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  • ELSEVIER SCIENCE BV
  • International Union of Crystallography
  • National Academy of Sciences
  • 2020-2023  (21)
  • 2020-2022
  • 2020-2020
  • 2010-2014
  • 2005-2009
  • 2022  (21)
  • 2022  (21)
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  • 2020-2023  (21)
  • 2020-2022
  • 2020-2020
  • 2010-2014
  • 2005-2009
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  • 1
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    Sediment oxygen consumption: Role in the global marine carbon cycle (2022)
    ELSEVIER SCIENCE BV
    In:  EPIC3Earth-Science Reviews, ELSEVIER SCIENCE BV, 228, pp. 103987, ISSN: 0012-8252
    Details
    Publication Date: 2022-03-30
    Description: The seabed plays a key role in the marine carbon cycle as a) the terminal location of aerobic oxidation of organic matter, b) the greatest anaerobic bioreactor, and c) the greatest repository for reactive organic carbon on Earth. We compiled data on the oxygen uptake of marine sediments with the objective to understand the constraints on mineralization rates of deposited organic matter and their relation to key environmental parameters. The compiled database includes nearly 4000 O 2 uptake data and is available as supplementary material. It includes also information on bottom water O 2 concentration, O 2 penetration depth, geographic position, water depth, and full information on the data sources. We present the different in situ and ex situ approaches to measure the total oxygen uptake (TOU) and the diffusive oxygen uptake (DOU) of sediments and discuss their robustness towards methodological errors and statistical uncertainty. We discuss O 2 transport through the benthic and diffusive boundary layers, the diffusion- and fauna-mediated O 2 uptake, and the coupling of aerobic respiration to anaerobic processes. Five regional examples are presented to illustrate the diversity of the seabed: Eutrophic seas, oxygen minimum zones, abyssal plains, mid-oceanic gyres, and hadal trenches. A multiple correlation analysis shows that seabed O 2 uptake is primarily controlled by ocean depth and sea surface primary productivity. The O2 penetration depth scales with the DOU according to a power law that breaks down under the abyssal ocean gyres. The developed multiple correlation model was used to draw a global map of seabed O2 uptake rates. Respiratory coefficients, differentiated for depth regions of the ocean, were used to convert the global O 2 uptake to organic carbon oxidation. The resulting global budget shows an oxidation of 212 Tmol C yr − 1 in marine sediments with a 5-95% confidence interval of 175-260 Tmol C yr − 1 . A comparison with the global flux of particulate organic carbon (POC) from photic surface waters to the deep sea, determined from multiple sediment trap studies, suggests a deficit in the sedimentation flux at 2000 m water depth of about 70% relative to the carbon turnover in the underlying seabed. At the ocean margins, the flux of organic carbon from rivers and from vegetated coastal ecosystems contributes greatly to the budget and may even exceed the phytoplankton production on the inner continental shelf.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    Controls on the distributions of GDGTs and n-alkane isotopic compositions in sediments of the Amazon River Basin (2022)
    ELSEVIER SCIENCE BV
    In:  EPIC3Chemical Geology, ELSEVIER SCIENCE BV, 594, pp. 120777, ISSN: 0009-2541
    Details
    Publication Date: 2022-02-26
    Description: ARTICLE INFO Keywords: Amazonia GDGT Amazon River Biomarkers Compound-specific isotopes N-Alkanes Paleoclimate proxies Plant waxes ABSTRACT Lipid biomarker proxies from terrigenous sediments have been extensively used to understand variations in paleoenvironmental conditions, but many of the mechanisms affecting these proxies during riverine transport are still poorly understood. Here, we analyze glycerol dialkyl glycerol tetraether (GDGT) distributions and n-alkane isotopic compositions of soils and sediments from the Amazon River Basin. Our dataset includes suspended sediments of the Amazon River and its main tributaries, as well as soils and sediments of the Xingu River, a large clearwater tributary draining the easternmost part of the Amazon River Basin. Our sampling design aimed at understanding the processes behind spatially distinct GDGT distributions and n-alkane isotopic signatures across lowland Amazonia. Gradual changes in the fractional abundances of isoprenoid GDGTs and in 5- and 6- methyl branched GDGT ratios in suspended sediments of the Amazon River towards its mouth suggest that riverine production is an increasingly important control on the distribution of GDGTs in the lower parts of the system, while values from the western parts are more in line with a dominant soil sourcing. In the Xingu River, indices based on the fractional abundances of branched GDGTs and long-chain n-alkanes demonstrate a strong contri- bution of terrestrial organic material during the high-water season and an important aquatic component during low-water season. Meanwhile, average stable carbon (δ13C) and hydrogen (δD) isotopic signatures of long-chain n-alkanes in soils, riverbed and suspended sediments of the Xingu River are similar and reinforce the relatively conservative behaviour of these proxies within large river systems. The average compound-specific δ13C signa- tures of sediments in the Xingu River are within the expected range for C3 vegetation and do not seem to capture the signals from the nearby deforested areas. n-Alkanes δD signals in the Xingu Basin are similar to values ob- tained in the Amazon River mouth and indicate that n-alkanes sourced from easternmost Amazonian lowlands may predominate over signals from western areas.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Eastern Lomonosov Ridge: Constraints for a variable ice mass thickness during former glaciations (2022)
    ELSEVIER SCIENCE BV
    In:  EPIC3Geomorphology, ELSEVIER SCIENCE BV, 413(108328), pp. 1-10, ISSN: 0169-555X
    Details
    Publication Date: 2022-07-13
    Description: Here we present dense acoustic and swath bathymetry data sets as well as geological age constraints that allow a new view on past glacial processes at the Siberian termination of Lomonosov Ridge in the Arctic Ocean between 81° and 84° 20′ N. Here, the seabed is marked by three sets of streamlined glacial lineations observed at present water depths of ~760 m to 1250 m. The shallower streamlined glacial lineations were likely formed during MIS 6 and the deeper ones during MIS 12. Other observations include recessional moraines and pockmarks on a flattened ridge crest. In the subsurface, an acoustically transparent unit above well stratified strata is interpreted as subglacial diamicton overlying pre-glacial sediments at an erosional contact. Furthermore, the diamicton is interpreted to have been deposited as lenses in glacially-eroded proximal settings. In contrast, some parts of the seafloor and subsurface show no glacial overprint in water depths as shallow as 819 m. To explain these findings, we propose that the Siberian termination of Lomonosov Ridge was covered by an ice mass of spatial and temporal variable thickness between ~780 to ~1250 m, that was likely composed of sea ice and thick icebergs calved from ice shelves.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 4
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    Sub‐micrometer focusing setup for high‐pressure crystallography at the Extreme Conditions beamline at PETRA III (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2022-06-24
    Description: Scientific tasks aimed at decoding and characterizing complex systems and processes at high pressures set new challenges for modern X‐ray diffraction instrumentation in terms of X‐ray flux, focal spot size and sample positioning. Presented here are new developments at the Extreme Conditions beamline (P02.2, PETRA III, DESY, Germany) that enable considerable improvements in data collection at very high pressures and small scattering volumes. In particular, the focusing of the X‐ray beam to the sub‐micrometer level is described, and control of the aberrations of the focusing compound refractive lenses is made possible with the implementation of a correcting phase plate. This device provides a significant enhancement of the signal‐to‐noise ratio by conditioning the beam shape profile at the focal spot. A new sample alignment system with a small sphere of confusion enables single‐crystal data collection from grains of micrometer to sub‐micrometer dimensions subjected to pressures as high as 200 GPa. The combination of the technical development of the optical path and the sample alignment system contributes to research and gives benefits on various levels, including rapid and accurate diffraction mapping of samples with sub‐micrometer resolution at multimegabar pressures.
    Description: Facing the challenges of X‐ray diffraction from tiny samples subjected to multimegabar pressures, instrumentation developments are presented that enable, among other studies, single‐crystal data collection from micrometer‐ to sub‐micrometer‐sized grains. The developments are based on a sub‐micrometer beam capability employing compound refractive lenses operating with a phase correcting plate and a precise motorization solution.
    Keywords: ddc:548
    Language: English
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  • 5
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    Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dommain, R., Riedl, S., Olaka, L. A., deMenocal, P., Deino, A. L., Owen, R. B., Muiruri, V., Müller, J., Potts, R., & Strecker, M. R. Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients. Proceedings of the National Academy of Sciences of the United States of America, 119(28),(2022): e2121388119, https://doi.org/10.1073/pnas.2121388119.
    Description: East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.
    Description: R.D. was funded by a Smithsonian Human Origins Postdoctoral Fellowship and by Geo.X—the Research Network for Geosciences in Berlin and Potsdam. Fig. 1 D, E, and G and SI Appendix, Figs. S1 and S3 are based on the TanDEM-X Science DEM granted to L.A.O. and S.R. by the German Aerospace Center (DLR) in 2017. L.A.O. acknowledges the Volkswagen Foundation for funding this study with Grant No. 89369. M.R.S. and S.R. were supported by funds from Potsdam University and the Geothermal Development Company of Kenya, and R.B.O. and V.M. were supported by the Hong Kong General Research Fund. We acknowledge support from the National Museums of Kenya and the Kenya Government permission granted by the Ministry of Sports, Culture and the Arts, and by the National Commission for Science, Technology and Innovation (NACOSTI) Permits P/14/7709/683 (to R.P.) and P/16/11924/11448 (to L.A.O.). This work is a contribution of the Olorgesailie Drilling Project, for which support from the National Museums of Kenya, the Oldonyo Nyokie Group Ranch, the Peter Buck Fund for Human Origins Research (Smithsonian Institution), the William H. Donner Foundation, the Ruth and Vernon Taylor Foundation, Whitney and Betty MacMillan, and the Smithsonian Human Origins Program is gratefully acknowledged. LacCore is acknowledged for support in drilling and core storage.
    Keywords: East Africa ; Biogeography ; Biodiversity ; Hydrological connectivity ; Holocene
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  • 7
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    Nutrient availability and senescence spatially structure the dynamics of a foundation species (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bell, T. W., & Siegel, D. A. Nutrient availability and senescence spatially structure the dynamics of a foundation species. Proceedings of the National Academy of Sciences of the United States of America, 119(1), (2021): e2105135118, https://doi.org/10.1073/pnas.2105135118.
    Description: Disentangling the roles of the external environment and internal biotic drivers of plant population dynamics is challenging due to the absence of relevant physiological and abundance information over appropriate space and time scales. Remote observations of giant kelp biomass and photosynthetic pigment concentrations are used to show that spatiotemporal patterns of physiological condition, and thus growth and production, are regulated by different processes depending on the scale of observation. Nutrient supply was linked to regional scale (〉1 km) physiological condition dynamics, and kelp forest stands were more persistent where nutrient levels were consistently high. However, on local scales (〈1 km), internal senescence processes related to canopy age demographics determined patterns of biomass loss across individual kelp forests despite uniform nutrient conditions. Repeat measurements of physiology over continuous spatial fields can provide insights into complex dynamics that are unexplained by the environmental drivers thought to regulate abundance. Emerging remote sensing technologies that provide simultaneous estimates of abundance and physiology can quantify the roles of environmental change and demographics governing plant population dynamics for a wide range of aquatic and terrestrial ecosystems.
    Description: This work was supported by the US NSF (Grants OCE 1232779 and 1831937), by the US Department of Energy (Cooperative Agreement DE-AR0000922), and by NASA (Grant NNX14AR62A) and the NASA Earth and Space Sciences Fellowship program in support of T.W.B.
    Keywords: Physiology ; Population ; Biomass ; Hyperspectral ; Giant kelp
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  • 8
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    Trivalent chromium isotopes in the eastern tropical North Pacific oxygen-deficient zone (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(8), (2021): e1918605118, https://doi.org/10.1073/pnas.1918605118.
    Description: Changes in chromium (Cr) isotope ratios due to fractionation between trivalent [Cr(III)] and hexavalent [Cr(VI)] are being utilized by geologists to infer oxygen conditions in past environments. However, there is little information available on Cr in the modern ocean to ground-truth these inferences. Transformations between the two chromium species are important processes in oceanic Cr cycling. Here we present profiles of hexavalent and trivalent Cr concentrations and stable isotope ratios from the eastern tropical North Pacific (ETNP) oxygen-deficient zone (ODZ) which support theoretical and experimental studies that predict that lighter Cr is preferentially reduced in low-oxygen environments and that residual dissolved Cr becomes heavier due to removal of particle-reactive Cr(III) on sinking particles. The Cr(III) maximum dominantly occurs in the upper portion of the ODZ, implying that microbial activity (dependent on the sinking flux of organic matter) may be the dominant mechanism for this transformation, rather than a simple inorganic chemical conversion between the species depending on the redox potential.
    Description: We thank chief scientist Gabrielle Rocap for accommodating us on cruises Roger Revelle 1804-5 and Kilo Moana 19-20 (sponsored by NSF Grant DEB-1542240 to G. Rocap, A. Devol, R. Kiel, and C. Deutch), Jim Moffett for helping with sampling on these cruises, and Mark Altabet and Frank Stewart for collecting the samples from station 2T on cruise New Horizon 1410. This research was supported by NSF Grant OCE-1736996 (to E.A.B.) and by a fellowship from the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Oceanography.
    Keywords: Chromium isotopes ; Oxygen-deficient zones ; Trace elements ; Trivalent chromium ; Hexavalent ; Chromium
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  • 9
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    Robust approaches for model‐free small‐angle scattering data analysis (2022)
    Bender, Philipp ; Honecker, Dirk ; Bersweiler, Mathias ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2022-10-04
    Description: The small‐angle neutron scattering data of nanostructured magnetic samples contain information regarding their chemical and magnetic properties. Often, the first step to access characteristic magnetic and structural length scales is a model‐free investigation. However, due to measurement uncertainties and a restricted q range, a direct Fourier transform usually fails and results in ambiguous distributions. To circumvent these problems, different methods have been introduced to derive regularized, more stable correlation functions, with the indirect Fourier transform being the most prominent approach. Here, the indirect Fourier transform is compared with the singular value decomposition and an iterative algorithm. These approaches are used to determine the correlation function from magnetic small‐angle neutron scattering data of a powder sample of iron oxide nanoparticles; it is shown that with all three methods, in principle, the same correlation function can be derived. Each method has certain advantages and disadvantages, and thus the recommendation is to combine these three approaches to obtain robust results.
    Description: Three different approaches are compared for determination of the correlation function from the small‐angle neutron scattering data of a powder sample of iron oxide nanoparticles.
    Keywords: ddc:548
    Language: English
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  • 10
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    Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Womersley, F. C., Humphries, N. E., Queiroz, N., Vedor, M., da Costa, I., Furtado, M., Tyminski, J. P., Abrantes, K., Araujo, G., Bach, S. S., Barnett, A., Berumen, M. L., Bessudo Lion, S., Braun, C. D., Clingham, E., Cochran, J. E. M., de la Parra, R., Diamant, S., Dove, A. D. M., Dudgeon, C. L., Erdmann, M. V., Espinoza, E., Fitzpatrick, R., González Cano, J., Green, J. R., Guzman, H. M., Hardenstine, R., Hasan, A., Hazin, F. H. V., Hearn, A. R., Hueter, R. E., Jaidah, M. Y., Labaja, J., Ladinol, F., Macena, B. C. L., Morris Jr., J. J., Norman, B. M., Peñaherrera-Palmav, C., Pierce, S. J., Quintero, L. M., Ramırez-Macías, D., Reynolds, S. D., Richardson, A. J., Robinson, D. P., Rohner, C. A., Rowat, D. R. L., Sheaves, M., Shivji, M. S., Sianipar, A. B., Skomal, G. B., Soler, G., Syakurachman, I., Thorrold, S. R., Webb, D. H., Wetherbee, B. M., White, T. D., Clavelle, T., Kroodsma, D. A., Thums, M., Ferreira, L. C., Meekan, M. G., Arrowsmith, L. M., Lester, E. K., Meyers, M. M., Peel, L. R., Sequeira, A. M. M., Eguıluz, V. M., Duarte, C. M., & Sims, D. W. Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark. Proceedings of the National Academy of Sciences of the United States of America, 119(20), (2022): e2117440119, https://doi.org/10.1073/pnas.2117440119.
    Description: Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (〉300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
    Description: Funding for data analysis was provided by the UK Natural Environment Research Council (NERC) through a University of Southampton INSPIRE DTP PhD Studentship to F.C.W. Additional funding for data analysis was provided by NERC Discovery Science (NE/R00997/X/1) and the European Research Council (ERC-AdG-2019 883583 OCEAN DEOXYFISH) to D.W.S., Fundação para a Ciência e a Tecnologia (FCT) under PTDC/BIA/28855/2017 and COMPETE POCI-01–0145-FEDER-028855, and MARINFO–NORTE-01–0145-FEDER-000031 (funded by Norte Portugal Regional Operational Program [NORTE2020] under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund–ERDF) to N.Q. FCT also supported N.Q. (CEECIND/02857/2018) and M.V. (PTDC/BIA-COM/28855/2017). D.W.S. was supported by a Marine Biological Association Senior Research Fellowship. All tagging procedures were approved by institutional ethical review bodies and complied with all relevant ethical regulations in the jurisdictions in which they were performed. Details for individual research teams are given in SI Appendix, section 8. Full acknowledgments for tagging and field research are given in SI Appendix, section 7. This research is part of the Global Shark Movement Project (https://www.globalsharkmovement.org).
    Keywords: ship strike ; marine megafauna ; conservation ; movement ecology ; human impact
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  • 11
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    Phosphonate production by marine microbes: exploring new sources and potential function (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-06-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Acker, M., Hogle, S. L., Berube, P. M., Hackl, T., Coe, A., Stepanauskas, R., Chisholm, S. W., & Repeta, D. J. Phosphonate production by marine microbes: exploring new sources and potential function. Proceedings of the National Academy of Sciences of the United States of America, 119(11), (2022): e2113386119, https://doi.org/10.1073/pnas.2113386119.
    Description: Phosphonates are organophosphorus metabolites with a characteristic C-P bond. They are ubiquitous in the marine environment, their degradation broadly supports ecosystem productivity, and they are key components of the marine phosphorus (P) cycle. However, the microbial producers that sustain the large oceanic inventory of phosphonates as well as the physiological and ecological roles of phosphonates are enigmatic. Here, we show that phosphonate synthesis genes are rare but widely distributed among diverse bacteria and archaea, including Prochlorococcus and SAR11, the two major groups of bacteria in the ocean. In addition, we show that Prochlorococcus can allocate over 40% of its total cellular P-quota toward phosphonate production. However, we find no evidence that Prochlorococcus uses phosphonates for surplus P storage, and nearly all producer genomes lack the genes necessary to degrade and assimilate phosphonates. Instead, we postulate that phosphonates are associated with cell-surface glycoproteins, suggesting that phosphonates mediate ecological interactions between the cell and its surrounding environment. Our findings indicate that the oligotrophic surface ocean phosphonate pool is sustained by a relatively small fraction of the bacterioplankton cells allocating a significant portion of their P quotas toward secondary metabolism and away from growth and reproduction.
    Description: This work was supported in part by grants from the NSF (OCE-1153588 and DBI-0424599 to S.W.C.; OCE-1335810 and OIA-1826734 to R.S.; and OCE-1634080 to D.J.R.), the Gordon and Betty Moore Foundation (no. 6000 to D.J.R.), and the Simons Foundation (Life Sciences Project Award IDs 337262 and 647135 to S.W.C.; 510023 to R.S.; and Simons Collaboration on Ocean Processes and Ecology [SCOPE] Award ID 329108 to S.W.C. and D.J.R.).
    Keywords: phosphonate ; Prochlorococcus ; marine ; biogeochemistry ; phosphorus
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  • 12
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    Structure determination from unindexed powder data from scratch by a global optimization approach using pattern comparison based on cross‐correlation functions (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2022-06-16
    Description: A method of ab initio crystal structure determination from powder diffraction data for organic and metal–organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit‐cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL‐GO (`FIt with DEviating Lattice parameters ‐ Global Optimization'). FIDEL‐GO uses a similarity measure based on cross‐correlation functions, which allows the comparison of simulated and experimental powder data even if the unit‐cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit‐cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi‐step procedure with built‐in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user‐controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11‐difluoro‐, 2,9‐dichloro‐ and 2,9‐dichloro‐6,13‐dihydro‐quinacridone, which were solved from powder patterns with 14–20 peaks only, and of the coordination polymer dichloro‐bis(pyridine‐N)copper(II).
    Description: A new method for the structure determination of molecular crystals from unindexed powder data has been developed and successfully applied. The method performs a global optimization using pattern comparison based on cross‐correlation functions.
    Keywords: ddc:548
    Language: English
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  • 13
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    Site dependence of the magnetocaloric effect in Mn5−xFexSi3 (2022)
    Ait Haddouch, Mohammed ; Abboushi, Nour ; Sharma, Neetika ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2022-12-06
    Description: The nuclear and magnetic structures of Mn3Fe2Si3 are investigated in the temperature range from 20 to 300 K. The magnetic properties of Mn3Fe2Si3 were measured on a single crystal. The compound undergoes a paramagnetic to antiferromagnetic transition at TN2 ≃ 120 K and an antiferromagnetic to antiferromagnetic transition at TN1 ≃ 69 K. A similar sequence of magnetic phase transitions is found for the parent compound Mn5Si3 upon temperature variation, but the field‐driven transition observed in Mn5Si3 is not found in Mn3Fe2Si3, resulting in a strongly reduced magnetocaloric effect. Structurally, the hexagonal symmetry found for both compounds under ambient conditions is preserved in Mn3Fe2Si3 through both magnetic transitions, indicating that the crystal structure is only weakly affected by the magnetic phase transition, in contrast to Mn5Si3 where both transitions distort the nuclear structure. Both compounds feature a collinear high‐temperature magnetic phase AF2 and transfer into a non‐collinear phase AF1 at low temperature. While one of the distinct crystallographic sites remains disordered in the AF2 phase in the parent compound, the magnetic structure in the AF2 phase involves all magnetic atoms in Mn3Fe2Si3. These observations imply that the distinct sites occupied by the magnetic atoms play an important role in the magnetocaloric behaviour of the family.
    Description: The nuclear and magnetic structures of Mn3Fe2Si3 are determined and the magnetic properties are compared with those of the parent compound Mn5Si3. The results imply that the distinct magnetic sites play an important role in the magnetocaloric behaviour of the family. image
    Keywords: ddc:548 ; magnetocaloric effect ; magnetic structure ; neutron diffraction ; synchrotron diffraction ; site dependence
    Language: English
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  • 14
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    Macrobenthic diversity response to the atlantification of the Arctic Ocean (Fram Strait, 79°N) – A taxonomic and functional trait approach (2022)
    ELSEVIER SCIENCE BV
    In:  EPIC3Ecological Indicators, ELSEVIER SCIENCE BV, 144(109464), ISSN: 1470-160X
    Details
    Publication Date: 2022-11-03
    Description: This is the first study presenting temporal changes of the macrofauna biodiversity along the bathymetric gradient from the shelf to abyssal depths in the eastern Fram Striat. In this region, between 2004 and 2008, a significant increase in surface water temperature was observed due to the transport of Atlantic water from lower latitudes and was defined as a Warm Water Anomaly (WWA). Effects of the WWA in the eastern Fram Strait were observed across the entire food web, from the pelagic to the deep seafloor. The material for our study was collected before (in 2000) and after the WWA (in 2010 and 2017) at station depths ranging from 203 m to 5561 m. Samples of macrofauna and surface sediments were collected with use of a box corer to analyze species composition and functional traits, and environmental characteristics in sediments. We explore the influence of environmental changes on the structure (species composition and diversity) and functioning (functional trait composition and diversity) of macrofauna communities. An increase of primary production in surface waters during and after the WWA was reflected in a higher food availability at the seafloor from shelf to abyssal depths. Warming induced environmental changes led to an increase of macrofauna density and taxonomic diversity at all water depths. Macrofauna species composition significantly changed after the WWA. At all study sites, macrofauna functional diversity increased after the warm period. Functional trait composition changed significantly along the bathymetric transect. Despite changes in the taxonomic composition, macrofauna communities at the shallowest stations showed high functional redundancy, i.e., trait composition remained unchanged after the WWA. At water depths below 1500 m, where functional redundancy was significantly lower, functional trait composition changed significantly after the WWA. Our results suggest that macrofauna communities on the shelves are more resistant to environmental changes compared to deep-sea assemblages in the eastern Fram Strait.
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
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    Microplastics in two German wastewater treatment plants: Year-long effluent analysis with FTIR and Py-GC/MS (2022)
    ELSEVIER SCIENCE BV
    In:  EPIC3Science of The Total Environment, ELSEVIER SCIENCE BV, 817(152619), ISSN: 0048-9697
    Details
    Publication Date: 2022-11-07
    Description: Microplastics (MP) have been recorded in various environments around the globe. For a better understanding of distribution patterns and for providing a basis for risk assessments, detailed data on MP concentrations and polymer compositions are required. This study investigated the effluents of two German wastewater treatment plants (WWTP) monthly over one year, in order to better understand their temporal input of MP into the receiving river systems. MP item data down to 11 μm were obtained by means of Fourier Transform Infrared (FTIR) spectroscopy under the application of an improved polymer database. Complementary mass data were obtained by pyrolysis gas chromatography–mass spectrometry (Py-GC/MS) (for one WWTP). Both FTIR and Py-GC/MS analysis revealed a homogeneous polymer composition over the year, with a general dominance of polyolefins. Elevated MP item and mass concentrations (maximum: 3 × 104 items m−3 and 3.8 × 103 μg m−3) were observed during winter months and were accompanied by either heavy rainfall (increased discharge and total organic carbon) or elevated turbidity values. These observations emphasize the need for the assessment of background parameters in future MP monitoring studies. By providing monthly data over one year on MP items and masses in WWTP effluents, this study helps enhancing the understanding of temporal MP dynamics and can act as a valuable reference point for future assessments.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    The Earth BioGenome Project 2020: starting the clock (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.
    Description: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.
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  • 17
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    High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bekaert, D. V., Gazel, E., Turner, S., Behn, M. D., de Moor, J. M., Zahirovic, S., Manea, V. C., Hoernle, K., Fischer, T. P., Hammerstrom, A., Seltzer, A. M., Kulongoski, J. T., Patel, B. S., Schrenk, M. O., Halldórsson, S. A., Nakagawa, M., Ramírez, C. J., Krantz, J. A., Yücel, M., Ballentine, C. J., Giovannelli, D., Lloyd, K. G., Barry, P. H. High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume. Proceedings of the National Academy of Sciences of the United States of America, 118(47), (2021): e2110997118, https://doi.org/10.1073/pnas.2110997118.
    Description: It is well established that mantle plumes are the main conduits for upwelling geochemically enriched material from Earth's deep interior. The fashion and extent to which lateral flow processes at shallow depths may disperse enriched mantle material far (〉1,000 km) from vertical plume conduits, however, remain poorly constrained. Here, we report He and C isotope data from 65 hydrothermal fluids from the southern Central America Margin (CAM) which reveal strikingly high 3He/4He (up to 8.9RA) in low-temperature (≤50 °C) geothermal springs of central Panama that are not associated with active volcanism. Following radiogenic correction, these data imply a mantle source 3He/4He 〉10.3RA (and potentially up to 26RA, similar to Galápagos hotspot lavas) markedly greater than the upper mantle range (8 ± 1RA). Lava geochemistry (Pb isotopes, Nb/U, and Ce/Pb) and geophysical constraints show that high 3He/4He values in central Panama are likely derived from the infiltration of a Galápagos plume–like mantle through a slab window that opened ∼8 Mya. Two potential transport mechanisms can explain the connection between the Galápagos plume and the slab window: 1) sublithospheric transport of Galápagos plume material channeled by lithosphere thinning along the Panama Fracture Zone or 2) active upwelling of Galápagos plume material blown by a “mantle wind” toward the CAM. We present a model of global mantle flow that supports the second mechanism, whereby most of the eastward transport of Galápagos plume material occurs in the shallow asthenosphere. These findings underscore the potential for lateral mantle flow to transport mantle geochemical heterogeneities thousands of kilometers away from plume conduits.
    Description: This work was principally supported by Grant G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. We also acknowledge the NSF awards (1144559, 1923915, and 2015789) to P.H.B., which partially supported this work. S.Z. was supported by the Australian Research Council Grant DE210100084 and a University of Sydney Robinson Fellowship. D.G. was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG. This study was also supported in part by NSF award No. EAR 1826673 to E.G. Folkmar Hauff is acknowledged for contributing to the analysis of the La Providencia samples at GEOMAR.
    Keywords: Helium ; Mantle plume ; Slab window ; Mantle flow ; Geochemistry
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  • 18
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    Microplastic ingestion in zooplankton from the Fram Strait in the Arctic (2022)
    ELSEVIER SCIENCE BV
    In:  EPIC3Science of The Total Environment, ELSEVIER SCIENCE BV, pp. 154886-154886, ISSN: 0048-9697
    Details
    Publication Date: 2022-11-28
    Description: Some of the highest microplastic concentrations in marine environments have been reported from the Fram Strait in the Arctic. This region supports a diverse ecosystem dependent on high concentrations of zooplankton at the base of the food web. Zooplankton samples were collected during research cruises using Bongo and MOCNESS nets in the boreal summers of 2018 and 2019. Using FTIR scanning spectroscopy in combination with an automated polymer identification approach, we show that all five species of Arctic zooplankton investigated had ingested microplastics. Amphipod species, found in surface waters or closely associated with sea ice, had ingested significantly more microplastic per individual (Themisto libellula: 1.8, Themisto abyssorrum: 1, Apherusa glacialis: 1) than copepod species (Calanus hyperboreus: 0.21, Calanus glacialis/finmarchicus: 0.01). The majority of microplastics ingested were below 50 μm in size, all were fragments and several different polymer types were present. We quantified microplastics in water samples collected at six of the same stations as the Calanus using an underway sampling system (inlet at 6.5 m water depth). Fragments of several polymer types and anthropogenic cellulosic fibres were present, with an average concentration of 7 microplastic particles (MP) L−1 (0–18.5 MP L−1). In comparison to the water samples, those microplastics found ingested by zooplankton were significantly smaller, highlighting that the smaller-sized microplastics were being selected for by the zooplankton. High levels of microplastic ingestion in zooplankton have been associated with negative effects on growth, development, and fecundity. As Arctic zooplankton only have a short window of biological productivity, any negative effect could have broad consequences. As global plastic consumption continues to increase and climate change continues to reduce sea ice cover, releasing ice-bound microplastics and leaving ice free areas open to exploitation, the Arctic could be exposed to further plastic pollution which could place additional strain on this fragile ecosystem.
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Orvis, J., Albertin, C., Shrestha, P., Chen, S., Zheng, M., Rodriguez, C., Tallon, L., Mahurkar, A., Zimin, A., Kim, M., Liu, K., Kandel, E., Fraser, C., Sossin, W., & Abrams, T. The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia. Proceedings of the National Academy of Sciences of the United States of America, 119(28), (2022): e2122301119, https://doi.org/10.1073/pnas.2122301119.
    Description: The gastropod mollusk Aplysia is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate an improved Aplysia nervous system transcriptome. This improved transcriptome enabled us to explore the evolution of cognitive capacity at the molecular level. Were there evolutionary expansions of neuronal genes between this relatively simple gastropod Aplysia (20,000 neurons) and Octopus (500 million neurons), the invertebrate with the most elaborate neuronal circuitry and greatest behavioral complexity? Are the tremendous advances in cognitive power in vertebrates explained by expansion of the synaptic proteome that resulted from multiple rounds of whole genome duplication in this clade? Overall, the complement of genes linked to neuronal function is similar between Octopus and Aplysia. As expected, a number of synaptic scaffold proteins have more isoforms in humans than in Aplysia or Octopus. However, several scaffold families present in mollusks and other protostomes are absent in vertebrates, including the Fifes, Lev10s, SOLs, and a NETO family. Thus, whereas vertebrates have more scaffold isoforms from select families, invertebrates have additional scaffold protein families not found in vertebrates. This analysis provides insights into the evolution of the synaptic proteome. Both synaptic proteins and synaptic plasticity evolved gradually, yet the last deuterostome-protostome common ancestor already possessed an elaborate suite of genes associated with synaptic function, and critical for synaptic plasticity.
    Description: This work was supported by NSF EAGER Award IOS-1255695 and NIH grant R01 MH 55880 grant to T.W.A.; by a Natural Sciences and Engineering Research Council of Canada Discovery grant and Canadian Institutes of Health Research project grant 340328 to W.S.; by funding from the HHMI to E.R.K.; and by a Hibbitt Early Career Fellowship to C.A. W.S. is James McGill Professor at McGill University.
    Keywords: Neural plasticity ; Synaptic plasticity ; Evolution ; Neuromodulation ; Aplysia
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  • 20
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    Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McDermott, J. M., Parnell-Turner, R., Barreyre, T., Herrera, S., Downing, C. C., Pittoors, N. C., Pehr, K., Vohsen, S. A., Dowd, W. S., Wu, J.-N., Marjanović, M., & Fornari, D. J. Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise. Proceedings of the National Academy of Sciences of the United States of America, 119(30), (2022): e2205602119, https://doi.org/10.1073/pnas.2205602119.
    Description: Comprehensive knowledge of the distribution of active hydrothermal vent fields along midocean ridges is essential to understanding global chemical and heat fluxes and endemic faunal distributions. However, current knowledge is biased by a historical preference for on-axis surveys. A scarcity of high-resolution bathymetric surveys in off-axis regions limits vent identification, which implies that the number of vents may be underestimated. Here, we present the discovery of an active, high-temperature, off-axis hydrothermal field on a fast-spreading ridge. The vent field is located 750 m east of the East Pacific Rise axis and ∼7 km north of on-axis vents at 9° 50′N, which are situated in a 50- to 100-m-wide trough. This site is currently the largest vent field known on the East Pacific Rise between 9 and 10° N. Its proximity to a normal fault suggests that hydrothermal fluid pathways are tectonically controlled. Geochemical evidence reveals deep fluid circulation to depths only 160 m above the axial magma lens. Relative to on-axis vents at 9° 50′N, these off-axis fluids attain higher temperatures and pressures. This tectonically controlled vent field may therefore exhibit greater stability in fluid composition, in contrast to more dynamic, dike-controlled, on-axis vents. The location of this site indicates that high-temperature convective circulation cells extend to greater distances off axis than previously realized. Thorough high-resolution mapping is necessary to understand the distribution, frequency, and physical controls on active off-axis vent fields so that their contribution to global heat and chemical fluxes and role in metacommunity dynamics can be determined.
    Description: Financial support was provided by the NSF Awards OCE-1949938 (to J.M.M.), OCE-1948936 (to R.P.-T.), and OCE-1949485 (to D.J.F. and T.B.).
    Keywords: Hydrothermal activity ; Midocean ridge ; Ocean chemistry ; Chemosynthetic ecosystem ; East Pacific Rise
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  • 21
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    HTD2: a single‐crystal X‐ray diffractometer for combined high‐pressure/low‐temperature experiments at laboratory scale (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2022-12-15
    Description: High‐pressure (HP) X‐ray diffraction experiments at low temperature (LT) require dedicated instruments as well as non‐standard sample environments and measuring strategies. This is especially true when helium cryogenic temperatures below 80 K are targeted. Furthermore, only experiments on single‐crystalline samples provide the prerequisites to study subtle structural changes in the p–T phase diagram under extreme LT and HP conditions in greater detail. Due to special hardware requirements, such measurements are usually in the realm of synchrotron beamlines. This contribution describes the design of an LT/HP diffractometer (HTD2) to perform single‐crystal X‐ray diffraction experiments using a laboratory source in the temperature range 400 〉 T 〉 2 K while applying pressures of up to 20 GPa.
    Description: The design and operation of a newly commissioned single‐crystal X‐ray diffractometer (HTD2) are presented. The device enables experiments under simultaneous low‐temperature and high‐pressure conditions using a laboratory X‐ray source.
    Keywords: ddc:548 ; HTD2 ; low temperature ; high pressure ; single crystals ; instrumentation
    Language: English
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