Wakeham Stuart G.

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Stuart G.

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  • Preprint
    Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea : a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids
    ( 2006-07-03) Coolen, Marco J. L. ; Abbas, Ben ; van Bleijswijk, Judith ; Hopmans, Ellen C. ; Kuypers, Marcel M. M. ; Wakeham, Stuart G. ; Sinninghe Damste, Jaap S.
    Within the upper 400 m at western, central, and eastern stations in the world’s largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alfa-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether (GDGT) of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 μM including layers where previously anammox bacteria were described (Kuypers et al., 2003). Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared to the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 μM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared to the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.
  • Article
    Transfer of organic carbon through marine water columns to sediments – insights from stable and radiocarbon isotopes of lipid biomarkers
    (Copernicus Publications on behalf of the European Geosciences Union, 2014-12-10) Wakeham, Stuart G. ; McNichol, Ann P.
    Compound-specific 13C and 14C compositions of diverse lipid biomarkers (fatty acids, alkenones, hydrocarbons, sterols and fatty alcohols) were measured in sinking particulate matter collected in sediment traps and from underlying surface sediments in the Black Sea, the Arabian Sea and the Ross Sea. The goal was to develop a multiparameter approach to constrain relative inputs of organic carbon (OC) from marine biomass, terrigenous vascular-plant and relict-kerogen sources. Using an isotope mass balance, we calculate that marine biomass in sediment trap material from the Black Sea and Arabian Sea accounted for 66–100% of OC, with lower terrigenous (3–8%) and relict (4–16%) contributions. Marine biomass in sediments constituted lower proportions of OC (66–90%), with consequentially higher proportions of terrigenous and relict carbon (3–17 and 7–13%, respectively). Ross Sea data were insufficient to allow similar mass balance calculations. These results suggest that, whereas particulate organic carbon is overwhelmingly marine in origin, pre-aged allochthonous terrigenous and relict OC become proportionally more important in sediments, consistent with pre-aged OC being better preserved during vertical transport to and burial at the seafloor than the upper-ocean-derived marine OC.
  • Article
    Analytical and computational advances, opportunities, and challenges in marine organic biogeochemistry in an era of "Omics"
    (Frontiers Media, 2020-09-02) Steen, Andrew D. ; Kusch, Stephanie ; Abdulla, Hussain A. ; Cakić, Nevenka ; Coffinet, Sarah ; Dittmar, Thorsten ; Fulton, James M. ; Galy, Valier ; Hinrichs, Kai-Uwe ; Ingalls, Anitra ; Koch, Boris P. ; Kujawinski, Elizabeth B. ; Liu, Zhanfei ; Osterholz, Helena ; Rush, Darci ; Seidel, Michael ; Sepulveda, Julio ; Wakeham, Stuart G.
    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.
  • Article
    Ancient DNA derived from alkenone-biosynthesizing haptophytes and other algae in Holocene sediments from the Black Sea
    (American Geophysical Union, 2006-02-18) Coolen, Marco J. L. ; Boere, Arjan C. ; Abbas, Ben ; Baas, Marianne ; Wakeham, Stuart G. ; Sinninghe Damste, Jaap S.
    Holocene sea surface temperatures (SST) of the Black Sea have been reconstructed using sedimentary C37 unsaturated alkenones assumed to be derived from the coccolithophorid haptophyte Emiliania huxleyi, whose fossil coccoliths are an important constituent of the unit I sediments. However, alkenones can also be biosynthesized by haptophyte species that do not produce microscopic recognizable coccoliths. A species-specific identification of haptophytes is important in such U 37 K′-based past SST reconstructions since different species have different alkenone-SST calibrations. We showed that 18S rDNA of E. huxleyi made up only a very small percentage (less than 0.8%) of the total eukaryotic 18S rDNA within the up to 3600-year-old fossil record obtained from the depocenter (>2000 m) of the Black Sea. The predominant fossil 18S rDNA was derived from dinoflagellates (Gymnodinium spp.), which are predominant members of the summer phytoplankton bloom in the modern Black Sea. Using a polymerase chain reaction/denaturing gradient gel electrophoresis method selective for haptophytes, we recovered substantial numbers of a preserved 458-base-pair (bp)-long 18S rDNA fragment of E. huxleyi from the Holocene Black Sea sediments. Additional fossil haptophyte sequences were not detected, indicating that the E. huxleyi alkenone-SST calibration can be applied for at least the last ∼3600 years. The ancient E. huxleyi DNA was well protected against degradation since the DNA/alkenone ratio did not significantly decrease throughout the whole sediment core and 20% of ∼2700-year-old fossil E. huxleyi DNA was still up to 23,000 base pairs long. We showed that fossil DNA offers great potential to study the Holocene paleoecology and paleoenvironment of anoxic deep-sea settings in unprecedented detail.
  • Technical Report
    Fatty acids and fatty acid esters of particulate matter collected in sediment traps in the Peru upwelling area R/V Knorr Cruise 73, February/March 1978
    (Woods Hole Oceanographic Institution, 1983-09) Wakeham, Stuart G. ; Livramento, Joaquim B. ; Farrington, John W.
    Particulate matter samples were collected using free-drifting sediment traps in the Peru upwelling area in 1978 to assess the vertical flux and organic composition of lipids associated with particles sinking out of the euphotic zone. Samples have been analyzed for a variety of lipids, including hydrocarbons, fatty acids, wax esters, steryl esters, triacylglycerols, alkyldiacylglycerols, fatty alcohols, sterols, and steroid ketones. The purpose of this report is to collate the fatty acid and fatty acid ester (wax ester, steryl ester, triacylglycerol, and alkyldiacylglycerol) for the 20 floating sediment traps which were deployed.
  • Technical Report
    Volatile organic compounds in Narragansett Bay, Rhode Island
    (Woods Hole Oceanographic Institution, 1982-08) Wakeham, Stuart G. ; Goodwin, Jeffrey T. ; Davis, Alan C.
    Volatile organic compounds (VOC) have been determined in Narragansett Bay, Rhode Island, water samples as part of an investigation into the sources, fates, and transport of volatile organic compounds in estuarine and coastal seawater. This report tabulates the concentrations of a wide range of VOC along a transect 1n Narragansett Bay for two summer and two winter sampling cruises.
  • Preprint
    Natural-abundance radiocarbon as a tracer of assimilation of petroleum carbon by bacteria in salt marsh sediments
    ( 2005-12-29) Wakeham, Stuart G. ; McNichol, Ann P. ; Kostka, Joel E. ; Pease, Tamara K.
    The natural abundance of radiocarbon (14C) provides unique insight into the source and cycling of sedimentary organic matter. Radiocarbon analysis of bacterial phospholipid lipid fatty acids (PLFAs) in salt-marsh sediments of southeast Georgia (USA) – one heavily contaminated by petroleum residues – was used to assess the fate of petroleum-derived carbon in sediments and incorporation of fossil carbon into microbial biomass. PLFAs that are common components of eubacterial cell membranes (e.g., branched C15 and C17, 10-methyl-C16) were depleted in 14C in the contaminated sediment (mean Δ14C value of +25 ± 19 ‰ for bacterial PLFAs) relative to PLFAs in uncontaminated “control” sediment (Δ14C = +101 ± 12‰). We suggest that the 14C-depletion in bacterial PLFAs at the contaminated site results from microbial metabolism of petroleum and subsequent incorporation of petroleum-derived carbon into bacterial membrane lipids. A mass balance calculation indicates that 6-10% of the carbon in bacterial PLFAs at the oiled site could derive from petroleum residues. These results demonstrate that even weathered petroleum may contain components of sufficient lability to be a carbon source for biomass production by marsh sediment microorganisms. Furthermore, a small but significant fraction of fossil carbon is assimilated even in the presence of a much larger pool of presumably more-labile and faster-cycling carbon substrates.
  • Article
    Selective preservation of organic matter in marine environments; processes and impact on the sedimentary record
    (Copernicus Publications on behalf of the European Geosciences Union, 2010-02-05) Zonneveld, K. A. F. ; Versteegh, G. J. M. ; Kasten, S. ; Eglinton, Timothy I. ; Emeis, Kay-Christian ; Huguet, Carme ; Koch, Boris P. ; de Lange, Gert J. ; de Leeuw, J. W. ; Middelburg, Jack J. ; Mollenhauer, Gesine ; Prahl, Fredrick G. ; Rethemeyer, J. ; Wakeham, Stuart G.
    The present paper is the result of a workshop sponsored by the DFG Research Center/Cluster of Excellence MARUM "The Ocean in the Earth System", the International Graduate College EUROPROX, and the Alfred Wegener Institute for Polar and Marine Research. The workshop brought together specialists on organic matter degradation and on proxy-based environmental reconstruction. The paper deals with the main theme of the workshop, understanding the impact of selective degradation/preservation of organic matter (OM) in marine sediments on the interpretation of the fossil record. Special attention is paid to (A) the influence of the molecular composition of OM in relation to the biological and physical depositional environment, including new methods for determining complex organic biomolecules, (B) the impact of selective OM preservation on the interpretation of proxies for marine palaeoceanographic and palaeoclimatic reconstruction, and (C) past marine productivity and selective preservation in sediments. It appears that most of the factors influencing OM preservation have been identified, but many of the mechanisms by which they operate are partly, or even fragmentarily, understood. Some factors have not even been taken carefully into consideration. This incomplete understanding of OM breakdown hampers proper assessment of the present and past carbon cycle as well as the interpretation of OM based proxies and proxies affected by OM breakdown. To arrive at better proxy-based reconstructions "deformation functions" are needed, taking into account the transport and diagenesis-related molecular and atomic modifications following proxy formation. Some emerging proxies for OM degradation may shed light on such deformation functions. The use of palynomorph concentrations and selective changes in assemblage composition as models for production and preservation of OM may correct for bias due to selective degradation. Such quantitative assessment of OM degradation may lead to more accurate reconstruction of past productivity and bottom water oxygenation. Given the cost and effort associated with programs to recover sediment cores for paleoclimatological studies, as well as with generating proxy records, it would seem wise to develop a detailed sedimentological and diagenetic context for interpretation of these records. With respect to the latter, parallel acquisition of data that inform on the fidelity of the proxy signatures and reveal potential diagenetic biases would be of clear value.