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  • 1
    Publication Date: 2020-09-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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  • 2
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Format: application/pdf
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  • 3
    Publication Date: 2022-02-21
    Description: Soil bacteria rank among the most diverse groups of organisms on Earth and actively impact global processes of carbon cycling, especially in the emission of greenhouse gases like methane, CO2 and higher gaseous hydrocarbons. An abundant group of soil bacteria are the mycobacteria, which colonize various terrestrial, marine and anthropogenic environments due to their impermeable cell envelope that contains remarkable lipids. These bacteria have been found to be highly abundant at petroleum and gas seep areas, where they might utilize the released hydrocarbons. However, the function and the lipid biomarker inventory of these soil mycobacteria are poorly studied. Here, soils from the Fuoco di Censo seep, an everlasting fire (gas seep) in Sicily, Italy, were investigated for the presence of mycobacteria via 16S rRNA gene sequencing and fatty acid profiling. The soils contained high relative abundances (up to 34% of reads assigned) of mycobacteria, phylogenetically close to the Mycobacterium simiae complex and more distant from the wellstudied M. tuberculosis and hydrocarbon-utilizing M. paraffinicum. The soils showed decreasing abundances of mycocerosic acids (MAs), fatty acids unique for mycobacteria, with increasing distance from the seep. The major MAs at this seep were tentatively identified as 2,4,6,8-tetramethyl tetracosanoic acid and 2,4,6,8,10-pentamethyl hexacosanoic acid. Unusual MAs with mid-chain methyl branches at positions C-12 and C-16 (i.e., 2,12-dimethyl eicosanoic acid and 2,4,6,8,16-pentamethyl tetracosanoic acid) were also present. The molecular structures of the Fuoco di Censo MAs are different from those of the well-studied mycobacteria like M. tuberculosis or M. bovis and have relatively 13C-depleted values (􀀀38‰ to 􀀀48 ‰), suggesting a direct or indirect utilization of the released seep gases like methane or ethane. The structurally unique MAs in combination with their depleted 13C values identified at the Fuoco di Censo seep offer a new tool to study the role of soil mycobacteria as hydrocarbon gas consumers in the carbon cycle.
    Description: Published
    Description: 1463–1479
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 4
    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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  • 5
    Publication Date: 2023-03-11
    Keywords: 64PE406; 64PE406-E1; Bacteriohopanetetrol stereoisomer (peak area), per unit mass total organic carbon; Carbon, organic, total; Carbon, organic, total, standard deviation; DEPTH, sediment/rock; NESSC EAST MED; NIOZ_UU; NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University; PC; Pelagia; Piston corer; see reference(s); δ13C; δ15N
    Type: Dataset
    Format: text/tab-separated-values, 150 data points
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  • 6
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    In:  Supplement to: Rush, Darci; Wakeham, Stuart G; Hopmans, Ellen C; Schouten, Stefan; Sinninghe Damsté, Jaap S (2012): Biomarker evidence for anammox in the oxygen minimum zone of the Eastern Tropical North Pacific. Organic Geochemistry, 53, 80-87, https://doi.org/10.1016/j.orggeochem.2012.02.005
    Publication Date: 2023-05-12
    Description: Anaerobic oxidation of ammonium (anammox) is an important process in the marine nitrogen cycle. It has been estimated to contribute up to 50% of nitrogen loss from the ocean, and is especially prevalent within oxygen minimum zones (OMZs). Here we studied the presence and distribution of anammox in the extended OMZ of the Eastern Tropical North Pacific (ETNP) using ladderane fatty acids, specific biomarkers for anammox bacteria. The validity of ladderane fatty acids as proxies for anammox bacteria was demonstrated by their excellent correspondence with anammox 16S rRNA functional gene abundances and their expression and intact polar ladderane lipid concentrations in suspended particulate matter (SPM) from the Arabian Sea. In the ETNP, SPM was collected from various water depths at four stations along a northwest to southeast cruise transect and ladderane fatty acids were analyzed at each station. In all SPM samples where ladderane lipids were detected, C18 ladderane fatty acids were on average 5 fold more abundant than C20 ladderane fatty acids. Maximum concentrations in ladderane fatty acids (1.1 - 2.3 ng/l) were recorded at 400-600 m water depth, often corresponding to the depth of the secondary nitrite maximum. In one of the four stations, a second maximum in the ladderane fatty acid concentration was noted at a shallower depth (i.e. at 85 m), coinciding with higher nitrite concentrations at this water depth. The availability of nitrite probably limits anammox activity in the ETNP. Anammox lipids were abundant within the OMZ at all stations and concentrations were comparable to those in other OMZs, suggesting that anammox may be responsible for a significant loss of nitrogen in the OMZ of the ETNP.
    Keywords: NIOZ_UU; NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 7
    Publication Date: 2023-05-12
    Keywords: 64PE301; Biodegradation products; Calculated; DEPTH, water; Fatty acid methyl esters; Index of Ladderane lipids with 5 cyclobutane rings; NIOZ_UU; NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University; PASOM; PASOM_10_WS; Pelagia; Sea surface temperature, annual mean; Water sample; WS
    Type: Dataset
    Format: text/tab-separated-values, 38 data points
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  • 8
    Publication Date: 2023-06-27
    Keywords: Bacteriohopanetetrol stereoisomer, per unit mass, total organic carbon; CALYPSO; Calypso Corer; Core; DEPTH, sediment/rock; Ladderane per unit organic carbon mass; LC21, LC-21; Marion Dufresne (1995); MD81; MD81-LC21; Mediterranean Sea; NIOZ_UU; NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University; PALAEOFLUX; Sapropel layer; Section position; see reference(s)
    Type: Dataset
    Format: text/tab-separated-values, 113 data points
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  • 9
    Publication Date: 2023-05-12
    Keywords: 64PE301; Arabian Sea; Biodegradation products; Biodegradation products per unit sediment mass; Calculated; DEPTH, sediment/rock; Fatty acid methyl esters; Fatty acid methyl esters per unit sediment mass; Index of Ladderane lipids with 5 cyclobutane rings; MUC; MultiCorer; NIOZ_UU; NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University; PASOM; PASOM_01B; Pelagia; Sea surface temperature, annual mean
    Type: Dataset
    Format: text/tab-separated-values, 120 data points
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  • 10
    Publication Date: 2023-05-12
    Keywords: Cariaco-Basin; DEPTH, water; Ladderane fatty acid methyl esters I-IV; Ladderane fatty acid methyl esters I-IV, standard deviation; NIOZ_UU; NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University
    Type: Dataset
    Format: text/tab-separated-values, 24 data points
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