Placing an upper limit on cryptic marine sulphur cycling.

A quantitative understanding of sources and sinks of fixed nitrogen in low-oxygen waters is required to explain the role of oxygen-minimum zones (OMZs) in controlling the fixed nitrogen inventory of the global ocean. Apparent imbalances in geochemical nitrogen budgets have spurred numerous studies to measure the contributions of heterotrophic and autotrophic N2-producing metabolisms (denitrification and anaerobic ammonia oxidation, respectively). Recently, 'cryptic' sulphur cycling was proposed as a partial solution to the fundamental biogeochemical problem of closing marine fixed-nitrogen budgets in intensely oxygen-deficient regions. The degree to which the cryptic sulphur cycle can fuel a loss of fixed nitrogen in the modern ocean requires the quantification of sulphur recycling in OMZ settings. Here we provide a new constraint for OMZ sulphate reduction based on isotopic profiles of oxygen ((18)O/(16)O) and sulphur ((33)S/(32)S, (34)S/(32)S) in seawater sulphate through oxygenated open-ocean and OMZ-bearing water columns. When coupled with observations and models of sulphate isotope dynamics and data-constrained model estimates of OMZ water-mass residence time, we find that previous estimates for sulphur-driven remineralization and loss of fixed nitrogen from the oceans are near the upper limit for what is possible given in situ sulphate isotope data.

Nitrous oxide dynamics in a braided river system, New Zealand.

Recently the Intergovernmental Panel on Climate Change (IPCC) emission factor EF5-r was revised downward to a value of 0.0025 kg N2O-N per kg NO3-N leached. It was not reduced further due to the continued uncertainty surrounding the dynamics of N2O in river systems. There have been few studies where river system N2O yields and fluxes have been measured. In this study, we examined the relationship between NO3-N and N2O-N fluxes at 10 sites along a braided river system (84 km) over a 397-d period. Isotopic analysis of NO3-N river water samples and the potential agricultural nitrogen (N) sources demonstrated that the NO3-N came from agricultural or sewage sources. Percent saturation of N2O varied with site and date (average, 114%) and correlated with river N2O-N concentrations. Modeled N2O fluxes (16-30 µg m(-2) h(-1)) from five sites were strongly related to river NO3-N concentrations ( r² = 0.86). The modeled N2O-N fluxes ranged from 39 to 81% of the IPCC-derived emissions based on the NO3-N load in the river over 397 d and do not support further lowering of the EF5-r. Further in situ river studies are required to verify the N2O-N fluxes and the calculated gas transfer velocity values for these braided river systems.

Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria.

The presence of a copper-containing dissimilatory nitrite reductase gene (nirK) was discovered in several isolates of beta-subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were designed based on published nirK sequences from denitrifying bacteria and used to amplify a 540-bp fragment of the nirK gene from Nitrosomonas marina and five additional isolates of ammonia-oxidizing bacteria. Amplification products of the expected size were cloned and sequenced. Alignment of the nucleic acid and deduced amino acid (AA) sequences shows significant similarity (62 to 75% DNA, 58 to 76% AA) between nitrite reductases present in these nitrifiers and the copper-containing nitrite reductase found in classic heterotrophic denitrifiers. While the presence of a nitrite reductase in Nitrosomonas europaea is known from early biochemical work, preliminary sequence data from its genome indicate a rather low similarity to the denitrifier nirKs. Phylogenetic analysis of the partial nitrifier nirK sequences indicates that the topology of the nirK tree corresponds to the 16S rRNA and amoA trees. While the role of nitrite reduction in the metabolism of nitrifying bacteria is still uncertain, these data show that the nirK gene is present in closely related nitrifying isolates from many oceanographic regions and suggest that nirK sequences retrieved from the environment may include sequences from ammonia-oxidizing bacteria.

Using dual-bacterial denitrification to improve delta15N determinations of nitrates containing mass-independent 17O.

The bacterial denitrification method for isotopic analysis of nitrate using N(2)O generated from Pseudomonas aureofaciens may overestimate delta(15)N values by as much as 1-2 per thousand for samples containing atmospheric nitrate because of mass-independent (17)O variations in such samples. By analyzing such samples for delta(15)N and delta(18)O using the denitrifier Pseudomonas chlororaphis, one obtains nearly correct delta(15)N values because oxygen in N(2)O generated by P. chlororaphis is primarily derived from H(2)O. The difference between the apparent delta(15)N value determined with P. aureofaciens and that determined with P. chlororaphis, assuming mass-dependent oxygen isotopic fractionation, reflects the amount of mass-independent (17)O in a nitrate sample. By interspersing nitrate isotopic reference materials having substantially different delta(18)O values with samples, one can normalize oxygen isotope ratios and determine the fractions of oxygen in N(2)O derived from the nitrate and from water with each denitrifier. This information can be used to improve delta(15)N values of nitrates having excess (17)O. The same analyses also yield estimates of the magnitude of (17)O excess in the nitrate (expressed as Delta(17)O) that may be useful in some environmental studies. The 1-sigma uncertainties of delta(15)N, delta(18)O and Delta(17)O measurements are +/-0.2, +/-0.3 and +/-5 per thousand, respectively.

Measurement of the oxygen isotopic composition of nitrate in seawater and freshwater using the denitrifier method.

We report a novel method for measurement of the oxygen isotopic composition (18O/16O) of nitrate (NO3-) from both seawater and freshwater. The denitrifier method, based on the isotope ratio analysis of nitrous oxide generated from sample nitrate by cultured denitrifying bacteria, has been described elsewhere for its use in nitrogen isotope ratio (15N/14N) analysis of nitrate. (1) Here, we address the additional issues associated with 18O/16O analysis of nitrate by this approach, which include (1) the oxygen isotopic difference between the nitrate sample and the N20 analyte due to isotopic fractionation associated with the loss of oxygen atoms from nitrate and (2) the exchange of oxygen atoms with water during the conversion of nitrate to N2O. Experiments with 18O-labeled water indicate that water exchange contributes less than 10%, and frequently less than 3%, of the oxygen atoms in the N20 product for Pseudomonas aureofaciens. In addition, both oxygen isotope fractionation and oxygen atom exchange are consistent within a given batch of analyses. The analysis of appropriate isotopic reference materials can thus be used to correct the measured 18O/16O ratios of samples for both effects. This is the first method tested for 18O/16O analysis of nitrate in seawater. Benefits of this method, relative to published freshwater methods, include higher sensitivity (tested down to 10 nmol and 1 microM NO3-), lack of interference by other solutes, and ease of sample preparation.

A bacterial method for the nitrogen isotopic analysis of nitrate in seawater and freshwater.

We report a new method for measurement of the isotopic composition of nitrate (NO3-) at the natural-abundance level in both seawater and freshwater. The method is based on the isotopic analysis of nitrous oxide (N20) generated from nitrate by denitrifying bacteria that lack N2O-reductase activity. The isotopic composition of both nitrogen and oxygen from nitrate are accessible in this way. In this first of two companion manuscripts, we describe the basic protocol and results for the nitrogen isotopes. The precision of the method is better than 0.2/1000 (1 SD) at concentrations of nitrate down to 1 microM, and the nitrogen isotopic differences among various standards and samples are accurately reproduced. For samples with 1 microM nitrate or more, the blank of the method is less than 10% of the signal size, and various approaches may reduce it further.