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  • Elemental nitrogen oxidation A new bacterial process in the nitrogen cycle; ELNOX; Event label; EXP; Experiment; Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS); Hydrogen/Carbon ratio; Mass-to-charge ratio; Molecular formula; Oxygen/Carbon ratio; Peak intensity; Pseudovibrio_ASW_EXP; Pseudovibrio_SW_EXP; Standard deviation; Treatment  (1)
  • FT-ICR-MS  (1)
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  • 1
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    PANGAEA
    In:  Supplement to: Schwedt, Anne; Seidel, Michael; Dittmar, Thorsten; Simon, Meinhard; Bondarev, Vladimir N; Romano, Stefano; Lavik, Gaute; Schulz-Vogt, Heide N (2015): Substrate use of Pseudovibrio sp. growing in ultra-oligotrophic seawater. PLoS ONE, 10(3), e0121675, https://doi.org/10.1371/journal.pone.0121675
    Publication Date: 2023-09-07
    Description: Marine planktonic bacteria often live in habitats with extremely low concentrations of dissolved organic matter (DOM). To study the use of trace amounts of DOM by the facultatively oligotrophic Pseudovibrio sp. FO-BEG1, we investigated the composition of artificial and natural seawater before and after growth. We determined the concentrations of dissolved organic carbon (DOC), total dissolved nitrogen (TDN), free and hydrolysable amino acids, and the molecular composition of DOM by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR-MS). The DOC concentration of the artificial seawater we used for cultivation was 4.4 µmol C/l, which was eight times lower compared to the natural oligotrophic seawater we used for parallel experiments (36 µmol C/l). During the three-week duration of the experiment, cell numbers increased from 40 cells/ml to 2x10**4 cells/ml in artificial and to 3x10**5 cells/ml in natural seawater. No nitrogen fixation and minor CO2 fixation (〈 1% of cellular carbon) was observed. Our data show that in both media, amino acids were not the main substrate for growth. Instead, FT-ICR-MS analysis revealed usage of a variety of different dissolved organic molecules, belonging to a wide range of chemical compound groups, also containing nitrogen. The present study shows that marine heterotrophic bacteria are able to proliferate with even lower DOC concentrations than available in natural ultra-oligotrophic seawater, using unexpected organic compounds to fuel their energy, carbon and nitrogen requirements.
    Keywords: Elemental nitrogen oxidation A new bacterial process in the nitrogen cycle; ELNOX; Event label; EXP; Experiment; Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS); Hydrogen/Carbon ratio; Mass-to-charge ratio; Molecular formula; Oxygen/Carbon ratio; Peak intensity; Pseudovibrio_ASW_EXP; Pseudovibrio_SW_EXP; Standard deviation; Treatment
    Type: Dataset
    Format: text/tab-separated-values, 9716 data points
    Location Call Number Limitation Availability
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  • 2
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Steen, A. D., Kusch, S., Abdulla, H. A., Cakic, N., Coffinet, S., Dittmar, T., Fulton, J. M., Galy, V., Hinrichs, K., Ingalls, A. E., Koch, B. P., Kujawinski, E., Liu, Z., Osterholz, H., Rush, D., Seidel, M., Sepulveda, J., & Wakeham, S. G. Analytical and computational advances, opportunities, and challenges in marine organic biogeochemistry in an era of "Omics". Frontiers in Marine Science, 7, (2020): 718, doi:10.3389/fmars.2020.00718.
    Description: Advances in sampling tools, analytical methods, and data handling capabilities have been fundamental to the growth of marine organic biogeochemistry over the past four decades. There has always been a strong feedback between analytical advances and scientific advances. However, whereas advances in analytical technology were often the driving force that made possible progress in elucidating the sources and fate of organic matter in the ocean in the first decades of marine organic biogeochemistry, today process-based scientific questions should drive analytical developments. Several paradigm shifts and challenges for the future are related to the intersection between analytical progress and scientific evolution. Untargeted “molecular headhunting” for its own sake is now being subsumed into process-driven targeted investigations that ask new questions and thus require new analytical capabilities. However, there are still major gaps in characterizing the chemical composition and biochemical behavior of macromolecules, as well as in generating reference standards for relevant types of organic matter. Field-based measurements are now routinely complemented by controlled laboratory experiments and in situ rate measurements of key biogeochemical processes. And finally, the multidisciplinary investigations that are becoming more common generate large and diverse datasets, requiring innovative computational tools to integrate often disparate data sets, including better global coverage and mapping. Here, we compile examples of developments in analytical methods that have enabled transformative scientific advances since 2004, and we project some challenges and opportunities in the near future. We believe that addressing these challenges and capitalizing on these opportunities will ensure continued progress in understanding the cycling of organic carbon in the ocean.
    Description: The Hanse-Wissenschaftskolleg Delmenhorst, Germany, sponsored the “Marine Organic Biogeochemistry” workshop in April 2019, of which this working group report was a part. The workshop was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number: 422798570. The Geochemical Society provided additional funding for the conference. AS was supported by DOE grant DE-SC0020369.
    Keywords: Chemometrics ; Natural marine organic matter ; FT-ICR-MS ; Analytical challenges ; HR-NMR ; Marine organic biogeochemistry
    Repository Name: Woods Hole Open Access Server
    Type: Article
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