Nitrogen removal in marine environments: recent findings and future research challenges

Respiratory reduction of nitrate (denitrification) is recognized as the most important process converting biologically available (fixed) nitrogen to N2. In current N cycle models, a major proportion of global marine denitrification (50–70%) is assumed to take place on the sea floor, particularly in organic rich continental margin sediments. Recent observations indicate that present conceptual views of denitrification and pathways of nitrate reduction and N2 formation are incomplete. Alternative N cycle pathways, particularly in sediments, include anaerobic ammonium oxidation to nitrite, nitrate and N2 by Mn-oxides, and anaerobic ammonium oxidation coupled to nitrite reduction and subsequent N2 mobilization. The discovery of new links and feedback mechanisms between the redox cycles of, e.g., C, N, S, Mn and Fe casts doubt on the present general understanding of the global N cycle. Recent models of the oceanic N budget indicate that total inputs are significantly smaller than estimated fixed N removal. The occurrence of alternative N reaction pathways further exacerbates the apparent imbalance as they introduce additional routes of N removal. In this contribution, we give a brief historical background of the conceptual understanding of N cycling in marine ecosystems, emphasizing pathways of aerobic and anaerobic N mineralization in marine sediments, and the implications of recently recognized metabolic pathways for N removal in marine environments

New Perspectives on Nitrogen Fixation Measurements Using 15N2 Gas

Recently, the method widely used to determine 15N2 fixation rates in marine and freshwater environments was found to underestimate rates because the dissolution of the added 15N2 gas bubble in seawater takes longer than theoretically calculated. As a solution to the potential underestimate of rate measurements, the usage of the enriched water method was proposed to provide constant 15N2 enrichment. Still, the superiority of enriched water method over the previously used bubble injection remains inconclusive. To clarify this issue, we performed laboratory based experiments and implemented the results into an error analysis of 15N2 fixation rates. Moreover, we conducted a literature search on the comparison of the two methods to calculate a mean effect size using a meta-analysis approach. Our results indicate that the error potentially introduced by an equilibrium phase of the 15N2 gas is −72% at maximum for experiments with very short incubation times of 1 h. In contrast, the underestimation was negligible for incubations lasting 12–24 h (error is −0.2%). Our meta-analysis indicates that 84% of the measurements in the two groups will overlap and there is a 61% chance that a sample picked at random from the enriched water group will have a higher value than one picked at random from the bubble group. Overall, the underestimation of N2 fixation rates when using the bubble method relative to the enriched water method is highly dependent on incubation time and other experimental conditions and cannot be generalized

New Perspectives on Nitrogen Fixation Measurements Using ¹⁵N₂ Gas

International audienc

Oxygen at Nanomolar Levels Reversibly Suppresses Process Rates and Gene Expression in Anammox and Denitrification in the Oxygen Minimum Zone off Northern Chile

A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O[subscript 2] and the sensitivity of the anaerobic N[subscript 2]-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O[subscript 2] at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N[subscript 2] and N[subscript 2]O production by denitrification was achieved at 205 and 297 nM O[subscript 2], respectively, whereas anammox was 50% inhibited at 886 nM O2. Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase (nosZ), nitrite reductase (nirS), and nitric oxide reductase (norB) decreased in relative abundance above 200 nM O[subscript 2]. This O[subscript 2] concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG, whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O[subscript 2] inhibition kinetics but strongly stimulated N[subscript 2]O production by denitrification. These results identify new O[subscript 2] thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses.Gordon and Betty Moore FoundationAgouron InstituteDanish National Research Foundation (Grant DNRF53

Continuous daylight in the high-Arctic summer supports high plankton respiration rates compared to those supported in the dark

Plankton respiration rate is a major component of global CO2 production and is forecasted to increase rapidly in the Arctic with warming. Yet, existing assessments in the Arctic evaluated plankton respiration in the dark. Evidence that plankton respiration may be stimulated in the light is particularly relevant for the high Arctic where plankton communities experience continuous daylight in spring and summer. Here we demonstrate that plankton community respiration evaluated under the continuous daylight conditions present in situ, tends to be higher than that evaluated in the dark. The ratio between community respiration measured in the light (Rlight) and in the dark (Rdark) increased as the 2/3 power of Rlight so that the Rlight:Rdark ratio increased from an average value of 1.37 at the median Rlight measured here (3.62 µmol O2 L-1 d-1) to an average value of 17.56 at the highest Rlight measured here (15.8 µmol O2 L-1 d-1). The role of respiratory processes as a source of CO2 in the Arctic has, therefore, been underestimated and is far more important than previously believed, particularly in the late spring, with 24 h photoperiods, when community respiration rates are highest

Sea ice and primary production proxies in surface sediments from a High Arctic Greenland fjord : Spatial distribution and implications for palaeoenvironmental studies

In order to establish a baseline for proxy-based reconstructions for the Young Sound-Tyrolerfjord system (Northeast Greenland), we analysed the spatial distribution of primary production and sea ice proxies in surface sediments from the fjord, against monitoring data from the Greenland Ecosystem Monitoring Programme. Clear spatial gradients in organic carbon and biogenic silica contents reflected marine influence, nutrient availability and river-induced turbidity, in good agreement with in situ measurements. The sea ice proxy IP25 was detected at all sites but at low concentrations, indicating that IP25 records from fjords need to be carefully considered and not directly compared to marine settings. The sea ice-associated biomarker HBI III revealed an open-water signature, with highest concentrations near the mid-July ice edge. This proxy evaluation is an important step towards reliable palaeoenvironmental reconstructions that will, ultimately, contribute to better predictions for this High Arctic ecosystem in a warming climate.Peer reviewe

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for “challenging” microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4–13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations