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ArticleAnalytical 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.
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ArticleAn interlaboratory study of TEX86 and BIT analysis using high-performance liquid chromatography–mass spectrometry(American Geophysical Union, 2009-03-20) Schouten, Stefan ; Hopmans, Ellen C. ; van der Meer, Jaap ; Mets, Anchelique ; Bard, Edouard ; Bianchi, Thomas S. ; Diefendorf, Aaron ; Escala, Marina ; Freeman, Katharine H. ; Furukawa, Yoshihiro ; Huguet, Carme ; Ingalls, Anitra ; Menot, Guillemette ; Nederbragt, Alexandra J. ; Oba, Masahiro ; Pearson, Ann ; Pearson, Emma J. ; Rosell-Mele, Antoni ; Schaeffer, Philippe ; Shah, Sunita R. ; Shanahan, Timothy M. ; Smith, Richard W. ; Smittenberg, Rienk ; Talbot, Helen M. ; Uchida, Masao ; Van Mooy, Benjamin A. S. ; Yamamoto, Masanobu ; Zhang, Zhaohui ; Sinninghe Damste, Jaap S.Recently, two new proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs) were proposed, i.e., the TEX86 proxy for sea surface temperature reconstructions and the BIT index for reconstructing soil organic matter input to the ocean. In this study, fifteen laboratories participated in a round robin study of two sediment extracts with a range of TEX86 and BIT values to test the analytical reproducibility and repeatability in analyzing these proxies. For TEX86 the repeatability, indicating intra-laboratory variation, was 0.028 and 0.017 for the two sediment extracts or ±1–2°C when translated to temperature. The reproducibility, indicating among-laboratory variation, of TEX86 measurements was substantially higher, i.e., 0.050 and 0.067 or ±3–4°C when translated to temperature. The latter values are higher than those obtained in round robin studies of Mg/Ca and U37 k′ paleothermometers, suggesting the need to primarily improve compatibility between labs. The repeatability of BIT measurements for the sediment with substantial amounts of soil organic matter input was relatively small, 0.029, but reproducibility was large, 0.410. This large variance could not be attributed to specific equipment used or a particular data treatment. We suggest that this may be caused by the large difference in the molecular weight in the GDGTs used in the BIT index, i.e., crenarchaeol versus the branched GDGTs. Potentially, this difference gives rise to variable responses in the different mass spectrometers used. Calibration using authentic standards is needed to establish compatibility between labs performing BIT measurements.
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ArticleProchlorococcus extracellular vesicles: molecular composition and adsorption to diverse microbes(Society for Applied Microbiology, 2021-11-12) Biller, Steven J. ; Lundeen, Rachel A. ; Hmelo, Laura R. ; Becker, Kevin W. ; Arellano, Aldo A. ; Dooley, Keven ; Heal, Katherine R. ; Carlson, Laura Truxal ; Van Mooy, Benjamin A. S. ; Ingalls, Anitra ; Chisholm, Sallie W.Extracellular vesicles are small (~50–200 nm diameter) membrane-bound structures released by cells from all domains of life. While vesicles are abundant in the oceans, their functions, both for cells themselves and the emergent ecosystem, remain a mystery. To better characterize these particles – a prerequisite for determining function – we analysed the lipid, protein, and metabolite content of vesicles produced by the marine cyanobacterium Prochlorococcus. We show that Prochlorococcus exports a diverse array of cellular compounds into the surrounding seawater enclosed within discrete vesicles. Vesicles produced by two different strains contain some materials in common, but also display numerous strain-specific differences, reflecting functional complexity within vesicle populations. The vesicles contain active enzymes, indicating that they can mediate extracellular biogeochemical reactions in the ocean. We further demonstrate that vesicles from Prochlorococcus and other bacteria associate with diverse microbes including the most abundant marine bacterium, Pelagibacter. Together, our data point toward hypotheses concerning the functional roles of vesicles in marine ecosystems including, but not limited to, possibly mediating energy and nutrient transfers, catalysing extracellular biochemical reactions, and mitigating toxicity of reactive oxygen species.
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ArticlePerspectives on Chemical Oceanography in the 21st century : participants of the COME ABOARD Meeting examine aspects of the field in the context of 40 years of DISCO(Elsevier, 2017-09-08) Fassbender, Andrea ; Palevsky, Hilary I. ; Martz, Todd R. ; Ingalls, Anitra ; Gledhill, Martha ; Fawcett, Sarah E. ; Brandes, Jay A. ; Aluwihare, Lihini I. ; COME ABOARD ; DISCO XXVThe questions that chemical oceanographers prioritize over the coming decades, and the methods we use to address these questions, will define our field's contribution to 21st century science. In recognition of this, the U.S. National Science Foundation and National Oceanic and Atmospheric Administration galvanized a community effort (the Chemical Oceanography MEeting: A BOttom-up Approach to Research Directions, or COME ABOARD) to synthesize bottom-up perspectives on selected areas of research in Chemical Oceanography. Representing only a small subset of the community, COME ABOARD participants did not attempt to identify targeted research directions for the field. Instead, we focused on how best to foster diverse research in Chemical Oceanography, placing emphasis on the following themes: strengthening our core chemical skillset; expanding our tools through collaboration with chemists, engineers, and computer scientists; considering new roles for large programs; enhancing interface research through interdisciplinary collaboration; and expanding ocean literacy by engaging with the public. For each theme, COME ABOARD participants reflected on the present state of Chemical Oceanography, where the community hopes to go and why, and actionable pathways to get there. A unifying concept among the discussions was that dissimilar funding structures and metrics of success may be required to accommodate the various levels of readiness and stages of knowledge development found throughout our community. In addition to the science, participants of the concurrent Dissertations Symposium in Chemical Oceanography (DISCO) XXV, a meeting of recent and forthcoming Ph.D. graduates in Chemical Oceanography, provided perspectives on how our field could show leadership in addressing long-standing diversity and early-career challenges that are pervasive throughout science. Here we summarize the COME ABOARD Meeting discussions, providing a synthesis of reflections and perspectives on the field.
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ArticleAn interlaboratory study of TEX86 and BIT analysis of sediments, extracts, and standard mixtures(John Wiley & Sons, 2013-12-20) Schouten, Stefan ; Hopmans, Ellen C. ; Rosell-Mele, Antoni ; Pearson, Ann ; Adam, Pierre ; Bauersachs, Thorsten ; Bard, Edouard ; Bernasconi, Stefano M. ; Bianchi, Thomas S. ; Brocks, Jochen J. ; Carlson, Laura Truxal ; Castaneda, Isla S. ; Derenne, Sylvie ; Selver, Ayca Dogrul ; Dutta, Koushik ; Eglinton, Timothy I. ; Fosse, Celine ; Galy, Valier ; Grice, Kliti ; Hinrichs, Kai-Uwe ; Huang, Yongsong ; Huguet, Arnaud ; Huguet, Carme ; Hurley, Sarah ; Ingalls, Anitra ; Jia, Guodong ; Keely, Brendan ; Knappy, Chris ; Kondo, Miyuki ; Krishnan, Srinath ; Lincoln, Sara ; Lipp, Julius S. ; Mangelsdorf, Kai ; Martínez-Garcia, Alfredo ; Menot, Guillemette ; Mets, Anchelique ; Mollenhauer, Gesine ; Ohkouchi, Naohiko ; Ossebaar, Jort ; Pagani, Mark ; Pancost, Richard D. ; Pearson, Emma J. ; Peterse, Francien ; Reichart, Gert-Jan ; Schaeffer, Philippe ; Schmitt, Gaby ; Schwark, Lorenz ; Shah, Sunita R. ; Smith, Richard W. ; Smittenberg, Rienk H. ; Summons, Roger E. ; Takano, Yoshinori ; Talbot, Helen M. ; Taylor, Kyle W. R. ; Tarozo, Rafael ; Uchida, Masao ; van Dongen, Bart E. ; Van Mooy, Benjamin A. S. ; Wang, Jinxiang ; Warren, Courtney ; Weijers, Johan W. H. ; Werne, Josef P. ; Woltering, Martijn ; Xie, Shucheng ; Yamamoto, Masanobu ; Yang, Huan ; Zhang, Chuanlun L. ; Zhang, Yige ; Zhao, Meixun ; Sinninghe Damste, Jaap S.Two commonly used proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs) are the TEX86 (TetraEther indeX of 86 carbon atoms) paleothermometer for sea surface temperature reconstructions and the BIT (Branched Isoprenoid Tetraether) index for reconstructing soil organic matter input to the ocean. An initial round-robin study of two sediment extracts, in which 15 laboratories participated, showed relatively consistent TEX86 values (reproducibility ±3–4°C when translated to temperature) but a large spread in BIT measurements (reproducibility ±0.41 on a scale of 0–1). Here we report results of a second round-robin study with 35 laboratories in which three sediments, one sediment extract, and two mixtures of pure, isolated GDGTs were analyzed. The results for TEX86 and BIT index showed improvement compared to the previous round-robin study. The reproducibility, indicating interlaboratory variation, of TEX86 values ranged from 1.3 to 3.0°C when translated to temperature. These results are similar to those of other temperature proxies used in paleoceanography. Comparison of the results obtained from one of the three sediments showed that TEX86 and BIT indices are not significantly affected by interlaboratory differences in sediment extraction techniques. BIT values of the sediments and extracts were at the extremes of the index with values close to 0 or 1, and showed good reproducibility (ranging from 0.013 to 0.042). However, the measured BIT values for the two GDGT mixtures, with known molar ratios of crenarchaeol and branched GDGTs, had intermediate BIT values and showed poor reproducibility and a large overestimation of the “true” (i.e., molar-based) BIT index. The latter is likely due to, among other factors, the higher mass spectrometric response of branched GDGTs compared to crenarchaeol, which also varies among mass spectrometers. Correction for this different mass spectrometric response showed a considerable improvement in the reproducibility of BIT index measurements among laboratories, as well as a substantially improved estimation of molar-based BIT values. This suggests that standard mixtures should be used in order to obtain consistent, and molar-based, BIT values.