van Kaam, Rianne J M; Chen, Yunru; Friedrich, Michael W; Zabel, Matthias: Labeled experiment of samples from Mauritania and Namibia [dataset]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.997117 (dataset in review), In: van Kaam, RJM et al.: Incubation experiments on iron(III) reduction with Shewanella loihica and characterized desert dust samples from an ephemeral river in Namibia and a sabkha in Mauritania [dataset bundled publication]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.997118 (dataset in review)
Abstract:
In the labeled experiment, the Namibian dust was loaded with a 5% ¹³C-labeled Spirulina extract via adsorption. This organic matter solution is not metabolizable by S. loihica. This setup allowed us to test whether the bacteria used associated organic carbon instead of the provided lactate. Differences in iron reduction between the labeled and unlabeled dust treatment may reflect changes in the use of associated organic carbon or in iron(III) bioavailability.
Keyword(s):
References:
Lovley, Derek R; Phillips, Elizabeth J P (1987): Rapid Assay for Microbially Reducible Ferric Iron in Aquatic Sediments. Applied and Environmental Microbiology, 53(7), 1536-1540, https://doi.org/10.1128/aem.53.7.1536-1540.1987
Stookey, Lawrence L (1970): Ferrozine - A new spectrophotometric reagent for iron. Analytical Chemistry, 42, 779-781, https://doi.org/10.1021/ac60289a016
Widdel, Friedrich (1980): Anaerober Abbau von Fettsäuren und Benzoesäure durch neu isolierte Arten Sulfat-reduzierender Bakterien [thesis]. Georg-August-Universität, Göttingen, Germany
Widdel, Friedrich; Kohring, Gert-Wieland; Mayer, Frank (1983): Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. Archives of Microbiology, 134(4), 286-294, https://doi.org/10.1007/BF00407804
Widdel, Friedrich; Pfennig, Norbert (1981): Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. Archives of Microbiology, 129(5), 395-400, https://doi.org/10.1007/BF00406470
Project(s):
Funding:
German Research Foundation (DFG), grant/award no. 390741603: EXC 2077: The Ocean Floor – Earth's Uncharted Interface
Event(s):
Comment:
Cell culturing:
Shewanella loihica PV-4 strain was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ, DSM No. 17748). Lyophilized cells were revived in marine broth at 18°C, 200 rpm (Innova 40, New Brunswick Scientific). At log phase, cultures were frozen in 25% glycerol and stored at -80°C until experimental use. Prior to use in incubation experiments, S. loihica was revived from glycerol into marine broth and pre-grown for ~2 days under the above conditions. Cells were harvested (3000 × g, 10 min), washed three times with the defined medium, and resuspended in this medium before addition to the incubations.
Defined medium:
The defined medium was a salt solution according to Widdel (1980), containing 20 g NaCl, 3 g MgCl₂∙6H₂O, 0.2 g KH₂PO₄, 0.25 g NH₄Cl, 0.5 g KCl and 0.15 g CaCl₂∙2H₂O in 1 L ultrapure water. The solution was sterilized by autoclaving under N₂, then supplemented with 1 M NaHCO₃ together with trace elements (Widdel et al., 1983), selenite–tungstate (Widdel, 1980), and vitamins (Widdel & Pfennig, 1981). pH was set to ca. 7.2. A sodium-lactate was used as electron donor and carbon source (final conc. 13 mM).
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Event label | Event | van Kaam, Rianne J M | |||
| 2 | Optional event label | Event 2 | van Kaam, Rianne J M | |||
| 3 | Comment of event | Comment | van Kaam, Rianne J M | |||
| 4 | Type of study | Study type | van Kaam, Rianne J M | |||
| 5 | Sample type | Samp type | van Kaam, Rianne J M | |||
| 6 | Treatment | Treat | van Kaam, Rianne J M | |||
| 7 | Sample code/label | Sample label | van Kaam, Rianne J M | |||
| 8 | Treatment: dust, added | T:dust add | g | van Kaam, Rianne J M | ||
| 9 | Treatment: solution | T:solution | ml | van Kaam, Rianne J M | Salt | |
| 10 | Treatment: solution | T:solution | ml | van Kaam, Rianne J M | Lactate | |
| 11 | Treatment: cells | T:cells | ml | van Kaam, Rianne J M | ||
| 12 | Treatment: solution | T:solution | ml | van Kaam, Rianne J M | Spirulina | |
| 13 | Time in days | Time d | days | van Kaam, Rianne J M | ||
| 14 | Iron II, dissolved | Fe(ll) diss | µmol/l | van Kaam, Rianne J M | VantaStar microplate reader, BMG Labtech | Extraction according to Lovley and Phillips (1987; doi:10.1128/aem.53.7.1536-1540.1987). Analysis through colorimetrically with ferrozine according to Stookey (1970; doi:10.1021/ac60289a016). |
| 15 | Acetate | Acetate | µmol/l | van Kaam, Rianne J M | VantaStar microplate reader, BMG Labtech | Enzymatically analysis, Acetic Acid Assay Kit (K-ACET), Megazyme (Bray, Ireland). |
| 16 | Carbon, organic, dissolved | DOC | µmol/l | van Kaam, Rianne J M | Carbon analyzer, Dimatec, Dimatoc; Multi N/C analyzer, Analytik Jena, 2100S | |
| 17 | Carbon, inorganic, dissolved | DIC | µmol/l | van Kaam, Rianne J M | Carbon analyzer, Dimatec, Dimatoc; Multi N/C analyzer, Analytik Jena, 2100S | |
| 18 | δ13C, dissolved inorganic carbon | δ13C DIC | ‰ PDB | van Kaam, Rianne J M | Flash Isotope Ratio Mass Spectrometer (IRMS); coupled with Mass Spectrometer Delta V Advantage via Conflo IV interface | vs. VPDB |
| 19 | Hydrogen gas | H2 | µmol/l | van Kaam, Rianne J M | Gas analyzer, Los Gatos Research and Gas chromatograph, SRI Instruments USA, SRI8610 | |
| 20 | Carbon, organic, total | TOC | % | van Kaam, Rianne J M | Flash Isotope Ratio Mass Spectrometer (IRMS); coupled with Mass Spectrometer Delta V Advantage via Conflo IV interface | [wt%] |
| 21 | δ13C, dissolved organic carbon | δ13C DOC | ‰ PDB | van Kaam, Rianne J M | Flash Isotope Ratio Mass Spectrometer (IRMS); coupled with Mass Spectrometer Delta V Advantage via Conflo IV interface | vs. VPDB |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0) (License comes into effect after moratorium ends)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
1436 data points