Sokoll, Sarah; Holtappels, Moritz (2012): Benthic anammox and dentrification rates measured in a slurry incubation experiments at four different stations in the Arabian Sea off Pakistan during the METEOR cruise M74/2 in 2007 [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.828672, In supplement to: Sokoll, Sarah; Holtappels, Moritz; Lam, Phyllis; Collins, Gavin; Schlüter, Michael; Lavik, Gaute; Kuypers, Marcel MM (2012): Benthic nitrogen loss in the Arabian Sea off Pakistan. Frontiers in Microbiology, 3, https://doi.org/10.3389/fmicb.2012.00395
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Abstract:
Vertical distributions of benthic denitrification and anammox rates within the sediment were estimated from slurry incubation experiments. Rates were used to calculate the contribution of anammox and denitrification to the total N-loss. Briefly, MUC sediment cores were sliced in 2 cm intervals and the sediment was diluted and incubated with degassed bottom water in a gas tight bag. After pre-incubating the bags for 2 h, 15N-labeled substrates were injected into the bags and the slurries were thoroughly mixed. Incubations were performed in the dark at in situ temperatures. The N2 isotope ratio (28N2, 29N2, and 30N2) was determined by gas chromatography-isotopic ratio mass spectrometry (VG Optima, Micromass) and calculated according to Kuypers et al. (2005) and Holtappels et al. (2011), respectively.Furthermore, total organic carbon and nitrogen concentrations were measured of core sediment layers corresponding to those used for rate measurements. Concentrations of organic carbon and nitrogen were determined by combustion/gas chromatography (Carlo Erba NA-1500 CNS analyzer) of dried sediment samples after acidification. The same sediment layer were also used to extract nucleic acids. The concentrations of the DNA in the samples were measured spectrophotometrically with a NanoDrop instrument (Thermo Fisher Scientific Inc.). The biomarker functional gene nirS, encoding the cd1-containing nitrite reductase, for both denitrifiers and marine anammox bacteria were quantified with real-time PCR, using the primers cd3aF/R3cd (5'-GTSAACGTSAAGGARACSGG-3' (Michotey et al., 2000)/5'-GASTTCGGRTGSGTCTTGA-3'; Throback et al., 2004) and Scnir372F/Scnir845R (5'-TGTAGCCAGCATTGTAGCGT-3'/5'-TCAAGCCAGACCCATTTGCT-3'; Lam et al., 2009).
Related to:
Lam, Phyllis; Lavik, Gaute; Jensen, Marlene M; van de Vossenberg, Jack; Schmidt, Markus; Woebken, Dagmar; Gutièrrez, Dimitri; Amann, Rudolf; Jetten, Mike S M; Kuypers, Marcel MM (2009): Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proceedings of the National Academy of Sciences, 106(12), 4752-4757, https://doi.org/10.1073/pnas.0812444106
Michotey, Valérie; Méjean, Vincent; Bonin, Patricia (2000): Comparison of Methods for Quantification of Cytochrome cd1-Denitrifying Bacteria in Environmental Marine Samples. Applied and Environmental Microbiology, 66(4), 1564-1571, https://doi.org/10.1128/AEM.66.4.1564-1571.2000
Throbäck, I N; Enwall, K; Jarvis, Ian; Hallin, James S (2004): Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology, 49(3), 401-417, https://doi.org/10.1016/j.femsec.2004.04.011
Project(s):
Coverage:
Median Latitude: 24.853991 * Median Longitude: 63.072855 * South-bound Latitude: 24.766330 * West-bound Longitude: 62.997830 * North-bound Latitude: 24.895160 * East-bound Longitude: 63.267160
Date/Time Start: 2007-10-13T17:20:00 * Date/Time End: 2007-10-24T14:41:00
Minimum DEPTH, sediment/rock: 0.01 m * Maximum DEPTH, sediment/rock: 0.07 m
Event(s):
GeoB12204-4 (M74/2_969-1) * Latitude Start: 24.882650 * Longitude Start: 63.026600 * Latitude End: 24.882650 * Longitude End: 63.026600 * Date/Time Start: 2007-10-13T17:20:00 * Date/Time End: 2007-10-13T18:10:00 * Elevation: -691.0 m * Campaign: M74/2 * Basis: Meteor (1986) * Method/Device: MultiCorer (MUC)
GeoB12208-2 (M74/2_976-2) * Latitude Start: 24.766660 * Longitude Start: 62.999830 * Latitude End: 24.766330 * Longitude End: 62.999830 * Date/Time Start: 2007-10-16T07:42:00 * Date/Time End: 2007-10-16T08:49:00 * Elevation: -1430.0 m * Campaign: M74/2 * Basis: Meteor (1986) * Method/Device: MultiCorer (MUC)
GeoB12210-3 (M74/2_979-3) * Latitude Start: 24.895160 * Longitude Start: 63.267160 * Latitude End: 24.895160 * Longitude End: 63.267160 * Date/Time Start: 2007-10-22T07:20:00 * Date/Time End: 2007-10-22T07:43:00 * Elevation: -363.0 m * Campaign: M74/2 * Basis: Meteor (1986) * Method/Device: MultiCorer (MUC)
Parameter(s):
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
Size:
228 data points
Data
| 1 Event | 2 Latitude | 3 Longitude | 4 Elevation [m] | 5 Depth sed [m] | 6 Depth top [m] | 7 Depth bot [m] | 8 TOC [%] (Element analyser, Carlo Erba ...) | 9 N org [%] (Element analyser, Carlo Erba ...) | 10 C/N [mol/mol] | 11 DNA/sed [ng/mg] (Spectrophotometer NanoDrop (T...) | 12 Std dev [±] (Spectrophotometer NanoDrop (T...) | 13 Anammox nirS/sed [gene copies/mg] (using the primer Scnir372F/Sc...) | 14 Std dev [±] (Real-time quantitative polyme...) | 15 Denitrifier nirS/sed [gene copies/mg] (using the primer cd3aF/R3cd, ...) | 16 Std dev [±] (Real-time quantitative polyme...) | 17 Anammox rate [nmol/cm3/day] (15N-stable Isotpe pairing tec...) | 18 Std dev [±] (15N-stable Isotpe pairing tec...) | 19 Denitrifi rate [nmol/cm3/day] (15N-stable Isotpe pairing tec...) | 20 Std dev [±] (15N-stable Isotpe pairing tec...) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GeoB12204-4 | 24.882650 | 63.026600 | -691 | 0.01 | 0.00 | 0.02 | 2.21 | 0.31 | 8.42 | 9.18 | 0.65 | 132.96 | 74.60 | 2561.52 | 180.47 | 11.95 | 1.16 | 91.31 | 9.92 |
| GeoB12204-4 | 24.882650 | 63.026600 | -691 | 0.03 | 0.02 | 0.04 | 1.96 | 0.28 | 8.07 | 5.04 | 0.59 | 105.23 | 11.71 | 2205.91 | 371.89 | 3.17 | 0.84 | 13.99 | 2.14 |
| GeoB12204-4 | 24.882650 | 63.026600 | -691 | 0.05 | 0.04 | 0.06 | 1.91 | 0.25 | 8.80 | 6.42 | 0.84 | 0.00 | 0.00 | 1500.89 | 170.06 | 4.10 | 0.34 | 9.64 | 0.58 |
| GeoB12204-4 | 24.882650 | 63.026600 | -691 | 0.07 | 0.06 | 0.08 | 1.81 | 0.26 | 8.14 | 3.96 | 0.33 | 42.47 | 3.68 | 1705.74 | 344.76 | 1.28 | 0.12 | ||
| GeoB12208-2 | 24.766660 | 62.999830 | -1430 | 0.01 | 0.00 | 0.02 | 1.73 | 0.24 | 8.25 | 6.48 | 0.41 | 1727.85 | 197.94 | 7244.69 | 813.20 | 44.71 | 2.16 | 73.18 | 8.35 |
| GeoB12208-2 | 24.766660 | 62.999830 | -1430 | 0.03 | 0.02 | 0.04 | 1.56 | 0.23 | 7.78 | 5.13 | 0.21 | 182.57 | 40.65 | 1662.49 | 342.58 | 39.43 | 9.12 | 46.99 | 7.31 |
| GeoB12208-2 | 24.766660 | 62.999830 | -1430 | 0.05 | 0.04 | 0.06 | 1.44 | 0.21 | 7.93 | 5.62 | 0.40 | 203.49 | 43.53 | 1245.98 | 205.93 | 15.77 | 3.05 | ||
| GeoB12208-2 | 24.766660 | 62.999830 | -1430 | 0.07 | 0.06 | 0.08 | 1.18 | 0.19 | 7.42 | 2.70 | 0.08 | 174.73 | 33.59 | 444.92 | 152.83 | 14.35 | 1.08 | ||
| GeoB12210-3 | 24.895160 | 63.267160 | -363 | 0.01 | 0.00 | 0.02 | 1.58 | 0.26 | 7.16 | 4.92 | 0.03 | 78.58 | 12.99 | 6989.53 | 272.22 | 10.55 | 1.68 | 136.40 | 3.28 |
| GeoB12210-3 | 24.895160 | 63.267160 | -363 | 0.03 | 0.02 | 0.04 | 1.51 | 0.23 | 7.78 | 3.69 | 0.23 | 101.11 | 52.28 | 3475.87 | 81.91 | 2.30 | 0.18 | 22.43 | 3.29 |
| GeoB12210-3 | 24.895160 | 63.267160 | -363 | 0.05 | 0.04 | 0.06 | 1.47 | 0.21 | 8.19 | 3.47 | 0.23 | 0.00 | 0.00 | 1048.36 | 163.23 | 1.16 | 0.05 | 23.12 | 3.11 |
| GeoB12210-3 | 24.895160 | 63.267160 | -363 | 0.07 | 0.06 | 0.08 | 1.25 | 0.21 | 7.10 | 3.05 | 0.24 | 108.03 | 10.70 | 2590.06 | 226.06 | 0.19 | 0.02 | ||
| GeoB12216-5 | 24.871660 | 62.997830 | -970 | 0.01 | 0.00 | 0.02 | 2.37 | 0.31 | 8.99 | 5.08 | 0.14 | 1727.85 | 197.94 | 7244.69 | 813.20 | 26.45 | 2.64 | 96.79 | 12.06 |
| GeoB12216-5 | 24.871660 | 62.997830 | -970 | 0.03 | 0.02 | 0.04 | 2.09 | 0.28 | 8.59 | 5.61 | 0.49 | 753.90 | 88.98 | 3804.42 | 228.82 | 15.60 | 1.50 | 25.40 | 1.50 |
| GeoB12216-5 | 24.871660 | 62.997830 | -970 | 0.05 | 0.04 | 0.06 | 2.00 | 0.27 | 8.74 | 4.43 | 0.43 | 106.68 | 62.53 | 971.41 | 155.01 | 5.08 | 0.21 | ||
| GeoB12216-5 | 24.871660 | 62.997830 | -970 | 0.07 | 0.06 | 0.08 | 1.33 | 0.19 | 7.95 | 3.12 | 0.41 | 0.00 | 0.00 | 205.85 | 14.05 | 0.87 | 0.20 |