproduce many of the observed patterns such as high 16 subsurface values in water column denitrification zones and the meridional and vertical 17 gradients in the Southern Ocean. The observed pronounced subsurface minimum in the 18 Atlantic is underestimated by the model presumably owing to too little simulated 19 nitrogen fixation there. Sensitivity experiments reveal that algal NO3 uptake, nitrogen 20 fixation, and water column denitrification have the strongest effects on the simulated 21 distribution of nitrogen isotopes, whereas the effect from zooplankton excretion is 22 weaker. Both water column and sedimentary denitrification also have important indirect 23 effects on the nitrogen isotope distribution by reducing the fixed nitrogen inventory, 24 which creates an ecological niche for nitrogen fixers and, thus, stimulates additional N2 25 fixation in the model. Important model deficiencies are identified, and strategies for 26 future improvement and possibilities for model application are outlined.

NC10 bacteria in marine oxygen minimum zones

Bacteria of the NC10 phylum link anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophy pathway. A niche for NC10 in the pelagic ocean has not been confirmed. We show that NC10 bacteria are present and transcriptionally active in oceanic oxygen minimum zones (OMZs) off northern Mexico and Costa Rica. NC10 16S rRNA genes were detected at all sites, peaking in abundance in the anoxic zone with elevated nitrite and methane concentrations. Phylogenetic analysis of particulate methane monooxygenase genes further confirmed the presence of NC10. rRNA and mRNA transcripts assignable to NC10 peaked within the OMZ and included genes of the putative nitrite-dependent intra-aerobic pathway, with high representation of transcripts containing the unique motif structure of the nitric oxide (NO) reductase of NC10 bacteria, hypothesized to participate in O2-producing NO dismutation. These findings confirm pelagic OMZs as a niche for NC10, suggesting a role for this group in OMZ nitrogen, methane and oxygen cycling.

N-loss isotope effects in the Peru oxygen minimum zone studied using a mesoscale eddy as a natural tracer experiment

Mesoscale eddies in Oxygen Minimum Zones (OMZs) have been identified as important fixed nitrogen (N) loss hotspots that may significantly impact both the global rate of N-loss as well as the oceans N isotope budget. They also represent ‘natural tracer experiments’ with intensified biogeochemical signals that can be exploited to understand the large-scale processes that control N-loss and associated isotope effects (e; the ‰ deviation from 1 in the ratio of reaction rate constants for the light versus the heavy isotopologues). We observed large ranges in the concentrations and N and O isotopic compositions of nitrate (NO3−), nitrite (NO2−) and biogenic N2 associated with an anticyclonic eddy in the Peru OMZ during two cruises in November and December 2012. In the eddys center where NO3− was nearly exhausted, we measured the highest δ15N values for both NO3− and NO2− (up to ~70‰ and 50‰) ever reported for an OMZ. Correspondingly, N deficit and biogenic N2-N concentrations were also the highest near the eddys center (up to ~40 µmol L−1). δ15N-N2 also varied with biogenic N2 production, following kinetic isotopic fractionation during NO2− reduction to N2 and, for the first time, provided an independent assessment of N isotope fractionation during OMZ N-loss. We found apparent variable e for NO3− reduction (up to ~30‰ in the presence of NO2−). However, the overall e for N-loss was calculated to be only ~13-14‰ (as compared to canonical values of ~20-30‰) assuming a closed system and only slightly higher assuming an open system (16-19‰). Our results were similar whether calculated from the disappearance of DIN (NO3− + NO2−) or from the appearance of N2 and changes in isotopic composition. Further, we calculated the separate e for NO3− reduction to NO2− and NO2− reduction to N2 of ~16-21‰ and ~12‰, respectively, when the effect of NO2− oxidation could be removed. These results, together with the relationship between N and O of NO3− isotopes and the difference in δ15N between NO3− and NO2-, confirm a role for NO2− oxidation in increasing the apparent e associated with NO3− reduction. The lower e for NO3− and NO2− reduction as well as N-loss calculated in this study could help reconcile the current imbalance in the global N budget if they are representative of OMZ N-loss.

N2O production and consumption from stable isotopic and concentration data in the Peruvian coastal upwelling system

The ocean is an important source of nitrous oxide (N2O) to the atmosphere, yet the factors controlling N2O production and consumption in oceanic environments are still not understood nor constrained. We measured N2O concentrations and isotopomer ratios, as well as O2, nutrient and biogenic N2 concentrations, and the isotopic compositions of nitrate and nitrite at several coastal stations during two cruises off the Peru coast (~5–16°S, 75–81°W) in December 2012 and January 2013. N2O concentrations varied from below equilibrium values in the oxygen deficient zone (ODZ) to up to 190 nmol L−1 in surface waters. We used a 3-D-reaction-advection-diffusion model to evaluate the rates and modes of N2O production in oxic waters and rates of N2O consumption versus production by denitrification in the ODZ. Intramolecular site preference in N2O isotopomer was relatively low in surface waters (generally −3 to 14‰) and together with modeling results, confirmed the dominance of nitrifier-denitrification or incomplete denitrifier-denitrification, corresponding to an efflux of up to 0.6 Tg N yr−1 off the Peru coast. Other evidence, e.g., the absence of a relationship between ΔN2O and apparent O2 utilization and significant relationships between nitrate, a substrate during denitrification, and N2O isotopes, suggest that N2O production by incomplete denitrification or nitrifier-denitrification decoupled from aerobic organic matter remineralization are likely pathways for extreme N2O accumulation in newly upwelled surface waters. We observed imbalances between N2O production and consumption in the ODZ, with the modeled proportion of N2O consumption relative to production generally increasing with biogenic N2. However, N2O production appeared to occur even where there was high N loss at the shallowest stations.

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.