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1. Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Caputi, L, Carradec, Q, Eveillard, D, Kirilovsky, A, Pelletier, E, Pierella Karlusich, JJ, Rocha Jimenez Vieira, F, Villar, E, Chaffron, S, Malviya, S, Scalco, E, Acinas, SG, Alberti, A, Aury, JM, Benoiston, AS, Bertrand, A, Biard, T, Bittner, L, Boccara, M, Brum, JR, Brunet, C, Busseni, G, Carratalà, A, Claustre, H, Coelho, LP, Colin, S, D'Aniello, S, Da Silva, C, Del Core, M, Doré, H, Gasparini, S, Kokoszka, F, Jamet, JL, Lejeusne, C, Lepoivre, C, Lescot, M, Lima-Mendez, G, Lombard, F, Lukeš, J, Maillet, N, Madoui, MA, Martinez, E, Mazzocchi, MG, Néou, MB, Paz-Yepes, J, Poulain, J, Ramondenc, S, Romagnan, JB, Roux, S, Salvagio Manta, D, Sanges, R, Speich, S, Sprovieri, M, Sunagawa, S, Taillandier, V, Tanaka, A, Tirichine, L, Trottier, C, Uitz, J, Veluchamy, A, Veselá, J, Vincent, F, Yau, S, Kandels-Lewis, S, Searson, S, Dimier, C, Picheral, M, Bork, P, Boss, E, de Vargas, C, Follows, MJ, Grimsley, N, Guidi, L, Hingamp, P, Karsenti, E, Sordino, P, Stemmann, L, Sullivan, MB, Tagliabue, A, Zingone, A, Garczarek, L, d'Ortenzio, F, Testor, P, Not, F, d'Alcalà, MR, Wincker, P, Bowler, C, and Iudicone, D

Subjects
Genetics, Atmospheric Sciences, Geochemistry, Meteorology & Atmospheric Sciences, Oceanography
Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.

Published
2019

2. Modeling, Minimizing and Managing the Risk of Fatigue for Mechanical Components

Author

Bittner, L., Gottschalk, H., Gröger, M., Moch, N., Saadi, M., and Schmitz, S.

Subjects
Mathematics - Optimization and Control, 62N05, 49Q10, 65N75, 90B25
Abstract

Mechanical components that are exposed to cyclic mechanical loading fail at loads that are well below the ultimate tensile strength. This process is known as fatigue. The failure time, that is the time when a first crack forms, is highly random. In this work we review some recent developments in the modelling of probabilistic failure times, understood as the time to the formation of a fatigue crack. We also discuss the how probabilistic models can be used in shape design with the design intent of optimizing the component's reliability. We give review a recent existence result for optimal shapes and we discuss continuous and discrete shape derivatives. Another application is optimal service scheduling. The mathematical fields involved range from reliability statistics over stochastic point processes, multiscale modeling, PDEs on variable geometries, shape optimization and numerical analysis to operations research., Comment: 36 pages, 9 Figures

Published
2016

5. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Tara Oceans Coordinators, Villar, E., Farrant, G. K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J. R., Brunet, C., Casotti, R., Chase, A., Dolan, J. R., d'Ortenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C. N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S. M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M. B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., and Iudicone, D.

Published
2015

6. Determinants of community structure in the global plankton interactome

Author

Tara Oceans Coordinators, Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., d'Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sànchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., and Raes, J.

Published
2015

7. Eukaryotic plankton diversity in the sunlit ocean

Author

Tara Oceans Coordinators, de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., and Karsenti, E.

Published
2015

9. Revisiting afro-alpine Lake Garba Guracha in the Bale Mountains of Ethiopia: rationale, chronology, geochemistry, and paleoenvironmental implications

Author

Bittner, L., Bliedtner, M., Grady, D., Gil-Romera, G., Martin-Jones, C., Lemma, B., Mekonnen, B., Lamb, H. F., Yang, H., Glaser, B., Szidat, S., Salazar, G., Rose, N. L., Opgenoorth, L., Miehe, G., Zech, W., Zech, M., Heisenberg Chair of Physical Geography with Focus on Paleoenvironmental Research, Institute of Geography, Technical University of Dresden, Dresden, Germany, Department of Physical Geography, Institute of Geography, Friedrich-Schiller-University Jena, Jena, Germany, Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, UK, Department of Geo-Environmental Processes and Global Change, CSIC, Pyrenean Institute of Ecology, Zaragoza, Spain, Limnology Unit, Department of Biology, Ghent University, Gent, Belgium, Institute of Agronomy and Nutritional Sciences, Soil Biogeochemistry, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Environmental Change Research Centre, University College London, London, UK, Department of Chemistry and Biochemistry and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland, Department of Geography, University of Marburg, Marburg, Germany, Institute of Soil Science and Soil Geography, University of Bayreuth, Bayreuth, Germany, Bittner, L [0000-0003-2521-5596], Apollo - University of Cambridge Repository, and Bittner, L. [0000-0003-2521-5596]

Subjects
Radiocarbon dating, 010506 paleontology, 010504 meteorology & atmospheric sciences, Sedimentation rate, Aquatic Science, 01 natural sciences, law.invention, law, 540 Chemistry, Paleoclimatology, Afro-alpine, Sedimentary organic matter, Glacial period, Younger Dryas, Paleolimnology, Sedimentology, Holocene, 0105 earth and related environmental sciences, Earth-Surface Processes, Original Paper, ddc:551, XRF scanning, 570 Life sciences, biology, Physical geography, Geology, Biomarkers, Chronology
Abstract

Previous paleolimnological studies demonstrated that the sediments of Garba Guracha, situated at 3950 m asl in the afro-alpine zone of the Bale Mountains of Ethiopia, provide a complete Late Glacial and Holocene paleoclimate and environmental archive. We revisited Garba Guracha in order to retrieve new sediment cores and to apply new environmental proxies, e.g. charcoal, diatoms, biomarkers, and stable isotopes. Our chronology is established using 210Pb dating and radiocarbon dating of bulk sedimentary organic matter, bulk n-alkanes, and charcoal. Although bedrock was not reached during coring, basal ages confirm that sedimentation started at the earliest ~ 16 cal kyr BP. The absence of a systematic age offset for the n-alkanes suggests that “pre-aging” is not a prominent issue in this lake, which is characterised by a very small afro-alpine catchment. X-ray fluorescence scans and total organic carbon contents show a prominent transition from minerogenic to organic-rich sediments around 11 cal kyr BP coinciding with the Holocene onset. While an unambiguous terrestrial versus aquatic source identification seems challenging, the n-alkane-based Paq proxy, TOC/N ratios, δ13C values, and the sugar biomarker patterns suggest a predominantly autochthonous organic matter source. Supraregional climate events, such as the African Humid Period, the Younger Dryas (YD), a 6.5 cal kyr BP short drying event, and the 4.2 cal kyr BP transition to overall drier climate are recorded in our archive. The Garba Guracha record suggests that northern hemisphere forcings played a role in the Eastern African highland paleoclimate., Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659

Published
2020
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12. Eukaryotic plankton diversity in the sunlit ocean

Author

de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., and Karsenti, E.

Published
2015

13. Determinants of community structure in the global plankton interactome

Author

Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., dʼOvidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., and Raes, J.

Published
2015

14. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Villar, E., Farrant, G. K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J. R., Brunet, C., Casotti, R., Chase, A., Dolan, J. R., dʼOrtenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C. N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S. M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Acinas, S. G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M. B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., and Iudicone, D.

Published
2015

16. New infrared undulator beamline at FLASH

Author

Gensch, M., Bittner, L., Chesnov, A., Delsim-Hashemi, H., Drescher, M., Faatz, B., Feldhaus, J., Fruehling, U., Geloni, G.A., Gerth, Ch., Grimm, O., Hahn, U., Hesse, M., Kapitzki, S., Kocharyan, V., Kozlov, O., Matyushevsky, E., Morozov, N., Petrov, D., Ploenjes, E., Roehling, M., Rossbach, J., Saldin, E.L., Schmidt, B., Schmueser, P., Schneidmiller, E.A., Syresin, E., Willner, A., and Yurkov, M.V.

Published
2008
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18. The Holocene lake-evaporation history of the afro-alpine Lake Garba Guracha in the Bale Mountains, Ethiopia, based on δ18O records of sugar biomarkers and diatoms

Author

Bittner, L., Gil-Romera, G., Grady, D., Lamb, H. F., Lorenz, E., Weiner, Mikaela, Meyer, Hanno, Bromm, T., Glaser, B., Zech, Michael, Bittner, L., Gil-Romera, G., Grady, D., Lamb, H. F., Lorenz, E., Weiner, Mikaela, Meyer, Hanno, Bromm, T., Glaser, B., and Zech, Michael

Abstract

In eastern Africa, there are few long, high-quality records of environmental change at high altitudes, inhibiting a broader understanding of regional climate change. We investigated a Holocene lacustrine sediment archive from Lake Garba Guracha, Bale Mountains, Ethiopia, (3,950 m a.s.l.), and reconstructed high-altitude lake evaporation history using δ18O records derived from the analysis of compound-specific sugar biomarkers and diatoms. The δ18Odiatom and δ18Ofuc records are clearly correlated and reveal similar ranges (7.9‰ and 7.1‰, respectively). The lowest δ18O values occurred between 10 and 7 cal ka BP and were followed by a continuous shift towards more positive δ18O values. Due to the aquatic origin of the sugar biomarker and the similar trends of δ18Odiatom, we suggest that our lacustrine δ18Ofuc record reflects δ18Olake water. Therefore, without completely excluding the influence of the ‘amount-effect’ and the ‘source-effect‘, we interpret our record to reflect primarily the precipitation-to-evaporation ratio (P/E). We conclude that precipitation increased at the beginning of the Holocene, leading to an overflowing lake between ~10 and ~8 cal ka BP, indicated by low δ18Olake water values interpreted as reduced evaporative enrichment. This is followed by a continuous trend towards drier conditions, indicating at least a seasonally closed lake system.

Published
2021

21. Multiple ionization of atom clusters by intense soft X-rays from a free-electron laser

Author

Wabnitz, H., Bittner, L., de Castro, A. R. B., Dohrmann, R., Gurtler, P., Laarmann, T., Laasch, W., Schulz, J., Swiderski, A., von Haeften, K., Moller, T., Faatz, B., Fateev, A., Feldhaus, J., Gerth, C., Hahn, U., Saldin, E., Schneidmiller, E., Sytchev, K., Tiedtke, K., Treusch, R., and Yurkov, M.

Abstract

Author(s): H. Wabnitz [1]; L. Bittner [1]; A. R. B. de Castro [2]; R. Döhrmann [1]; P. Gürtler [1]; T. Laarmann [1]; W. Laasch [1]; J. Schulz [1]; A. Swiderski [...]

Published
2002
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23. Revisiting afro-alpine Lake Garba Guracha in the Bale Mountains of Ethiopia: rationale, chronology, geochemistry, and paleoenvironmental implications

Author

Bittner, L., primary, Bliedtner, M., additional, Grady, D., additional, Gil-Romera, G., additional, Martin-Jones, C., additional, Lemma, B., additional, Mekonnen, B., additional, Lamb, H. F., additional, Yang, H., additional, Glaser, B., additional, Szidat, S., additional, Salazar, G., additional, Rose, N. L., additional, Opgenoorth, L., additional, Miehe, G., additional, Zech, W., additional, and Zech, M., additional

Published
2020
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27. Functional trait‐based approaches as a common framework for aquatic ecologists

Author

Martini, S., Larras, Floriane, Boyé, A., Faure, E., Aberle, N., Archambault, P., Bacouillard, L., Beisner, B.E., Bittner, L., Castella, E., Danger, M., Gauthier, O., Karp‐Boss, L., Lombard, F., Maps, F., Stemmann, L., Thiébaut, E., Usseglio‐Polatera, P., Vogt, M., Laviale, M., Ayata, S.-D., Martini, S., Larras, Floriane, Boyé, A., Faure, E., Aberle, N., Archambault, P., Bacouillard, L., Beisner, B.E., Bittner, L., Castella, E., Danger, M., Gauthier, O., Karp‐Boss, L., Lombard, F., Maps, F., Stemmann, L., Thiébaut, E., Usseglio‐Polatera, P., Vogt, M., Laviale, M., and Ayata, S.-D.

Abstract

Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists, is needed to bridge communication gaps and foster knowledge sharing. This framework should transcend local specificities and taxonomy in order to provide a common ground and shareable tools to address common scientific challenges. Here, we advocate the use of functional trait‐based approaches (FTBAs) for aquatic ecologists and propose concrete paths to go forward. Firstly, we propose to unify existing definitions in FTBAs to adopt a common language. Secondly, we list the numerous databases referencing functional traits for aquatic organisms. Thirdly, we present a synthesis on traditional as well as recent promising methods for the study of aquatic functional traits, including imaging and genomics. Finally, we conclude with a highlight on scientific challenges and promising venues for which FTBAs should foster opportunities for future research. By offering practical tools, our framework provides a clear path forward to the adoption of trait‐based approaches in aquatic ecology.

Published
2020

29. Biological pump processes are driven by microbial networks in the global oligotrophic ocean

Author

Benoiston, A.S., Eveillard, E., Chaffron, S., Ayata, S., Bowler, C., Guidi, L., Delage, Erwan, Jean, Géraldine, Bittner, L., Corrdinators, Tara Oceans, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Laboratoire des Sciences du Numérique de Nantes (LS2N), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Nantes Université (Nantes Univ), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience

Published
2018

30. Assessing functional diversity of plankton communities from high throughput –omics data

Author

Ayata, Sakina-Dorothée, Faure, E., Benoiston, A.-S., Silva, O., Sonnet, V., Benedetti, F., Not, F., Aumont, Olivier, Guidi, L., Chaffron, S., Eveillard, D., Bittner, L., Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Nucleus for European Modeling of the Ocean (NEMO R&D ), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)

Subjects
poster, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience

Published
2018

33. Tomographic observation of injection procedures for fracture sealing

Author

Kulenkampff, J., Bittner, L., Gründig, M., and Lippmann-Pipke, J.

Subjects
positron emission tomography, nuclear waste disposal
Abstract

Networks of micro fissures may exist in rock salt in the excavation damage zone. Though they will not affect the integrity of the barrier function as a whole it might be advantageous to seal such likely permeable structures by means of impregnation procedures. However, the lasting effect of such procedures is difficult to judge from simple measurements of the decrease of porosity and permeability, because spatial distribution and penetration depth of the impregnation agent should be known. We therefore suggest evaluating such impregnation methods with the help of tomographic laboratory methods of macroscopic samples. The sample size should exceed the mean fracture distance. Therefore the size of standard drill cores with a diameter in the order of 100 mm is appropriate. This rather large size limits the achievable spatial resolution and thus the detectability of fractures with the otherwise well-established µCT-method. The low contrast between the density of the fracture fill and the solid material further complicates detection and segmentation of the structures. To overcome these issues, we apply positron emission tomography (PET). This tomographic modality yields quantitative images of the concentration of a positron emitting radiotracer with molecular sensitivity and a spatial resolution of 1 mm. We obtain images of the penetration of the labelled impregnation agent, as average tracer concentration over the voxel volume of 1 µL. As prove of principle, we applied waterglass (sodium silcate) labelled with 18F as agent that was injected into an artificially fractured sylvinite core (Z2KSTh) from Staßfurt. The sample was structurally characterized before and after impregnation with µCT, and the flow field was determined with PET process tomography of propagating saturated NaCl-solution labelled with 18F. Although we achieved a significant decrease of permeability by waterglass injection, no significant structural effect could be seen with µCT. In contrast, PET showed a superficial covering of the sample surface with solid waterglass and penetration into larger voids with a penetration depth of a few millimetres (Fig. 1). This rather small effect is a consequence of the experimental conditions – low injection rate and low pressure – that were chosen to keep the setup simple. Although it was not intended here to estimate the effectiveness of waterglass impregnation as method for improving the geological barrier, we experienced the delicate interplay between reaction kinetics of waterglass solidification and local flow rate which makes its prediction difficult. However, we could prove the applicability of the visualization method which is uncomplicated to adapt to other impregnation agents and materials, higher pressure and injection rate.

Published
2018

34. From plankton functional traits to marine ecosystem functions: Assessing functional diversity of plankton communities from high throughput -omics data and its impact on oceanic biogeochemical cycles

Author

Ayata, Sakina-Dorothée, Faure, E., Benoiston, A.-S., Not, F., Aumont, Olivier, Guidi, L, Chaffron, S., Eveillard, D., Bittner, L., Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Nucleus for European Modeling of the Ocean (NEMO R&D ), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)

Subjects
[SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience

Published
2018

38. A de novo approach to disentangle partner identity and function in holobiont systems

Author

Meng, A., Marchet, C., Corre, E., Peterlongo, P., Alberti, A., Da Silva, C., Wincker, P., Pelletier, E., Probert, I., Decelle, Johan, Le Crom, S., Not, F., Bittner, L., Meng, A., Marchet, C., Corre, E., Peterlongo, P., Alberti, A., Da Silva, C., Wincker, P., Pelletier, E., Probert, I., Decelle, Johan, Le Crom, S., Not, F., and Bittner, L.

Abstract

BackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.ResultsWe considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner’s transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited.ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or po

Published
2018

40. Plankton networks correlated to the biological carbon pump in the global ocean

Author

Benoiston, A.S., Bittner, L., Guidi, Lionel, Chaffron, S., Eveillard, D., Ayata, S.D., Jean, Géraldine, Pelletier, E., Pesant, S., de Vargas, C., Karsenti, E., Bowler, C., Gorsky, G., Consortium, Tara, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Nantes Université (Nantes Univ), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience

Published
2017

43. Das peptische Ulcus: Pathophysiologische Aspekte des präpylorischen Ulcus ventriculi

Author

M. Meves, H. G. Beger, R. Bittner, and Bittner L

Subjects
medicine.medical_specialty, Gastric emptying, business.industry, medicine.medical_treatment, Stomach, digestive, oral, and skin physiology, General Medicine, Gastroenterology, digestive system diseases, Pathophysiology, medicine.anatomical_structure, Internal medicine, medicine, Gastric mucosa, Gastric acid, Billroth I, Gastrectomy, business, Gastrin
Abstract

The secretory and motor function of the stomach and gastrin incretion were investigated in 68 patients with peptic ulcer of variable localization. In addition, a retrospective analysis of the course of prepyloric gastric ulcer and Billroth I resection was performed in 62 patients. Results show that gastric acid secretion and velocity of gastric emptying diminish significantly with increasing height of the localization of the ulcer. Prepyloric gastric ulcer cannot be likened to the duodenal ulcer. Moreover, experimental and clinical results suggest that prepyloric ulcer represents a disease entity per se requiring separate therapeutic approaches (gastric resection following Billroth I).

Published
2008
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47. A communal catalogue reveals Earth's multiscale microbial diversity

Author

Thompson, LR, Sanders, JG, McDonald, D, Amir, A, Ladau, J, Locey, KJ, Prill, RJ, Tripathi, A, Gibbons, SM, Ackermann, G, Navas-Molina, JA, Janssen, S, Kopylova, E, Vázquez-Baeza, Y, González, A, Morton, JT, Mirarab, S, Xu, ZZ, Jiang, L, Haroon, MF, Kanbar, J, Zhu, Q, Song, SJ, Kosciolek, T, Bokulich, NA, Lefler, J, Brislawn, CJ, Humphrey, G, Owens, SM, Hampton-Marcell, J, Berg-Lyons, D, McKenzie, V, Fierer, N, Fuhrman, JA, Clauset, A, Stevens, RL, Shade, A, Pollard, KS, Goodwin, KD, Jansson, JK, Gilbert, JA, Knight, R, Agosto Rivera, JL, Al-Moosawi, L, Alverdy, J, Amato, KR, Andras, J, Angenent, LT, Antonopoulos, DA, Apprill, A, Armitage, D, Ballantine, K, Bárta, J, Baum, JK, Berry, A, Bhatnagar, A, Bhatnagar, M, Biddle, JF, Bittner, L, Boldgiv, B, Bottos, E, Boyer, DM, Braun, J, Brazelton, W, Brearley, FQ, Campbell, AH ; https://orcid.org/0000-0002-2322-2840, Caporaso, JG, Cardona, C, Carroll, JL, Cary, SC, Casper, BB, Charles, TC, Chu, H, Claar, DC, Clark, RG, Clayton, JB, Clemente, JC, Cochran, A, Coleman, ML, Collins, G, Colwell, RR, Contreras, M, Crary, BB, Creer, S, Cristol, DA, Crump, BC, Cui, D, Daly, SE, Davalos, L, Dawson, RD, Defazio, J, Delsuc, F, Dionisi, HM, Dominguez-Bello, MG, Dowell, R, Dubinsky, EA, Dunn, PO, Ercolini, D, Espinoza, RE, Ezenwa, V, Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001, Munroe, Paul ; https://orcid.org/0000-0002-5091-2513, Steinberg, Peter ; https://orcid.org/0000-0002-1781-0726, Marzinelli, Ezequiel ; https://orcid.org/0000-0002-3762-3389, Nielsen, Shaun ; https://orcid.org/0000-0001-6855-4227, Moitinho e Silva, Lucas, Thompson, LR, Sanders, JG, McDonald, D, Amir, A, Ladau, J, Locey, KJ, Prill, RJ, Tripathi, A, Gibbons, SM, Ackermann, G, Navas-Molina, JA, Janssen, S, Kopylova, E, Vázquez-Baeza, Y, González, A, Morton, JT, Mirarab, S, Xu, ZZ, Jiang, L, Haroon, MF, Kanbar, J, Zhu, Q, Song, SJ, Kosciolek, T, Bokulich, NA, Lefler, J, Brislawn, CJ, Humphrey, G, Owens, SM, Hampton-Marcell, J, Berg-Lyons, D, McKenzie, V, Fierer, N, Fuhrman, JA, Clauset, A, Stevens, RL, Shade, A, Pollard, KS, Goodwin, KD, Jansson, JK, Gilbert, JA, Knight, R, Agosto Rivera, JL, Al-Moosawi, L, Alverdy, J, Amato, KR, Andras, J, Angenent, LT, Antonopoulos, DA, Apprill, A, Armitage, D, Ballantine, K, Bárta, J, Baum, JK, Berry, A, Bhatnagar, A, Bhatnagar, M, Biddle, JF, Bittner, L, Boldgiv, B, Bottos, E, Boyer, DM, Braun, J, Brazelton, W, Brearley, FQ, Campbell, AH ; https://orcid.org/0000-0002-2322-2840, Caporaso, JG, Cardona, C, Carroll, JL, Cary, SC, Casper, BB, Charles, TC, Chu, H, Claar, DC, Clark, RG, Clayton, JB, Clemente, JC, Cochran, A, Coleman, ML, Collins, G, Colwell, RR, Contreras, M, Crary, BB, Creer, S, Cristol, DA, Crump, BC, Cui, D, Daly, SE, Davalos, L, Dawson, RD, Defazio, J, Delsuc, F, Dionisi, HM, Dominguez-Bello, MG, Dowell, R, Dubinsky, EA, Dunn, PO, Ercolini, D, Espinoza, RE, Ezenwa, V, Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001, Munroe, Paul ; https://orcid.org/0000-0002-5091-2513, Steinberg, Peter ; https://orcid.org/0000-0002-1781-0726, Marzinelli, Ezequiel ; https://orcid.org/0000-0002-3762-3389, Nielsen, Shaun ; https://orcid.org/0000-0001-6855-4227, and Moitinho e Silva, Lucas

Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Published
2017

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