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529 results on '"Monterey Bay Aquarium Research Institute"'

1. Choanoflagellates alongside diverse uncultured predatory protists consume the abundant open-ocean cyanobacterium Prochlorococcus

Author: Monterey Bay Aquarium Research Institute, Gordon and Betty Moore Foundation, European Commission, Simons Foundation, Agencia Estatal de Investigación (España), Wilken, Susanne, Yung, Charmaine C.M., Poirier, Camille, Massana, Ramon, Jiménez, Valeria, Worden, Alexandra Z., Monterey Bay Aquarium Research Institute, Gordon and Betty Moore Foundation, European Commission, Simons Foundation, Agencia Estatal de Investigación (España), Wilken, Susanne, Yung, Charmaine C.M., Poirier, Camille, Massana, Ramon, Jiménez, Valeria, and Worden, Alexandra Z.
Abstract: Prochlorococcus is a key member of open-ocean primary producer communities. Despite its importance, little is known about the predators that consume this cyanobacterium and make its biomass available to higher trophic levels. We identify potential predators along a gradient wherein Prochlorococcus abundance increased from near detection limits (coastal California) to >200,000 cells mL−1 (subtropical North Pacific Gyre). A replicated RNA-Stable Isotope Probing experiment involving the in situ community, and labeled Prochlorococcus as prey, revealed choanoflagellates as the most active predators of Prochlorococcus, alongside a radiolarian, chrysophytes, dictyochophytes, and specific MAST lineages. These predators were not appropriately highlighted in multiyear conventional 18S rRNA gene amplicon surveys where dinoflagellates and other taxa had highest relative amplicon abundances across the gradient. In identifying direct consumers of Prochlorococcus, we reveal food-web linkages of individual protistan taxa and resolve routes of carbon transfer from the base of marine food webs
Published: 2023

2. Humpback whale song occurrence reflects ecosystem variability in feeding and migratory habitat of the northeast Pacific

Author: Monterey Bay Aquarium Research Institute, Southwest Fisheries Science Center, Oceanography, Ryan, John P., Cline, Danelle E., Joseph, John E., Margolina, Tetyana, Santora, Jarrod A., Kudela, Raphael M., Chavez, Francisco P., Pennington, J. Timothy, Wahl, Christopher, Michisaki, Reiko, Beniot-Bird, Kelly, Forney, Karin A., Stimpert, Alison K., DeVogelaere, Andrew, Black, Nancy, Fischer, Mark, Monterey Bay Aquarium Research Institute, Southwest Fisheries Science Center, Oceanography, Ryan, John P., Cline, Danelle E., Joseph, John E., Margolina, Tetyana, Santora, Jarrod A., Kudela, Raphael M., Chavez, Francisco P., Pennington, J. Timothy, Wahl, Christopher, Michisaki, Reiko, Beniot-Bird, Kelly, Forney, Karin A., Stimpert, Alison K., DeVogelaere, Andrew, Black, Nancy, and Fischer, Mark
Abstract: This study examines the occurrence of humpback whale (Megaptera novaeangliae) song in the northeast Pacific from three years of continuous recordings off central California (36.713˚N, 122.186˚W). Song is prevalent in this feeding and migratory habitat, spanning nine months of the year (September–May), peaking in winter (November–January), and reaching a maximum of 86% temporal coverage (during November 2017). From the rise of song in fall through the end of peak occurrence in winter, song length increases significantly from month to month. The seasonal peak in song coincides with the seasonal trough in day length and sighting-based evidence of whales leaving Monterey Bay, consistent with seasonal migration. During the seasonal song peak, diel variation shows maximum occurrence at night (69% of the time), decreasing during dawn and dusk (52%), and further decreasing with increasing solar elevation during the day, reaching a minimum near solar noon (30%). Song occurrence increased 44% and 55% between successive years. Sighting data within the acoustic detection range of the hydrophone indicate that variation in local population density was an unlikely cause of this large interannual variation. Hydrographic data and modeling of acoustic transmission indicate that changes in neither habitat occupancy nor acoustic transmission were probable causes. Conversely, the positive interannual trend in song paralleled major ecosystem variations, including similarly large positive trends in winddriven upwelling, primary productivity, and krill abundance. Further, the lowest song occurrence during the first year coincided with anomalously warm ocean temperatures and an extremely toxic harmful algal bloom that affected whales and other marine mammals in the region. These major ecosystem variations may have influenced the health and behavior of humpback whales during the study period.
Published: 2019

3. Natural-Language Retrieval of Images Based on Descriptive Captions

Author: Monterey Bay Aquarium Research Institute (MBARI) and the Naval Postgraduate School., Guglielmo, Eugene J., Rowe, Neil C., Monterey Bay Aquarium Research Institute (MBARI) and the Naval Postgraduate School., Guglielmo, Eugene J., and Rowe, Neil C.
Abstract: We describe a prototype intelligent information retrieval system that uses natural-language understanding to efficiently locate captioned data. Multimedia data generally require captions to explain their features and significance. Such descriptive captions often rely on long nominal compounds (strings of consecutive nouns) which create problems of disambiguating word sense. In our system, captions and user queries are parsed and interpreted to produce a logical form, using a detailed theory of the meaning of nominal compounds. A fine-grain match can then compare the logical form of the query to the logical forms for each caption. To improve system efficiency, we first perform a coarse-grain match with index files, using nouns and verbs extracted from the query. Our experiments with randomly selected queries and captions from an existing image library show an increase of 30% in precision and 50% in recall over the keyphrase approach currently used. Our processing times have a median of seven seconds as compared to eight minutes for the existing system, and our system is much easier to use.
Published: 1996

4. Viral coinfections in hospitalized Coronavirus disease 2019 patients recruited to the international severe acute respiratory and emerging infections consortium WHO clinical characterisation protocol UK study

Author: Vink, Elen, Davis, Chris, Maclean, Alasdair, Pascall, David, Mcdonald, Sarah, Gunson, Rory, Hardwick, Hayley, Oosthuyzen, Wilna, Openshaw, Peter, Baillie, J Kenneth, Semple, Malcolm, Ho, Antonia, Barclay, Wendy, Bogaert, Debby, Chand, Meera, Chechi, Kanta, Cooke, Graham, Filipe, Ana da Silva, Silva, Thushan De, Docherty, Annemarie, Correia, Gonçalo dos Santos, Dumas, Marc-Emmanuel, Dunning, Jake, Fletcher, Tom, Green, Christoper, Greenhalf, William, Griffin, Julian, Gupta, Rishi, Harrison, Ewen, Hiscox, Julian, Ho, Antonia Ying Wai, Holden, Karl, Horby, Peter, Ijaz, Samreen, Khoo, Saye, Klenerman, Paul, Law, Andrew, Lewis, Matthew, Liggi, Sonia, Lim, Wei Shen, Maslen, Lynn, Mentzer, Alexander, Merson, Laura, Meynert, Alison, Moore, Shona, Noursadeghi, Mahdad, Olanipekun, Michael, Osagie, Anthonia, Palmarini, Massimo, Palmieri, Carlo, Paxton, William, Pollakis, Georgios, Price, Nicholas, Rambaut, Andrew, Robertson, David, Russell, Clark, Sancho-Shimizu, Vanessa, Sands, Caroline, Scott, Janet, Sigfrid, Louise, Solomon, Tom, Sriskandan, Shiranee, Stuart, David, Summers, Charlotte, Swann, Olivia, Takats, Zoltan, Takis, Panteleimon, Tedder, Richard, Thompson, A, Thomson, Emma, Thwaites, Ryan, Turtle, Lance Cw, Zambon, Maria, Drake, Thomas, Fairfield, Cameron, Knight, Stephen, Mclean, Kenneth, Murphy, Derek, Norman, Lisa, Pius, Riinu, Shaw, Catherine, Connor, Marie, Dalton, Jo, Gamble, Carrol, Girvan, Michelle, Halpin, Sophie, Harrison, Janet, Jackson, Clare, Lee, James, Marsh, Laura, Plotkin, Daniel, Roberts, Stephanie, Saviciute, Egle, Clohisey, Sara, Hendry, Ross, Knight, Susan, Lahnsteiner, Eva, Leeming, Gary, Norris, Lucy, Scott-Brown, James, Tait, Sarah, Wham, Murray, Clark, Richard, Coutts, Audrey, Donnelly, Lorna, Fawkes, Angie, Gilchrist, Tammy, Hafezi, Katarzyna, Macgillivray, Louise, Maclean, Alan, Mccafferty, Sarah, Morrice, Kirstie, Murphy, Lee, Wrobel, Nicola, Adeniji, Kayode, Agranoff, Daniel, Agwuh, Ken, Ail, Dhiraj, Aldera, Erin, Alegria, Ana, Allen, Sam, Angus, Brian, Ashish, Abdul, Atkinson, Dougal, Bari, Shahedal, Barlow, Gavin, Barnass, Stella, Barrett, Nicholas, Bassford, Christopher, Basude, Sneha, Baxter, David, Beadsworth, Michael, Bernatoniene, Jolanta, Berridge, John, Berry, Colin, Best, Nicola, Bothma, Pieter, Brittain-Long, Robin, Bulteel, Naomi, Burden, Tom, Burtenshaw, Andrew, Caruth, Vikki, Chadwick, David, Chambler, Duncan, Chee, Nigel, Child, Jenny, Chukkambotla, Srikanth, Clark, Tom, Collini, Paul, Cosgrove, Catherine, Cupitt, Jason, Cutino-Moguel, Maria-Teresa, Dark, Paul, Dawson, Chris, Dervisevic, Samir, Donnison, Phil, Douthwaite, Sam, Drummond, Andrew, Durand, Ingrid, Dushianthan, Ahilanadan, Dyer, Tristan, Evans, Cariad, Eziefula, Chi, Fegan, Chrisopher, Finn, Adam, Fullerton, Duncan, Garg, Sanjeev, Garg, Atul, Gkrania-Klotsas, Effrossyni, Godden, Jo, Goldsmith, Arthur, Graham, Clive, Grammatikopoulos, Tassos, Hardy, Elaine, Hartshorn, Stuart, Harvey, Daniel, Havalda, Peter, Hawcutt, Daniel, Hobrok, Maria, Hodgson, Luke, Hormis, Anil, Howard, Joanne, Jacobs, Michael, Jain, Susan, Jennings, Paul, Kaliappan, Agilan, Kasipandian, Vidya, Kegg, Stephen, Kelsey, Michael, Kendall, Jason, Kerrison, Caroline, Kerslake, Ian, Koch, Oliver, Koduri, Gouri, Koshy, George, Laha, Shondipon, Laird, Steven, Larkin, Susan, Leiner, Tamas, Lillie, Patrick, Limb, James, Linnett, Vanessa, Little, Jeff, Lyttle, Mark, Macmahon, Michael, Macnaughton, Emily, Mankregod, Ravish, Masson, Huw, Matovu, Elijah, Mccullough, Katherine, Mcewen, Ruth, Meda, Manjula, Mills, Gary, Minton, Jane, Mirfenderesky, Mariyam, Mohandas, Kavya, Mok, Quen, Moon, James, Moore, Elinoor, Morgan, Patrick, Morris, Craig, Mortimore, Katherine, Moses, Samuel, Mpenge, Mbiye, Mulla, Rohinton, Murphy, Michael, Nagarajan, Thapas, Nagel, Megan, Nelson, Mark, Norris, Lillian, O'Shea, Matthew, Ostermann, Marlies, Otahal, Igor, Pais, Mark, Panchatsharam, Selva, Papakonstantinou, Danai, Papineni, Padmasayee, Paraiso, Hassan, Patel, Brij, Pattison, Natalie, Pepperell, Justin, Peters, Mark, Phull, Mandeep, Pintus, Stefania, Planche, Tim, Post, Frank, Price, David, Prout, Rachel, Rae, Nikolas, Reschreiter, Henrik, Reynolds, Tim, Richardson, Neil, Roberts, Mark, Roberts, Devender, Rose, Alistair, Rousseau, Guy, Ruge, Bobby, Ryan, Brendan, Saluja, Taranprit, Cole, Sarah, Schmid, Matthias, Shah, Aarti, Shankar-Hari, Manu, Shanmuga, Prad, Sharma, Anil, Shawcross, Anna, Pooni, Jagtur Singh, Sizer, Jeremy, Smith, Richard, Snelson, Catherine, Spittle, Nick, Staines, Nikki, Stambach, Tom, Stewart, Richard, Subudhi, Pradeep, Szakmany, Tamas, Tatham, Kate, Thomas, Jo, Thompson, Chris, Thompson, Robert, Tridente, Ascanio, Tupper-Carey, Darell, Twagira, Mary, Vallotton, Nick, Vancheeswaran, Rama, Vincent-Smith, Lisa, Visuvanathan, Shico, Vuylsteke, Alan, Waddy, Sam, Wake, Rachel, Walden, Andrew, Welters, Ingeborg, Whitehouse, Tony, Whittaker, Paul, Whittington, Ashley, Wijesinghe, Meme, Williams, Martin, Wilson, Lawrence, Winchester, Stephen, Wiselka, Martin, Wolverson, Adam, Wootton, Daniel, Workman, Andrew, Yates, Bryan, Young, Peter, Shaw, Victoria, Ahmed, Katie, Armstrong, Jane, Ashworth, Milton, Asiimwe, Innocent, Bakshi, Siddharth, Barlow, Samantha, Booth, Laura, Brennan, Benjamin, Bullock, Katie, Carlucci, Nicola, Cass, Emily, Catterall, Benjamin, Clark, Jordan, Clarke, Emily, Cooper, Louise, Cox, Helen, Davis, Christopher, Dincarslan, Oslem, Carracedo, Alejandra Doce, Dunn, Chris, Dyer, Philip, Elliott, Angela, Evans, Anthony, Finch, Lorna, Fisher, Lewis, Flaherty, Lisa, Foster, Terry, Garcia-Dorival, Isabel, Gunning, Philip, Hartley, Catherine, Holmes, Anthony, Jensen, Rebecca, Jones, Christopher, Jones, Trevor, Khandaker, Shadia, King, Katharine, Kiy, Robyn, Koukorava, Chrysa, Lake, Annette, Lant, Suzannah, Latawiec, Diane, Lavelle-Langham, Lara, Lefteri, Daniella, Lett, Lauren, Livoti, Lucia, Mancini, Maria, Massey, Hannah, Maziere, Nicole, Mcevoy, Laurence, Mclauchlan, John, Metelmann, Soeren, Miah, Nahida, Middleton, Joanna, Mitchell, Joyce, Murphy, Ellen, Penrice-Randal, Rebekah, Pilgrim, Jack, Prince, Tessa, Reynolds, Will, Ridley, P Matthew, Sales, Debby, Shears, Rebecca, Small, Benjamin, Subramaniam, Krishanthi, Szemiel, Agnieska, Taggart, Aislynn, Tanianis-Hughes, Jolanta, Thomas, Jordan, Trochu, Erwan, Tonder, Libby Van, Wilcock, Eve, Zhang, J Eunice, Keating, Seán, Donegan, Cara, Spencer, Rebecca, Donohue, Chloe, Griffiths, Fiona, Investigators, ISARIC4C, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, West of Scotland Specialist Virology Centre, Gartnavel General Hospital, Glasgow, National Heart and Lung Institute [London] (NHLI), Imperial College London-Royal Brompton and Harefield NHS Foundation Trust, University of Liverpool, Alder Hey Children's Hospital, Department of Infectious Disease Epidemiology [London] (DIDE), Imperial College London, Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Imperial College London - National Heart and Lung Institute, and Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK
Subjects: Infectious Diseases, PCR, rhinovirus, Oncology, SARS-CoV-2, [SDV]Life Sciences [q-bio], surveillance, disease severity, respiratory virus
Abstract: Background We conducted this study to assess the prevalence of viral coinfection in a well characterized cohort of hospitalized coronavirus disease 2019 (COVID-19) patients and to investigate the impact of coinfection on disease severity. Methods Multiplex real-time polymerase chain reaction testing for endemic respiratory viruses was performed on upper respiratory tract samples from 1002 patients with COVID-19, aged Results A coinfecting virus was detected in 20 (2.0%) participants. Multivariable analysis revealed no significant risk factors for coinfection, although this may be due to rarity of coinfection. Likewise, ordinal logistic regression analysis did not demonstrate a significant association between coinfection and increased disease severity. Conclusions Viral coinfection was rare among hospitalized COVID-19 patients in the United Kingdom during the first 18 months of the pandemic. With unbiased prospective sampling, we found no evidence of an association between viral coinfection and disease severity. Public health interventions disrupted normal seasonal transmission of respiratory viruses; relaxation of these measures mean it will be important to monitor the prevalence and impact of respiratory viral coinfections going forward.
Published: 2022

5. Basin-scale biogeochemical and ecological impacts of islands in the tropical Pacific Ocean

Author: Monique Messié, Anne Petrenko, Andrea M. Doglioli, Elodie Martinez, Séverine Alvain, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), and Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord])
Subjects: [SDU]Sciences of the Universe [physics], General Earth and Planetary Sciences
Abstract: International audience; In the relatively unproductive waters of the tropical ocean, islands can enhance phytoplankton biomass and create hotspots of productivity and biodiversity that sustain upper trophic levels, including fish that are crucial to the survival of islands' inhabitants. This phenomenon, termed the island mass effect 66 years ago, has been widely described. However, most studies focused on individual islands, and very few documented phytoplankton community composition. Consequently, basin-scale impacts on phytoplankton biomass, primary production and biodiversity remain largely unknown. Here we systematically identify enriched waters near islands from satellite chlorophyll concentrations (a proxy for phytoplankton biomass) to analyse the island mass effect for all tropical Pacific islands on a climatological basis. We find enrichments near 99% of islands, impacting 3% of the tropical Pacific Ocean. We quantify local and basin-scale increases in chlorophyll and primary production by contrasting island-enriched waters with nearby waters. We also reveal a significant impact on phytoplankton community structure and biodiversity that is identifiable in anomalies in the ocean colour signal. Our results suggest that, in addition to strong local biogeochemical impacts, islands may have even stronger and farther-reaching ecological impacts.
Published: 2022

6. A Global Ocean Oxygen Database and Atlas for Assessing and Predicting Deoxygenation and Ocean Health in the Open and Coastal Ocean

Author: Grégoire, Marilaure, Garçon, Véronique, Garcia, Hernan, Breitburg, Denise, Isensee, Kirsten, Oschlies, Andreas, Telszewski, Maciej, Barth, Alexander, Bittig, Henry C., Carstensen, Jacob, Carval, Thierry, Chai, Fei, Chavez, Francisco, Conley, Daniel, Coppola, Laurent, Crowe, Sean, Currie, Kim, Dai, Minhan, Deflandre, Bruno, Dewitte, Boris, Diaz, Robert, Garcia-Robledo, Emilio, Gilbert, Denis, Giorgetti, Alessandra, Glud, Ronnie, Gutierrez, Dimitri, Hosoda, Shigeki, Ishii, Masao, Jacinto, Gil, Langdon, Chris, Lauvset, Siv K., Levin, Lisa A., Limburg, Karin E., Mehrtens, Hela, Montes, Ivonne, Naqvi, Wajih, Paulmier, Aurélien, Pfeil, Benjamin, Pitcher, Grant, Pouliquen, Sylvie, Rabalais, Nancy, Rabouille, Christophe, Recape, Virginie, Roman, Michaël, Rose, Kenneth, Rudnick, Daniel, Rummer, Jodie, Schmechtig, Catherine, Schmidtko, Sunke, Seibel, Brad, Slomp, Caroline, Sumalia, U. Rashid, Tanhua, Toste, Thierry, Virginie, Uchida, Hiroshi, Wanninkhof, Rik, Yasuhara, Moriaki, Geochemistry, General geochemistry, Université de Liège, Centre National d'Études Spatiales [Toulouse] (CNES), National Oceanic and Atmospheric Administration (NOAA), Smithsonian Environmental Research Center (SERC), United Nations Educational, Scientific and Cultural Organization (UNESCO), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Institute of Oceanology, Polish Academy of Sciences (IO-PAN), Polska Akademia Nauk = Polish Academy of Sciences (PAN), GeoHydrodynamics and Environment Research (GHER), Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Aarhus University [Aarhus], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), University of Maine, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Lund University [Lund], 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), Department of Earth, Ocean and Atmospheric Sciences [Vancouver] (UBC EOAS), University of British Columbia (UBC), National Institute of Water and Atmospheric Research [Auckland] (NIWA), Xiamen University, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), University of Virginia, University of Cadiz, Maurice Lamontagne Institute, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy, Danish Meteorological Institute (DMI), Instituto Geofísico del Perú (IGP), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Meteorological Research Institute [Tsukuba] (MRI), Japan Meteorological Agency (JMA), University of the Philippines (UP System), Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami [Coral Gables], NORCE Norwegian Research Center, Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), State University of New York (SUNY), Council of Scientific and Industrial Research [India] (CSIR), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Bjerknes Centre for Climate Research (BCCR), Department of Biological Sciences [Bergen] (BIO / UiB), University of Bergen (UiB)-University of Bergen (UiB), University of Cape Town, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Observatoire de Versailles Saint-Quentin-en-Yvelines (OVSQ), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Department of Oceanography and Coastal Sciences, Louisiana State University (LSU), Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), University of Maryland System-University of Maryland System, The ARC Centre of Excellence for Coral Reefs Studies [Townsville, Australie] (ARC), The Scripps Research Institute [La Jolla, San Diego], College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Faculty of Geosciences [Utrecht], Utrecht University [Utrecht], The University of Hong Kong (HKU), 1190276, R20F0008-CEAZA, National Science Foundation, NSF: OCE-1840868, National Oceanic and Atmospheric Administration, NOAA: SFB754, Horizon, Fundação para a Ciência e a Tecnologia, FCT, Fonds De La Recherche Scientifique - FNRS, FNRS: T.1009.15, Belgian Federal Science Policy Office, BELSPO, Ministero dell’Istruzione, dell’Università e della Ricerca, MIUR, Norges Forskningsråd: 269753, All authors would like to thank IOC-UNESCO, International Ocean Carbon Coordination Project (IOCCP), NOAA, and the German SFB754. MG is funded by the Fonds National de la Recherche Scientifique (FRS-FNRS) and received fundings from the FNRS BENTHOX program grant T.1009.15, the Copernicus Marine Service (CMEMS), MG, VG, KI, and BDew are supported by the Project CE2COAST funded by ANR (FR), BELSPO (BE), FCT (PT), IZM (LV), MI (IE), MIUR (IT), Rannis (IS), and RCN (NO) through the 2019 ?Joint Transnational Call on Next Generation Climate Science in Europe for Oceans? initiated by JPI Climate and JPI Oceans. MT, KC, and VG acknowledge support from the United States National Science Foundation grant OCE-1840868 to the Scientific Committee on Oceanic Research (SCOR, United States). BoD also acknowledges support from ANID grants R20F0008-CEAZA and 1190276. CB, AP, VG, LC, BrD, VR, VT, and CS acknowledge support of the French CES ODATIS Oxygen through INSU funding. SKL acknowledges support from the Research Council of Norway (Grant No. 269753). This manuscript is a contribution to the UN Decade Global Ocean Oxygen (GOOD) Program., ANR-20-CE01-0021,CO2COAST,Analyse de la variabilité spatio-temporelle de pCO2 et du flux de CO2 à l'interface air-mer des eaux côtières globales sur les deux dernières décennies: une approche basée sur l'observation spatiale(2020), European Project: 869300,FutureMARES, and European Project: 0652976(2007)
Subjects: Global and Planetary Change, Ecology, observing, Ocean oxygen, deoxygenation, Ocean Engineering, Ocean observation, Aquatic Science, Environmental Science (miscellaneous), Oceanography, [SDU]Sciences of the Universe [physics], purl.org/pe-repo/ocde/ford#1.05.11 [https], atlas, data-products, mapping, open and coastal ocean, Life Below Water, oxygen, database, Water Science and Technology
Abstract: In this paper, we outline the need for a coordinated international effort toward the building of an open-access Global Ocean Oxygen Database and ATlas (GO 2DAT) complying with the FAIR principles (Findable, Accessible, Interoperable, and Reusable). GO 2DAT will combine data from the coastal and open ocean, as measured by the chemical Winkler titration method or by sensors (e.g., optodes, electrodes) from Eulerian and Lagrangian platforms (e.g., ships, moorings, profiling floats, gliders, ships of opportunities, marine mammals, cabled observatories). GO 2DAT will further adopt a community-agreed, fully documented metadata format and a consistent quality control (QC) procedure and quality flagging (QF) system. GO 2DAT will serve to support the development of advanced data analysis and biogeochemical models for improving our mapping, understanding and forecasting capabilities for ocean O 2 changes and deoxygenation trends. It will offer the opportunity to develop quality-controlled data synthesis products with unprecedented spatial (vertical and horizontal) and temporal (sub-seasonal to multi-decadal) resolution. These products will support model assessment, improvement and evaluation as well as the development of climate and ocean health indicators. They will further support the decision-making processes associated with the emerging blue economy, the conservation of marine resources and their associated ecosystem services and the development of management tools required by a diverse community of users (e.g., environmental agencies, aquaculture, and fishing sectors). A better knowledge base of the spatial and temporal variations of marine O 2 will improve our understanding of the ocean O 2 budget, and allow better quantification of the Earth’s carbon and heat budgets. With the ever-increasing need to protect and sustainably manage ocean services, GO 2DAT will allow scientists to fully harness the increasing volumes of O 2 data already delivered by the expanding global ocean observing system and enable smooth incorporation of much higher quantities of data from autonomous platforms in the open ocean and coastal areas into comprehensive data products in the years to come. This paper aims at engaging the community (e.g., scientists, data managers, policy makers, service users) toward the development of GO 2DAT within the framework of the UN Global Ocean Oxygen Decade (GOOD) program recently endorsed by IOC-UNESCO. A roadmap toward GO 2DAT is proposed highlighting the efforts needed (e.g., in terms of human resources).
Published: 2021

7. Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities

Author: Robert J. Miller, Francisco P. Chavez, Thomas Lamy, Christie E. Yorke, Kathleen J. Pitz, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Marine Science Institute [Santa Barbara] (MSI), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC)-University of California (UC), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), University of California [Santa Barbara] (UCSB), and University of California-University of California
Subjects: 0106 biological sciences, 0301 basic medicine, Science, [SDE.MCG]Environmental Sciences/Global Changes, Beta diversity, Biodiversity, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Environmental DNA, Community ecology, 14. Life underwater, Multidisciplinary, Conservation biology, Ecology, 15. Life on land, DNA, Environmental, Kelp forest, Kelp, 030104 developmental biology, Geography, Spatial ecology, Medicine, Spatial variability, Species richness, Molecular ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Monitoring
Abstract: Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifies species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms offers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fish communities on temperate rocky reefs in southern California. eDNA provided a more-detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species filtering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. Based on historical records in the region (2000–2018) we found that 6.9 times more UVC samples would be required to detect 50 taxa compared to eDNA. Our results show that eDNA metabarcoding can outperform diver counts to capture the spatial patterns in biodiversity at fine scales with less field effort and more power than traditional methods, supporting the notion that eDNA is a critical scientific tool for detecting biodiversity changes in aquatic ecosystems.
Published: 2021

8. Technical note: Interpreting pH changes

Author: Andrew G. Dickson, James C. Orr, Andrea J. Fassbender, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Modelling the Earth Response to Multiple Anthropogenic Interactions and Dynamics (MERMAID), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Scripps Institution of Oceanography (SIO - UC San Diego), University of California (UC)-University of California (UC), and ANR-16-CE01-0014,SOBUMS,Comprendre la réponse du cycle du carbone dans l'océan austral au stress climatique(2016)
Subjects: 0106 biological sciences, Hydrogen ion, 010504 meteorology & atmospheric sciences, lcsh:Life, Analytical chemistry, Ph changes, 01 natural sciences, lcsh:QH540-549.5, TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Earth-Surface Processes, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Chemistry, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Technical note, Ocean acidification, lcsh:Geology, lcsh:QH501-531, 13. Climate action, Spatial ecology, Absolute Change, lcsh:Ecology
Abstract: The number and quality of ocean pH measurements have increased substantially over the past few decades such that trends, variability, and spatial patterns of change are now being evaluated. However, comparing pH changes across domains with different initial pH values can be misleading because a pH change reflects a relative change in the hydrogen ion concentration ([H+], expressed in mol kg−1) rather than an absolute change in [H+]. We recommend that [H+] be used in addition to pH when describing such changes and provide three examples illustrating why.
Published: 2021

9. Small phytoplankton dominate western North Atlantic biomass

Author: Emmanuel Boss, Chang Jae Choi, Jason R. Graff, Nils Haëntjens, Robert T. O'Malley, Stephen J. Giovannoni, Françoise Morison, Toby K. Westberry, Alexandra Z. Worden, Peter Gaube, Lee Karp-Boss, Alison Chase, Michael J. Behrenfeld, Luis M. Bolaños, Susanne Menden-Deuer, Alice Della Penna, Oregon State University (OSU), University of Maine, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Department of Botany and Plant Pathology, Applied Physics Laboratory [Seattle] (APL-UW), University of Washington [Seattle], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Rhode Island (URI), This research was supported by NASA NAAMES grant no. NNX15AE70G. We thank Mark Dasenko and Oregon State University CGRB for amplicon library preparation and sequencing. We thank Captains A. Lund and D. Bergeron and R/V Atlantis crew. We thank the NAAMES community for their input. This study has been conducted using E.U. Copernicus Marine Service Information (CMEMS) and the Group for High Resolution Sea Surface Temperature (GHRSST) Multi-scale Ultra-high Resolution (MUR) SST data (obtained from the NASA EOSDIS Physical Oceanography Distributed Active Archive Center (PO.DAAC) at the Jet Propulsion Laboratory, Pasadena, CA). Phylogenetic analyses were supported in part by GBMF3788 and NSF DEB-1639033 to AZW. A. DP is grateful for the support of the Applied Physics Laboratory Science and Engineering Enrichment Development (SEED) fellowship and of funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 749591. We thank Mimi Lyon-Edmondson, Faith Hoyle, Emma Jourdain, Emma Dullaert and Gretchen Spencer for assistance with the classification of IFCB images., and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Water microbiology, Water mass, lineages, 010504 meteorology & atmospheric sciences, Cyanobacteria, 01 natural sciences, Microbiology, Article, diversity, 03 medical and health sciences, Algae, Phytoplankton, 14. Life underwater, Biomass, nanoplankton, Ecology, Evolution, Behavior and Systematics, Microbial biooceanography, 030304 developmental biology, 0105 earth and related environmental sciences, Diatoms, 0303 health sciences, Biomass (ecology), biology, variability, ACL, carbon, time-series, Community structure, Spring bloom, Plankton, Biogeochemistry, biology.organism_classification, Annual cycle, ocean, Oceanography, 13. Climate action, Seasons, fluorescence, Molecular ecology, community structure, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, export
Abstract: WOS:000522382500001; International audience; The North Atlantic phytoplankton spring bloom is the pinnacle in an annual cycle that is driven by physical, chemical, and biological seasonality. Despite its important contributions to the global carbon cycle, transitions in plankton community composition between the winter and spring have been scarcely examined in the North Atlantic. Phytoplankton composition in early winter was compared with latitudinal transects that captured the subsequent spring bloom climax. Amplicon sequence variants (ASVs), imaging flow cytometry, and flow-cytometry provided a synoptic view of phytoplankton diversity. Phytoplankton communities were not uniform across the sites studied, but rather mapped with apparent fidelity onto subpolar- and subtropical-influenced water masses of the North Atlantic. At most stations, cells \textless 20-mu m diameter were the main contributors to phytoplankton biomass. Winter phytoplankton communities were dominated by cyanobacteria and pico-phytoeukaryotes. These transitioned to more diverse and dynamic spring communities in which pico- and nano-phytoeukaryotes, including many prasinophyte algae, dominated. Diatoms, which are often assumed to be the dominant phytoplankton in blooms, were contributors but not the major component of biomass. We show that diverse, small phytoplankton taxa are unexpectedly common in the western North Atlantic and that regional influences play a large role in modulating community transitions during the seasonal progression of blooms.
Published: 2020

10. The delayed island mass effect: How islands can remotely trigger blooms in the oligotrophic ocean

Author: Sophie Bonnet, Anne Petrenko, Clement Aldebert, Thierry Moutin, Monique Messié, Elodie Martinez, Andrea Doglioli, Guillaume Koenig, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Horizon 2020, and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, 01 natural sciences, Algal bloom, Lagrangian analysis, 14. Life underwater, oligotrophic ocean, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 010604 marine biology & hydrobiology, Mass effect, fungi, phytoplankton bloom, 15. Life on land, nutrient supply, Geophysics, Oceanography, nitrogen fixation, 13. Climate action, Nitrogen fixation, island mass effect, General Earth and Planetary Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: In oligotrophic gyres of the tropical ocean, islands can enhance phytoplankton biomass and create hotspots of productivity and biodiversity. This “Island Mass Effect” (IME) is typically identified by increased chlorophyll concentrations next to an island. Here we use a simple plankton model in a Lagrangian framework to represent an unexplained open ocean bloom, demonstrating how islands could have triggered it remotely. This new type of IME, termed “delayed IME”, occurs when nitrate is limiting, N:P ratios are low, and excess phosphate and iron remain in water masses after an initial bloom associated to a “classical” IME. Nitrogen fixers then slowly utilize leftover phosphate and iron while water masses get advected away, resulting in a bloom decoupled in time (several weeks) and space (hundreds of km) from island‐driven nutrient supply. This study suggests that the fertilizing effect of islands on phytoplankton may have been largely underestimated. Plain language summary In the poor and nutrient‐depleted waters of the tropical Pacific, islands act as sources of nutrients fertilizing nearby waters. These nutrients are consumed by microscopic photosynthesizing algae, the phytoplankton. The resulting phytoplankton enrichments (blooms) in turn support productive ecosystems. This phenomenon, termed the “island mass effect”, has been known for sixty years and is classically defined by increased chlorophyll (representing phytoplankton biomass) next to an island. Blooms also occur in the open ocean and are usually attributed to vertical processes such as mixing or uplifting that locally supply nutrients from subsurface reservoirs. In this paper, we demonstrate that a different type of island mass effect exists, where the phytoplankton response is delayed because they grow very slowly. These blooms are supported by the nitrogen fixer Trichodesmium. Since phytoplankton get carried away from islands by oceanic currents while they grow, this can lead to a bloom located hundreds of km away with no apparent connection to the islands. Nutrient inputs by islands followed by advection can thus trigger remote blooms in the open ocean. Our study suggests that the fertilizing effect of islands may currently be largely underestimated, particularly in the warm waters of the tropical Pacific where Trichodesmimum is common.
Published: 2020

11. Research Priorities for Achieving Healthy Marine Ecosystems and Human Communities in a Changing Climate

Author: Whitney R. Friedman, Benjamin S. Halpern, Elizabeth McLeod, Michael W. Beck, Carlos M. Duarte, Carrie V. Kappel, Arielle Levine, Robert D. Sluka, Steven Adler, Casey C. O’Hara, Eleanor J. Sterling, Sebastian Tapia-Lewin, Iñigo J. Losada, Tim R. McClanahan, Linwood Pendleton, Margaret Spring, James P. Toomey, Kenneth R. Weiss, Hugh P. Possingham, Jensen R. Montambault, Universidad de Cantabria, University of California, The Nature Conservancy, King Abdullah University of Science and Technology (KAUST), San Diego State University (SDSU), University of California [Santa Barbara] (UCSB), American Museum of Natural History (AMNH), University of Cantabria, Wildlife Conservation Society (WCS), Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Public Health Genomics Unit, University of Queensland [Brisbane], Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), University of California (UC), and University of California [Santa Barbara] (UC Santa Barbara)
Subjects: 0106 biological sciences, social equity, 010504 meteorology & atmospheric sciences, Ecological health, lcsh:QH1-199.5, [SDE.MCG]Environmental Sciences/Global Changes, media_common.quotation_subject, Ocean Engineering, Context (language use), Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, Oceanography, human health, 01 natural sciences, [SHS]Humanities and Social Sciences, marine sustainability, Need to know, Multidisciplinary approach, Political science, 11. Sustainability, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, lcsh:Science, Environmental planning, 0105 earth and related environmental sciences, Water Science and Technology, media_common, Global and Planetary Change, priority research, Equity (economics), 010604 marine biology & hydrobiology, sustainable development goals, [SDE.ES]Environmental Sciences/Environmental and Society, climate change, 13. Climate action, [SDE]Environmental Sciences, Sustainability, lcsh:Q, Psychological resilience, Social equality
Abstract: International audience; The health of coastal human communities and marine ecosystems are at risk from a host of anthropogenic stressors, in particular, climate change. Because ecological health and human well-being are inextricably connected, effective and positive responses to current risks require multidisciplinary solutions. Yet, the complexity of coupled social–ecological systems has left many potential solutions unidentified or insufficiently explored. The urgent need to achieve positive social and ecological outcomes across local and global scales necessitates rapid and targeted multidisciplinary research to identify solutions that have the greatest chance of promoting benefits for both people and nature. To address these challenges, we conducted a forecasting exercise with a diverse, multidisciplinary team to identify priority research questions needed to promote sustainable and just marine social–ecological systems now and into the future, within the context of climate change and population growth. In contrast to the traditional reactive cycle of science and management, we aimed to generate questions that focus on what we need to know, before we need to know it. Participants were presented with the question, “If we were managing oceans in 2050 and looking back, what research, primary or synthetic, would wish we had invested in today?” We first identified major social and ecological events over the past 60 years that shaped current human relationships with coasts and oceans. We then used a modified Delphi approach to identify nine priority research areas and 46 questions focused on increasing sustainability and well-being in marine social–ecological systems. The research areas we identified include relationships between ecological and human health, access to resources, equity, governance, economics, resilience, and technology. Most questions require increased collaboration across traditionally distinct disciplines and sectors for successful study and implementation. By identifying these questions, we hope to facilitate the discourse, research, and policies needed to rapidly promote healthy marine ecosystems and the human communities that depend upon them. © Copyright © 2020 Friedman, Halpern, McLeod, Beck, Duarte, Kappel, Levine, Sluka, Adler, O’Hara, Sterling, Tapia-Lewin, Losada, McClanahan, Pendleton, Spring, Toomey, Weiss, Possingham and Montambault.
Published: 2020

12. Reemergence of anthropogenic carbon into the ocean's mixed layer strongly amplifies transient climate sensitivity

Author: Andrea J. Fassbender, Sarah Schlunegger, Masao Ishii, Keith B. Rodgers, Thomas L. Frölicher, Katsuya Toyama, Yves Plancherel, Olivier Aumont, Richard D. Slater, Pusan National University, Princeton University, Japan Meteorological Agency (JMA), University of Bern, Oeschger Centre for Climate Change Research (OCCR), Grantham Institute for Climate Change and the Environment, Imperial College London, 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), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, European Project: 8209899(1982), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), 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 de Paris (UP)-École normale supérieure - Paris (ENS Paris), 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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), and 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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)
Subjects: EFFICIENCY, 010504 meteorology & atmospheric sciences, Mixed layer, 530 Physics, %22">ocean, chemistry.chemical_element, Flux, feedback, BUDGET, %22">feedback, 010502 geochemistry & geophysics, Atmospheric sciences, 01 natural sciences, Carbon cycle, Atmosphere, carbon cycle, Meteorology & Atmospheric Sciences, 14. Life underwater, Geosciences, Multidisciplinary, ATMOSPHERIC CO2, FORMULATION, 0105 earth and related environmental sciences, %22">carbon cycle, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Science & Technology, FEEDBACK, Geology, modeling, ocean, Geophysics, chemistry, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, 13. Climate action, Physical Sciences, %22">modeling, General Earth and Planetary Sciences, Environmental science, Climate sensitivity, Seawater, Transient (oscillation), Carbon, SYSTEM, DIOXIDE
Abstract: International audience; A positive marine chemistry‐climate feedback was originally proposed by Revelle and Suess (1957, https://doi.org/10.3402/tellusa.v9i1.9075), whereby the invasion flux of anthropogenic carbon into the ocean serves to inhibit future marine CO2 uptake through reductions to the buffering capacity of surface seawater. Here we use an ocean circulation‐carbon cycle model to identify an upper limit on the impact of reemergence of anthropogenic carbon into the ocean's mixed layer on the cumulative airborne fraction of CO2 in the atmosphere. We find under an RCP8.5 emissions pathway (with steady circulation) that the cumulative airborne fraction of CO2 has a sevenfold reduction by 2100 when the CO2 buffering capacity of surface seawater is maintained at preindustrial levels. Our results indicate that the effect of reemergence of anthropogenic carbon into the mixed layer on the buffering capacity of CO2 amplifies the transient climate sensitivity of the Earth system.
Published: 2020

13. Inhibiting Pathogen Surface Adherence by Multilayer Polyelectrolyte Films Functionalized with Glucofuranose Derivatives

Author: Hernán E. Ríos, Angel Leiva, Francisco P. Chávez, Mohammed Ahmar, Valeria Villalobos, Marcela D. Urzúa, Jorge Pavez, Jenny M. Blamey, Yves Queneau, Carlos P. Silva, Centre d'Etudes en Sciences Sociales sur les Mondes Africains, Américains et Asiatiques (CESSMA), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD [France-Nord]), High-Assurance Software Laboratory [Braga, Portugal] ( HASLab ), University of Minho [Braga]-Institute for Systems and Computer Engineering, Technology and Science [Porto] (INESC TEC), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), and Monterey Bay Aquarium Research Institute
Subjects: Materials science, Surface Properties, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Biofilm, 02 engineering and technology, Microscopy, Atomic Force, 010402 general chemistry, 021001 nanoscience & nanotechnology, Polyelectrolytes, 01 natural sciences, Combinatorial chemistry, Polyelectrolyte, Anti-Bacterial Agents, 0104 chemical sciences, Biofilms, Wettability, General Materials Science, 0210 nano-technology, S typhimurium, Pathogen, ComputingMilieux_MISCELLANEOUS
Abstract: Inhibiting pathogenic bacterial adherence on surfaces is an ongoing challenge to prevent the development of biofilms. Multilayer polyelectrolyte films are feasible antibacterial materials. Here, we have designed new films made of carbohydrate polyelectrolytes to obtain antibacterial coatings that prevent biofilm formation. The polyelectrolyte films were constructed from poly(maleic anhydride- alt-styrene) functionalized with glucofuranose derivatives and quaternized poly(4-vinylpyridine) N-alkyl. These films prevent Pseudomonas aeruginosa and Salmonella Typhimurium, two important bacterial contaminants in clinical environments, from adhering to surfaces. When the film was composed of more than 10 layers, the bacterial population was greatly reduced, while the bacteria remaining on the film were morphologically damaged, as atomic force microscopy revealed. The antibacterial capacity of the polyelectrolyte films was determined by the combination of thickness, wettability, surface energy, and most importantly, the conformation that polyelectrolytes adopt the function of nature of the carbohydrate group. This polyelectrolyte film constitutes the first green approach to preventing pathogenic bacterial surface adherence and proliferation without killing the bacterial pathogen.
Published: 2018

14. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

Author: Worden, Alexandra [Monterey Bay Aquarium Research Institute, Moss Landing, CA (United States); Canadian Institute for Advanced Research, Toronto (Canada)]
Published: 2016
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15. Distribution and quantification of bioluminescence as an ecological trait in the deep sea benthos

Author: Jérôme Mallefet, Séverine Martini, Steven H. D. Haddock, Linda A. Kuhnz, 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), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Université Catholique de Louvain = Catholic University of Louvain (UCL), and UCL - SST/ELI/ELIB - Biodiversity
Subjects: 0106 biological sciences, Seamount, lcsh:Medicine, Remotely operated vehicle, 010603 evolutionary biology, 01 natural sciences, Deep sea, Article, Benthos, 14. Life underwater, lcsh:Science, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, geography, Multidisciplinary, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, lcsh:R, Pelagic zone, Biodiversity, Habitat, Benthic zone, Environmental science, lcsh:Q, Bay
Abstract: Bioluminescence is a prominent functional trait used for visual communication. A recent quantification showed that in pelagic ecosystems more than 75% of individual macro-planktonic organisms are categorized as able to emit light. In benthic ecosystems, only a few censuses have been done, and were based on a limited number of observations. In this study, our dataset is based on observations from remotely operated vehicle (ROV) dives conducted from 1991–2016, spanning 0–3,972 m depth. Data were collected in the greater Monterey Bay area in central California, USA and include 369,326 pelagic and 154,275 epibenthic observations at Davidson Seamount, Guide Seamount, Sur Ridge and Monterey Bay. Because direct observation of in situ bioluminescence remains a technical challenge, taxa from ROV observations were categorized based on knowledge gained from the literature to assess bioluminescence status. We found that between 30–41% of the individual observed benthic organisms were categorized as capable of emitting light, with a strong difference between benthic and pelagic ecosystems. We conclude that overall variability in the distribution of bioluminescent organisms is related to the major differences between benthic and pelagic habitats in the deep ocean. This study may serve as the basis of future investigations linking the optical properties of various habitats and the variability of bioluminescent organism distributions.
Published: 2019

16. Global Perspectives on Observing Ocean Boundary Current Systems

Author: Robert E. Todd, Francisco P. Chavez, Sophie Clayton, Sophie Cravatte, Marlos Goes, Michelle Graco, Xiaopei Lin, Janet Sprintall, Nathalie V. Zilberman, Matthew Archer, Javier Arístegui, Magdalena Balmaseda, John M. Bane, Molly O. Baringer, John A. Barth, Lisa M. Beal, Peter Brandt, Paulo H. R. Calil, Edmo Campos, Luca R. Centurioni, Maria Paz Chidichimo, Mauro Cirano, Meghan F. Cronin, Enrique N. Curchitser, Russ E. Davis, Marcus Dengler, Brad deYoung, Shenfu Dong, Ruben Escribano, Andrea J. Fassbender, Sarah E. Fawcett, Ming Feng, Gustavo J. Goni, Alison R. Gray, Dimitri Gutiérrez, Dave Hebert, Rebecca Hummels, Shin-ichi Ito, Marjorlaine Krug, François Lacan, Lucas Laurindo, Alban Lazar, Craig M. Lee, Matthieu Lengaigne, Naomi M. Levine, John Middleton, Ivonne Montes, Mike Muglia, Takeyoshi Nagai, Hilary I. Palevsky, Jaime B. Palter, Helen E. Phillips, Alberto Piola, Albert J. Plueddemann, Bo Qiu, Regina R. Rodrigues, Moninya Roughan, Daniel L. Rudnick, Ryan R. Rykaczewski, Martin Saraceno, Harvey Seim, Alex Sen Gupta, Lynne Shannon, Bernadette M. Sloyan, Adrienne J. Sutton, LuAnne Thompson, Anja K. van der Plas, Denis Volkov, John Wilkin, Dongxiao Zhang, Linlin Zhang, Woods Hole Oceanographic Institution (WHOI), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Océan du Large et Variabilité Climatique (OLVAC), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Instituto del Mar del Peru (IMARPE), Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, Fac. Ciencias del Mar, University of Las Palmas de Gran Canaria (ULPGC), European Centre for Medium-Range Weather Forecasts (ECMWF), Université Grenoble Alpes - Institut d'urbanisme et de géographie alpine (IUGA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Coastal & Marine Research Centre, University College Cork (UCC), Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), National Oceanic and Atmospheric Administration (NOAA), Millennium Institute of Oceanography, Universidad de Concepción [Chile], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Direccion de Investigaciones Oceanograficas, Océan et variabilité du climat (VARCLIM), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), 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 de Paris (UP)-École normale supérieure - Paris (ENS Paris), 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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-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)-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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), University of Southern California (USC), Departamento de Oceanografía [Concepción], Departamento de Oceanografia, Servicio de Hidrografía Naval, School of Ocean and Earth Science and Technology (SOEST), University of Hawai‘i [Mānoa] (UHM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Climate Change Research Centre [Sydney] (CCRC), University of New South Wales [Sydney] (UNSW), Marine Research Institute and Department of Biological Sciences, University of Cape Town, CSIRO, Oceans and Atmosphere, Hobart, TAS, Australia, Rutgers University System (Rutgers), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Scripps Institution of Oceanography (SIO - UC San Diego), University of California (UC)-University of California (UC), Universidad de Concepción - University of Concepcion [Chile], 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)), and 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)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, lcsh:QH1-199.5, Computer science, Climate system, Ocean Engineering, Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, drifters, Oceanography, 01 natural sciences, purl.org/becyt/ford/1 [https], purl.org/becyt/ford/1.5 [https], eastern boundary current systems, remote sensing, ocean observing systems, Global network, moorings, 14. Life underwater, western boundary current systems, lcsh:Science, ddc:3, 0105 earth and related environmental sciences, Water Science and Technology, Global Ocean Observing System, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, business.industry, 010604 marine biology & hydrobiology, Environmental resource management, Ocean current, article, autonomous underwater gliders, Boundary current, 13. Climate action, ddc:333.7, lcsh:Q, Current (fluid), time series, business
Abstract: Ocean boundary current systems are key components of the climate system, are home to highly productive ecosystems, and have numerous societal impacts. Establishment of a global network of boundary current observing systems is a critical part of ongoing development of the Global Ocean Observing System. The characteristics of boundary current systems are reviewed, focusing on scientific and societal motivations for sustained observing. Techniques currently used to observe boundary current systems are reviewed, followed by a census of the current state of boundary current observing systems globally. The next steps in the development of boundary current observing systems are considered, leading to several specific recommendations. Fil: Todd, Robert E.. Woods Hole Oceanographic Institution; Estados Unidos Fil: Chavez, Francisco. Monterey Bay Aquarium Research Institute; Estados Unidos Fil: Clayton, Sophie. Old Dominion University; Estados Unidos Fil: Cravatte, Sophie E.. Centre National de la Recherche Scientifique. Institut de Recherche pour le Développement; Francia. Universite de Toulouse; Francia Fil: Goes, Marlos P.. University of Miami; Estados Unidos Fil: Graco, Michelle I.. Instituto del Mar del Peru; Perú Fil: Lin, Xiaopei. Ocean University of China; China Fil: Sprintall, Janet. University of California; Estados Unidos Fil: Zilberman, Nathalie V.. University of California; Estados Unidos Fil: Archer, Matthew. California Institute of Technology; Estados Unidos Fil: Arístegui, Javier. Universidad de Las Palmas de Gran Canaria; España Fil: Balmaseda, Magdalena A.. European Centre for Medium-Range Weather Forecasts; Reino Unido Fil: Bane, John M.. University of North Carolina; Estados Unidos Fil: Baringer, Molly O.. Atlantic Oceanographic and Meteorological Laboratory ; Estados Unidos Fil: Barth, John A.. State University of Oregon; Estados Unidos Fil: Beal, Lisa M.. University of Miami; Estados Unidos Fil: Brandt, Peter. Geomar-Helmholtz Centre for Ocean Research Kiel; Alemania Fil: Calil, Paulo H.. Universidade Federal do Rio Grande; Brasil Fil: Campos, Edmo. Universidade de Sao Paulo; Brasil Fil: Centurioni, Luca R.. University of California; Estados Unidos Fil: Chidichimo, María Paz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Ministerio de Defensa. Armada Argentina. Servicio de Hidrografía Naval; Argentina Fil: Cirano, Mauro. Universidade Federal do Rio de Janeiro; Brasil Fil: Cronin, Meghan F.. National Oceanic and Atmospheric Administration. Pacific Marine Environmental Laboratory; Estados Unidos Fil: Curchitser, Enrique N.. Rutgers University; Estados Unidos Fil: Davis, Russ E.. University of California; Estados Unidos Fil: Dengler, Marcus. Geomar-Helmholtz Centre for Ocean Research Kiel; Alemania Fil: DeYoung, Brad. Memorial University of Newfoundland; Canadá Fil: Dong, Shenfu. University of Miami; Estados Unidos Fil: Escribano, Ruben. Universidad de Concepción; Chile Fil: Fassbender, Andrea J.. Monterey Bay Aquarium Research Institute; Estados Unidos
Published: 2019

17. Using fluorescence and bioluminescence sensors to characterize auto- and heterotrophic plankton communities

Author: Igor Shulman, Monique Messié, Séverine Martini, Steven H. D. Haddock, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Naval Research Laboratory at Stennis Space Center (NRL-SSC), Naval Research Laboratory (NRL), 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 Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Villefranche-sur-mer (OOVM), and 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)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, 010604 marine biology & hydrobiology, fungi, Heterotroph, Geology, Aquatic Science, Plankton, 01 natural sciences, Zooplankton, Oceanography, 13. Climate action, Phytoplankton, [SDE]Environmental Sciences, Bioluminescence, Upwelling, Environmental science, 14. Life underwater, Autotroph, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay, 0105 earth and related environmental sciences
Abstract: International audience; High-resolution autonomous sensors routinely measure physical (temperature, salinity), chemical (oxygen, nutrients) and biological (fluorescence) parameters. However, while fluorescence provides a proxy for phyto-plankton, heterotrophic populations remain challenging to monitor in real-time and at high resolution. Bathyphotometers, sensors which measure the light emitted by bioluminescent organisms when mechanically stimulated, provide the capability to identify bioluminescent dinoflagellates and zooplankton. In the coastal ocean, highly abundant dinoflagellates emitting low-intensity flashes generate a background bioluminescence signal, while rarer zooplankton emit bright flashes that can be individually resolved by high-frequency sensors. Bathyphotometers were deployed from ships and onboard autonomous underwater vehicles (AUVs) during three field campaigns in Monterey Bay, California. Ship-based in situ water samples were simultaneously collected and the plankton communities characterized. Plankton concentrations were matched with concurrent datasets of fluorescence and bioluminescence to develop proxies for autotrophic and heterotrophic dinoflagellates, other phytoplankton such as diatoms, copepods, larvaceans (appendicularians), and small jellies. The method extracts the bioluminescence background as a proxy for dinoflagellates, and exploits differences in bioluminescence flash intensity between several types of zooplankton to identify larvaceans, copepods and small jellies. Fluorescence is used to discriminate between autotrophic and heterotrophic dinoflagellates, and to identify other autotrophic plankton. Concurrent fluorometers and bathyphotometers onboard AUVs can thus provide a novel view of plankton diversity and phytoplankton/zooplankton interactions in the sea.
Published: 2019

18. Area-only method for underwater object tracking using autonomous vehicles

Author: Tom O'Reilly, Joaquin Del-Rio, Kakani Katija, Jacopo Aguzzi, I. Masmitja, Brian Kieft, Pierre-Jean Bouvet, Spartacus Gomáriz, Clara Fannjiang, Universitat Politècnica de Catalunya [Barcelona] (UPC), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Systèmes Embarqués, Acoustique et Télécommunications (LABISEN-SEACOM), Laboratoire ISEN (L@BISEN), Institut supérieur de l'électronique et du numérique (ISEN)-YNCREA OUEST (YO)-Institut supérieur de l'électronique et du numérique (ISEN)-YNCREA OUEST (YO), Department of Electrical Engineering and Computer Science [Berkeley] (EECS), University of California [Berkeley], and University of California-University of California
Subjects: 0106 biological sciences, [SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], 0209 industrial biotechnology, business.industry, Computer science, 010604 marine biology & hydrobiology, Real-time computing, Glider, Tracking system, 02 engineering and technology, Field tests, Tracking (particle physics), Track (rail transport), 01 natural sciences, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], 020901 industrial engineering & automation, Video tracking, 14. Life underwater, Underwater, business, Hidden Markov model, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, ComputingMilieux_MISCELLANEOUS
Abstract: OCEANS 2019, 17-20 June 2019, Marseille.-- 9 pages, 6 figures, 1 table, The use of autonomous underwater vehicles for ocean research has increased as they have a better cost/performance ratio than crewed oceanographic vessels. For example, autonomous vehicles (e.g. a Wave Glider) can be used to localise and track underwater targets. Whereas other researchers have been focused on target tracking using acoustic modems, here we present a novelty method called area-only target tracking. This method works with commercially available acoustic tags, thereby reducing the costs and complexity over other tracking systems. Moreover, this method can be used to track small targets such as jellyfishes due to the tag's size. The methodology behind the area-only technique is shown, and results from the first field tests conducted in Monterey Bay area are also presented.
Published: 2019

19. A BGC-Argo Guide: Planning, Deployment, Data Handling and Usage

Author: Bittig, Henry C., Maurer, Tanya L., Plant, Joshua N., Schmechtig, Catherine, Wong, Annie P. S., Claustre, Hervé, Trull, Thomas W., Udaya Bhaskar, T. V. S., Boss, Emmanuel, Dall’olmo, Giorgio, Organelli, Emanuele, Poteau, Antoine, Johnson, Kenneth S., Hanstein, Craig, Leymarie, Edouard, Le Reste, Serge, Riser, Stephen C., Rupan, A. Rick, Taillandier, Vincent, Thierry, Virginie, Xing, Xiaogang, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Observatoire des sciences de l'univers Ecce Terra (ECCE TERRA), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), University of Maine, Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, 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), REM/RDT/SI2M, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Unité de Mécanique (UME), École Nationale Supérieure de Techniques Avancées (ENSTA Paris), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Observatoire des sciences de l'univers Ecce Terra [Paris] (ECCE TERRA), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Observatoire des sciences de l'univers Ecce Terra [Paris] (OSU ECCE TERRA), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Océanographie Physique et Spatiale (LOPS), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: ocean optics, carbon cycle, ocean observation, best practices, ocean biogeochemical cycles, sensors, argo, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: The Biogeochemical-Argo program (BGC-Argo) is a new profiling-float-based, ocean wide, and distributed ocean monitoring program which is tightly linked to, and has benefited significantly from, the Argo program. The community has recommended for BGC-Argo to measure six additional properties in addition to pressure, temperature and salinity measured by Argo, to include oxygen, pH, nitrate, downwelling light, chlorophyll fluorescence and the optical backscattering coefficient. The purpose of this addition is to enable the monitoring of ocean biogeochemistry and health, and in particular, monitor major processes such as ocean deoxygenation, acidification and warming and their effect on phytoplankton, the main source of energy of marine ecosystems. Here we describe the salient issues associated with the operation of the BGC-Argo network, with information useful for those interested in deploying floats and using the data they produce. The topics include float testing, deployment and increasingly, recovery. Aspects of data management, processing and quality control are covered as well as specific issues associated with each of the six BGC-Argo sensors. In particular, it is recommended that water samples be collected during float deployment to be used for validation of sensor output.
Published: 2019

20. Episodic organic carbon fluxes from surface ocean to abyssal depths during long-term monitoring in NE Pacific

Author: Christine L. Huffard, Henry A. Ruhl, Monique Messié, Kenneth L. Smith, Mati Kahru, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, National Oceanography Centre [Southampton] (NOC), University of Southampton, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Scripps Institution of Oceanography (SIO - UC San Diego), and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, Total organic carbon, Remineralisation, Multidisciplinary, 010504 meteorology & atmospheric sciences, 010604 marine biology & hydrobiology, Sediment, Biological Sciences, Atmospheric sciences, 01 natural sciences, Deep sea, Carbon cycle, Abyssal zone, carbon flux, carbon budget, Flux (metallurgy), 13. Climate action, [SDE]Environmental Sciences, abyssal community, Environmental science, 14. Life underwater, Seabed, Environmental Sciences, 0105 earth and related environmental sciences
Abstract: Significance Ignoring temporal fluctuations in the oceanic carbon budget leads to a significant misrepresentation of the cycling of organic matter from production in surface waters to consumption and sequestration in the abyssal ocean. A 29-year time series (1989 to 2017) of particulate organic carbon (POC) fluxes and sea-floor measurements of sediment community oxygen consumption (SCOC) revealed episodic, high-magnitude events over the past 7 years. Time lags between changes in satellite-estimated export flux, POC flux and SCOC varied from 0 to 70 days. A commonly used model to estimate carbon flux through the water column significantly underestimated the measured carbon fluxes by almost 50%. Episodic pulses of organic carbon into the deep sea must be accounted for to balance the oceanic carbon budget., Growing evidence suggests substantial quantities of particulate organic carbon (POC) produced in surface waters reach abyssal depths within days during episodic flux events. A 29-year record of in situ observations was used to examine episodic peaks in POC fluxes and sediment community oxygen consumption (SCOC) at Station M (NE Pacific, 4,000-m depth). From 1989 to 2017, 19% of POC flux at 3,400 m arrived during high-magnitude episodic events (≥mean + 2 σ), and 43% from 2011 to 2017. From 2011 to 2017, when high-resolution SCOC data were available, time lags between changes in satellite-estimated export flux (EF), POC flux, and SCOC on the sea floor varied between six flux events from 0 to 70 days, suggesting variable remineralization rates and/or particle sinking speeds. Half of POC flux pulse events correlated with prior increases in EF and/or subsequent SCOC increases. Peaks in EF overlying Station M frequently translated to changes in POC flux at abyssal depths. A power-law model (Martin curve) was used to estimate abyssal fluxes from EF and midwater temperature variation. While the background POC flux at 3,400-m depth was described well by the model, the episodic events were significantly underestimated by ∼80% and total flux by almost 50%. Quantifying episodic pulses of organic carbon into the deep sea is critical in modeling the depth and intensity of POC sequestration and understanding the global carbon cycle.
Published: 2018

21. A global meta-analysis of marine predator nitrogen stable isotopes: Relationships between trophic structure and environmental conditions

Author: C. Anela Choy, Anne Lorrain, Petra M. Kuhnert, Robert J. Olson, Nathalie Bodin, John M. Logan, Leanne M. Duffy, Christophe E. Menkès, Valerie Allain, Heidi Pethybridge, Frédéric Ménard, Christopher J. Somes, Brian Fry, Jock W. Young, Clothilde Langlais, Alistair J. Hobday, CSIRO Marine and Atmosphere Research [Hobart], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, Pacific community (SPC), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Seychelles Fishing Authority (SFA) (SFA), Université des Seychelles, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Inter-American Tropical Tuna Commission (IATTC), Data61 [Canberra] (CSIRO), Australian National University (ANU)-Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Griffith University [Brisbane], Scripps Institution of Oceanography (SIO - UC San Diego), University of California (UC)-University of California (UC), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Yellowfin tuna, 010504 meteorology & atmospheric sciences, trophodynamics, Effects of global warming on oceans, Bigeye tuna, 01 natural sciences, biological oceanography, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, oxygen minimum zone, Marine ecosystem, 14. Life underwater, Biological oceanography, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Trophic level, Global and Planetary Change, Ecology, biology, 010604 marine biology & hydrobiology, ACL, yellowfin tuna, albacore tuna, biology.organism_classification, 13. Climate action, food webs, macroecology, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tuna, bigeye tuna, human activities, Thunnus
Abstract: International audience; AimWe examined potential environmental drivers of broad‐scale spatial patterns in the trophic structure of marine ecosystems as represented by nitrogen stable isotopes in globally distributed marine predators. Additionally, we assessed the effects of spatial scale on the predictive capabilities of environmental variables.LocationGlobal oceans.Time period2000 to 2015.Major taxa studiedTunas: Thunnus albacares , Thunnus obesus , Thunnus alalunga .MethodsWe undertook a global compilation and meta‐analysis of the bulk nitrogen stable isotope ratios (δ15N values) of three tuna species (n = 4,281). After adjusting for regional variations in baseline δ15N values using a global ocean biogeochemistry model, generalized additive mixed models were employed to infer global‐scale oceanographic controls of trophic structure, using cosmopolitan tuna species as a model.ResultsFor the three tuna species, variation in trophic position estimated using bulk δ15N values was largely explained by geographical location and the corresponding oxygen minimum layer depth. Tuna trophic positions declined in areas with reduced oxygen at depth. Food‐chain length, as captured by maximum trophic position, was longer in areas of the western Pacific Ocean and shorter in the northern Atlantic and eastern Pacific Oceans. Trophic adaptability of the tuna predators, as indicated by intraspecific variability, was highest in the western and central Pacific Ocean and lowest in the northern Atlantic Ocean. Our analysis demonstrated that while tunas share similar functional trophic roles, deeper‐foraging tuna species had higher trophic positions globally. The predictive capacity of environmental variables decreased at finer (regional) spatial scales.Main conclusionsOur work suggests that habitat compression resulting from the predicted global expansion of oxygen minimum zones with ocean warming will impact the trophic structure of marine food webs and the corresponding foraging habits of marine predators. Spatial scale analyses highlighted the importance of representing differences in regional ecological dynamics in global‐scale trophic and ecosystem models.
Published: 2018

22. Scanning Electron Microscopic Aids for Identification of Larval and Post-Larval Bivalves

Author: Marcel Le Pennec, Richard A. Lutz, S. Cynthia Fuller, Patrick E. Dabinett, Brad S. Baldwin, Shannon B. Johnson, Alan S. Pooley, Ronald Goldberg, Carter R. Newell, Jacob D. Goodwin, Joy Goodsell, Judith P. Grassle, Scott M. Gallager, Ya-Ping Hu, Richard G. Gustafson, Victor S. Kennedy, Arnold G. Eversole, Roger Mann, Samuel R. Chapman, Michael Castagna, Al Chestnut, Christopher V. Davis, Antonieto S. Tan, Herbert Hidu, Gavin Burnell, A. Partridge, Robert C. Vrijenhoek, David Jablonski, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), University College Cork (UCC), Virginia Institute of Marine Science (VIMS), University of Maine, Memorial University of Newfoundland [St. John's], Clemson University, Woods Hole Oceanographic Institution (WHOI), Northeast Fisheries Science Center (NEFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Northwest Fisheries Science Center (NWFSC), Department of Geophysical Sciences [Chicago], University of Chicago, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, University of Maryland Center for Environmental Science (UMCES), University of Maryland System, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Memorial University of Newfoundland = Université Memorial de Terre-Neuve [St. John's, Canada] (MUN), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Microscope, 010504 meteorology & atmospheric sciences, early developmental stages, Morphological similarity, Scanning electron microscope, species identification, larvae, chesapeake bay, Aquatic Science, Biology, 01 natural sciences, bivalve, law.invention, law, nested multiplex pcr, pallet morphology, shell development, 14. Life underwater, postlarvae, Shellfish, 0105 earth and related environmental sciences, new-zealand, Morphometrics, Larva, 010604 marine biology & hydrobiology, ACL, fungi, Plankton, cape-cod estuary, semiautomated image-analysis, oyster larvae, Evolutionary biology, Benthic zone, identification, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, scanning electron microscopy
Abstract: WOS:000435219000002; International audience; The identification of bivalve larvae and early postlarvae in plankton and benthic samples has long been a challenge, hampering both basic and applied research efforts in marine, estuarine, and freshwater environments. The usefulness of published optical micrographs of the early life-history stages of bivalves is limited because of the great morphological similarity of the imaged articulated shells, particularly at the early (straight-hinge) developmental stages. While a number of techniques have been refined in recent years and show promise for use in routine identifications of larval and post-larval bivalves (e.g., single-step nested multiplex polymerase chain reaction; in situ hybridization protocols through color coding with taxon-specific, dye-labeled DNA probes; coupled fluorescence in situ hybridization and cell sorting; and image analysis techniques using species-specific shell birefringence patterns under polarized light), no adequate comprehensive reference source exists that accurately depicts the morphology and morphometry of the shells of larval and post-larval stages of target bivalve species in a consistent format to assist in identification of such stages. To this end, scanning electron micrograph (SEM) sequences are presented of the disarticulated shell valves of laboratory-reared larval and post-larval stages of 56 species of bivalve molluscs from a wide spectrum of marine, estuarine, and freshwater habitats. Emphasis is placed on the usefulness of the morphology and morphometrics of consistently-oriented, disarticulated shell valves and associated hinge structures in discriminating the early life-history stages of these various bivalve species. Although the scanning electron micrograph sequences presented accurately depict the gross morphologies/morphometrics and hinge structures of the disarticulated shell valves of the larvae and/or postlarvae of the 56 species of bivalves, it is important to emphasize that a scanning electron microscope is not necessary to observe even fine hinge structures associated with the early ontogenetic stages of these species. Such structures are readily visible using a wide range of optical compound microscopes equipped with high-intensity reflected light sources, although the disarticulated shell valves must be viewed in several planes of focus to discern the often subtle details seen clearly in the scanning electron micrographs. These morphological characters provide researchers with invaluable aids for the routine identification of the early life-history stages of these species isolated from plankton and benthic samples.
Published: 2018

23. Advancing marine biological observations and data requirements of the complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) frameworks

Author: Frank E. Muller-Karger, Patricia Miloslavich, Nicholas J. Bax, Samantha Simmons, Mark J. Costello, Isabel Sousa Pinto, Gabrielle Canonico, Woody Turner, Michael Gill, Enrique Montes, Benjamin D. Best, Jay Pearlman, Patrick Halpin, Daniel Dunn, Abigail Benson, Corinne S. Martin, Lauren V. Weatherdon, Ward Appeltans, Pieter Provoost, Eduardo Klein, Christopher R. Kelble, Robert J. Miller, Francisco P. Chavez, Katrin Iken, Sanae Chiba, David Obura, Laetitia M. Navarro, Henrique M. Pereira, Valerie Allain, Sonia Batten, Lisandro Benedetti-Checchi, J. Emmett Duffy, Raphael M. Kudela, Lisa-Maria Rebelo, Yunne Shin, Gary Geller, Department of Psychiatry, Trinity College Dublin-St. James's Hospital, IEEE, Marine Geospatial Ecology Laboratory [USA], Nicholas School of the Environment, Duke University [Durham]-Duke University [Durham], Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University [Durham], United Nations Environment Programma World Conservation Monitoring Centre, International Oceanographic Data and Information Exchange (IODE) of the Intergovernmental Oceanographic Commission of UNESCO, Oostende, Massachusetts Institute of Technology (MIT), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Coastal Oceans Research and Development in the Indian Ocean - East Africa (CORDIO - East Africa), Secretariat of the Pacific Community, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Marine conservation, 010504 meteorology & atmospheric sciences, lcsh:QH1-199.5, [SDE.MCG]Environmental Sciences/Global Changes, Marine life, Ocean Engineering, Aquatic Science, Environmental Science (miscellaneous), global ocean observing system (GOOS), lcsh:General. Including nature conservation, geographical distribution, Oceanography, 01 natural sciences, 12. Responsible consumption, Ecosystem services, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, marine biodiversity observation network (MBON), 11. Sustainability, 14. Life underwater, lcsh:Science, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Water Science and Technology, ocean biogeographic information system (OBIS), Sustainable development, Essential biodiversity variables (EBV), Essential ocean variables (EOV), Global ocean observing system (GOOS), Integrated marine biosphere research (IMBeR), Marine biodiversity observation network (MBON), Marine global earth observatory (MarineGEO), Ocean biogeographic information system (OBIS), Global and Planetary Change, integrated marine biosphere research (IMBeR), business.industry, marine global earth observatory (MarineGEO), 010604 marine biology & hydrobiology, Environmental resource management, global ocean observing system(GOOS), 15. Life on land, Ocean Biogeographic Information System, ocean biogeographic information system(OBIS), 13. Climate action, Sustainability, essential ocean variables (EOV), lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Global biodiversity, Group on Earth Observations, essential biodiversity variables (EBV)
Abstract: Measurements of the status and trends of key indicators for the ocean and marine life are required to inform policy and management in the context of growing human uses of marine resources, coastal development, and climate change. Two synergistic efforts identify specific priority variables for monitoring: Essential Ocean Variables (EOVs) through the Global Ocean Observing System (GOOS), and Essential Biodiversity Variables (EBVs) from the Group on Earth Observations Biodiversity Observation Network (GEO BON) (see Data Sheet 1 in Supplementary Materials for a glossary of acronyms). Both systems support reporting against internationally agreed conventions and treaties. GOOS, established under the auspices of the Intergovernmental Oceanographic Commission (IOC), plays a leading role in coordinating global monitoring of the ocean and in the definition of EOVs. GEO BON is a global biodiversity observation network that coordinates observations to enhance management of the world's biodiversity and promote both the awareness and accounting of ecosystem services. Convergence and agreement between these two efforts are required to streamline existing and new marine observation programs to advance scientific knowledge effectively and to support the sustainable use and management of ocean spaces and resources. In this context, the Marine Biodiversity Observation Network (MBON), a thematic component of GEO BON, is collaborating with GOOS, the Ocean Biogeographic Information System (OBIS), and the Integrated Marine Biosphere Research (IMBeR) project to ensure that EBVs and EOVs are complementary, representing alternative uses of a common set of scientific measurements. This work is informed by the Joint Technical Commission for Oceanography and Marine Meteorology (JCOMM), an intergovernmental body of technical experts that helps international coordination on best practices for observing, data management and services, combined with capacity development expertise. Characterizing biodiversity and understanding its drivers will require incorporation of observations from traditional and molecular taxonomy, animal tagging and tracking efforts, ocean biogeochemistry, and ocean observatory initiatives including the deep ocean and seafloor. The partnership between large-scale ocean observing and product distribution initiatives (MBON, OBIS, JCOMM, and GOOS) is an expedited, effective way to support international policy-level assessments (e.g., the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services or IPBES), along with the implementation of international development goals (e.g., the United Nations Sustainable Development Goals).
Published: 2018

24. Marine algae and land plants share conserved phytochrome signaling systems

Author: Worden, Alexandra [Monterey Bay Aquarium Research Institute, Moss Landing, CA (United States); Canadian Institute for Advanced Research, Toronto, ON (Canada)]
Published: 2014
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25. Lessons learned from an ecosystem-based management approach to restoration of a California estuary

Author: Andrea Woolfolk, Mark Silberstein, Antonia Akhavan, Linwood Pendleton, Kerstin Wasson, Becky Suarez, Erin McCarthy, Monique C. Fountain, Judith Kildow, Kenneth S. Johnson, Dave Feliz, Department of Ecology and Evolutionary Biology [Santa Cruz], University of California [Santa Cruz] (UCSC), University of California-University of California, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Economics and Econometrics, Aquatic Science, Management, Monitoring, Policy and Law, decision making, California, Ecosystem services, [SHS]Humanities and Social Sciences, Environmental Science(all), environmental policy, Ecosystem, Resource management, 14. Life underwater, Human resources, estuarine ecosystem, restoration ecology, targeting, General Environmental Science, ecosystem management, geography, environmental restoration, geography.geographical_feature_category, business.industry, Environmental resource management, Estuary, 15. Life on land, coastal zone management, Ecosystem-based management, 6. Clean water, policy implementation, United States, ecosystem service, 13. Climate action, Salt marsh, Business, ecosystem approach, Coastal management, Law, Elkhorn Slough Estuary
Abstract: International audience; Ecosystem-based management (EBM) is the dominant paradigm, at least in theory, for coastal resource management. However, there are still relatively few case studies illustrating thorough application of principles of EBM by stakeholders and decision-makers. At Elkhorn Slough, a California estuary, we launched an EBM initiative in 2004. Stakeholders collaboratively developed and evaluated large-scale restoration alternatives designed to decrease two types of rapid habitat change occurring in the estuary, erosion of channels and dieback of salt marsh. In the end, decision-makers rejected large-scale alternatives altering the mouth of the estuary, and instead opted for small- to medium-scale restoration projects and recommended an added emphasis on reduction of nutrient-loading. We describe seven challenges encountered during the application of EBM principles: (1) interdisciplinary collaboration is difficult due to differences in professional culture and values, (2) roles and responsibilities of different participants are often not sufficiently clear, (3) implementing EBM is very costly in time and human resources, (4) an ecosystem services framework may not resonate with stakeholders already committed to biodiversity conservation, (5) conflicts arise from differences in desired restoration targets, (6) multiple geographic and jurisdictional scales cannot be simultaneously addressed, and (7) understanding of ecosystem drivers and processes may change rapidly. We recommend approaches to overcoming each of these challenges so that our experiences implementing EBM at one estuary can inform collaborative decision-making initiatives elsewhere. © 2015 The Authors.
Published: 2015
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26. Global trophic ecology of yellowfin, bigeye, and albacore tunas: Understanding predation on micronekton communities at ocean-basin scales

Author: Heidi Pethybridge, John M. Logan, C. Anela Choy, Frédéric Ménard, Michel Potier, Evgeny V. Romanov, Petra M. Kuhnert, Felipe Galván-Magaña, Valerie Allain, Robert J. Olson, Melanie Abecassis, Leanne M. Duffy, Nicolas Goñi, Jock W. Young, Monique Simier, Alistair J. Hobday, Michelle D. Staudinger, University of Tasmania (UTAS), UMR 212 EME 'écosystèmes marins exploités' (EME), Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Secretariat of the Pacific Community, Institut de Recherche pour le Développement (IRD), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Inter-American Tropical Tuna Commission (IATTC), Data61 [Canberra] (CSIRO), Australian National University (ANU)-Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Tasmania [Hobart, Australia] (UTAS), Massachusetts Division of Marine Fisheries, AZTI-Tecnalia, Marine Research Division, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Division of Ecosystem Sciences, The Commonwealth Scientific and Industrial Research Organisation, Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Classification trees, Inter-ocean comparison, Mesopelagic zone, Oceanography, 010603 evolutionary biology, 01 natural sciences, Ecosystems, Climate changes, Predatory fish, 14. Life underwater, Macroecology, ComputingMilieux_MISCELLANEOUS, Trophic level, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, biology, Ecology, Albacore, 010604 marine biology & hydrobiology, Food webs, Pelagic zone, 16. Peace & justice, biology.organism_classification, Fishery, Meta-analysis, [SDU]Sciences of the Universe [physics], Trophic relationships, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tuna, Thunnus
Abstract: International audience; Predator-prey interactions for three commercially valuable tuna species: yellowfin (Thunnus albacares), bigeye (T. obesus), and albacore (T. alalunga), collected over a 40-year period from the Pacific, Indian, and Atlantic Oceans, were used to quantitatively assess broad, macro-scale trophic patterns in pelagic ecosystems. Analysis of over 14,000 tuna stomachs, using a modified classification tree approach, revealed for the first time the global expanse of pelagic predatory fish diet and global patterns of micronekton diversity. Ommastrephid squids were consistently one of the top prey groups by weight across all tuna species and in most ocean bodies. Interspecific differences in prey were apparent, with epipelagic scombrid and mesopelagic paralepidid fishes globally important for yellowfin and bigeye tunas, respectively, while vertically-migrating euphausiid crustaceans were important for albacore tuna in the Atlantic and Pacific Oceans. Diet diversity showed global and regional patterns among tuna species. In the central and western Pacific Ocean, characterized by low productivity, a high diversity of micronekton prey was detected while low prey diversity was evident in highly productive coastal waters where upwelling occurs. Spatial patterns of diet diversity were most variable in yellowfin and bigeye tunas while a latitudinal diversity gradient was observed with lower diversity in temperate regions for albacore tuna. Sea-surface temperature was a reasonable predictor of the diets of yellowfin and bigeye tunas, whereas chlorophyll-a was the best environmental predictor of albacore diet. These results suggest that the ongoing expansion of warmer, less productive waters in the world's oceans may alter foraging opportunities for tunas due to regional changes in prey abundances and compositions.
Published: 2017

27. Quantification of bioluminescence from the surface to the deep sea demonstrates its predominance as an ecological trait

Author: Steven H. D. Haddock, Séverine Martini, Monterey Bay Aquarium Research Institute (MBARI), and Monterey Bay Aquarium Research Institute
Subjects: 0106 biological sciences, 0301 basic medicine, Aquatic Organisms, Video Recording, Marine Biology, 01 natural sciences, Deep sea, Article, 03 medical and health sciences, Chaetognatha, Bioluminescence, Animals, 14. Life underwater, Taxonomic rank, ComputingMilieux_MISCELLANEOUS, Marine biology, Multidisciplinary, Pacific Ocean, biology, Ecology, 010604 marine biology & hydrobiology, Scyphozoa, biology.organism_classification, Ctenophora, 030104 developmental biology, Taxon, Luminescent Measurements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The capability of animals to emit light, called bioluminescence, is considered to be a major factor in ecological interactions. Because it occurs across diverse taxa, measurements of bioluminescence can be powerful to detect and quantify organisms in the ocean. In this study, 17 years of video observations were recorded by remotely operated vehicles during surveys off the California Coast, from the surface down to 3,900 m depth. More than 350,000 observations are classified for their bioluminescence capability based on literature descriptions. The organisms represented 553 phylogenetic concepts (species, genera or families, at the most precise taxonomic level defined from the images), distributed within 13 broader taxonomic categories. The importance of bioluminescent marine taxa is highlighted in the water column, as we showed that 76% of the observed individuals have bioluminescence capability. More than 97% of Cnidarians were bioluminescent, and 9 of the 13 taxonomic categories were found to be bioluminescent dominant. The percentage of bioluminescent animals is remarkably uniform over depth. Moreover, the proportion of bioluminescent and non-bioluminescent animals within taxonomic groups changes with depth for Ctenophora, Scyphozoa, Chaetognatha, and Crustacea. Given these results, bioluminescence has to be considered an important ecological trait from the surface to the deep-sea.
Published: 2017
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28. Deep sediment resuspension and thick nepheloid layer generation by open-ocean convection

Author: Durrieu de Madron, Xavier, Ramondenc, S., Berline, L., Houpert, Loïc, Bosse, Anthony, Martini, S., Guidi, L., Conan, P., Curtil, C., Delsaut, N., Kunesch, S., Ghiglione, J.F., Marsaleix, Patrick, Pujo-Pay, M., Séverin, T., Testor, Pierre, Tamburini, Christian, Centre de Formation et de Recherche sur les Environnements Méditérranéens (CEFREM), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), 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 méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Scottish Association for Marine Science (SAMS), Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), 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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), 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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Laboratoire d'Océanographie Microbienne (LOMIC), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique des Particules de Marseille (CPPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Aix Marseille Université (AMU), Laboratoire d'aérologie (LA), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Marine Science Institute [Port Aransas], University of Texas at Austin [Austin], SOERE‐MOOSE, MISTRALS‐MERMEX, European Project: 287600,EC:FP7:ENV,FP7-OCEAN-2011,PERSEUS(2012), Université de Perpignan Via Domitia (UPVD), Université Pierre et Marie Curie - Paris 6 (UPMC), 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), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), ANTARES, 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), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'aérologie (LAERO), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: [PHYS]Physics [physics], [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDE.MCG]Environmental Sciences/Global Changes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; The Gulf of Lions in the northwestern Mediterranean is one of the few sites around the world ocean exhibiting deep open‐ocean convection. Based on 6 year long (2009–2015) time series from a mooring in the convection region, shipborne measurements from repeated cruises, from 2012 to 2015, and glider measurements, we report evidence of bottom thick nepheloid layer formation, which is coincident with deep sediment resuspension induced by bottom‐reaching convection events. This bottom nepheloid layer, which presents a maximum thickness of more than 2000 m in the center of the convection region, probably results from the action of cyclonic eddies that are formed during the convection period and can persist within their core while they travel through the basin. The residence time of this bottom nepheloid layer appears to be less than a year. In situ measurements of suspended particle size further indicate that the bottom nepheloid layer is primarily composed of aggregates between 100 and 1000 µm in diameter, probably constituted of fine silts. Bottom‐reaching open ocean convection, as well as deep dense shelf water cascading that occurred concurrently some years, lead to recurring deep sediments resuspension episodes. They are key mechanisms that control the concentration and characteristics of the suspended particulate matter in the basin, and in turn affect the bathypelagic biological activity.
Published: 2017

29. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Author: Beverley R. Green, Gernot Glöckner, Thomas Mock, Remo Sanges, James A. Raymond, Michael G. Janech, Barbara R. Lyon, Kerrie Barry, Florian Leese, Ansgar Gruber, Joel Martin, Erika Lindquist, Matthew D. Clark, Robert Otillar, Ben J. Ward, Alexandra Z. Worden, Christoph Mayer, Antonio Emidio Fortunato, Micaela S. Parker, Christopher L. Dupont, Maria Immacolata Ferrante, Stephan Frickenhaus, Klaus Valentin, Hadi Quesneville, Vincent Moulton, Rachel Hipkin, Angela Falciatore, Igor V. Grigoriev, Christiane Uhlig, Chris Bowler, Cock van Oosterhout, Ruben E. Valas, Asaf Salamov, Jeremy Schmutz, E. Virginia Armbrust, Andrew E. Allen, Alaguraj Veluchamy, Jan Strauss, Peter G. Kroth, Mark McMullan, Taoyang Wu, Andrew Toseland, Pirita Paajanen, Florian Maumus, School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Joint Genome Institute, United States Department of Energy, Hudson Alpha Institute, Sezione Ecologia Marina Integrata, Stazione Zoologica Anton Dohrn, School of Physics [NUI Galway], National University of Ireland [Galway] (NUI Galway), Infection et inflammation chronique (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Technical University of Munich (TUM), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Genomics Institute for Biochemistry I, University of Cologne, University of Innsbruck, Laboratoire Genome Population & Interactions, Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-ORSTOM, Department of Biology, University of Konstanz, Animal Ecology, Evolution and Biodiversity, Ruhr-Universität Bochum [Bochum], Univ Reading, Sch Chem Pharm & Food Biosci, Reading RG6 6AD, Berks, England, Canadian Institute for Advanced Research (CIAR), Université de Montréal [Montréal], Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, University of California [Santa Cruz] (UCSC), University of California, School of Oceanography [Seattle], University of Washington [Seattle], Johns Hopkins University School of Medicine [Baltimore], Department of Computer Science, DOE Joint Genome Institute [Walnut Creek], Stazione Zoologica Anton Dohrn (SZN), Infection et inflammation (2I), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Leopold Franzens Universität Innsbruck - University of Innsbruck, Université Montpellier 2 - Sciences et Techniques (UM2)-ORSTOM-Centre National de la Recherche Scientifique (CNRS), Canadian Institute for Advanced Research (CIFAR), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), ERC Advanced Grant ERC-2011-ADG (Diatomite) - Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 - NERC under grants NE/I001751/1, NE/K004530/1, MGF (NBAF) grant 197, The Royal Society grant RG090774 and the Earth & Life Systems Alliance in Norwich, European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Acclimatization, [SDV]Life Sciences [q-bio], 01 natural sciences, Mutation Rate, Settore BIO/13 - Biologia Applicata, Freezing, Alleles, Carbon Dioxide, Darkness, Diatoms, Gene Expression Profiling, Genetic Drift, Genome, Ice Cover, Iron, Oceans and Seas, Phylogeny, Recombination, Genetic, Transcriptome, Cold Temperature, Evolution, Molecular, Genomics, Multidisciplinary, biology, Ecology, Biologie, Biotechnology, Genome evolution, Evolution, General Science & Technology, 03 medical and health sciences, Genetic drift, Genetic, Cylindrus, Molecular evolution, ddc:570, Genetics, 14. Life underwater, Genome size, Human Genome, fungi, Molecular, biology.organism_classification, Recombination, 030104 developmental biology, Diatom, Adaptation, 010606 plant biology & botany
Abstract: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Published: 2017

30. Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms Using Molecular and Maritime Technology

Author: Meghan L. Powers, Monique Messié, Benjamin E. Erwin, Karen J. Osborn, C. Anela Choy, Darrin T. Schultz, P.R. Pugh, Séverine Martini, Christine E. Schnitzler, Erik V. Thuesen, Brad A. Seibel, Jacob R. Winnikoff, Rebeca Gasca, Steven H. D. Haddock, Sönke Johnsen, Susan von Thun, George I. Matsumoto, William E. Browne, Joseph F. Ryan, Kyra L. Schlining, Casey W. Dunn, Warren R. Francis, Claudia E. Mills, Lynne M. Christianson, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), and 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)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, 010604 marine biology & hydrobiology, Biodiversity, Marine technology, Oceanography, 01 natural sciences, Deep sea, 13. Climate action, Bioluminescence, Environmental science, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: Since its founding, the Monterey Bay Aquarium Research Institute (MBARI) has pioneered unique capabilities for accessing the deep ocean and its inhabitants through focused peer relationships between scientists and engineers. This focus has enabled breakthroughs in our understanding of life in the sea, leading to fundamental advances in describing the biology and the ecology of open-ocean and deep-sea animals. David Packard’s founding principle was the application of technological advances to studying the deep ocean, in part because he recognized the critical importance of this habitat in a global context. Among other fields, MBARI’s science has benefited from applying novel methodologies in molecular biology and genetics, imaging systems, and in situ observations. These technologies have allowed MBARI’s bioluminescence and biodiversity laboratory and worldwide collaborators to address centuries-old questions related to the biodiversity, behavior, and bio-optical properties of organisms living in the water column, from the surface into the deep sea. Many of the most interesting of these phenomena are in the midwater domain—the vast region of ocean between the sunlit surface waters and the deep seafloor.
Published: 2017
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31. A global neural network-based parameterization of biogeochemical water mass properties and processes based on GLODAP data

Author: Bittig, Henry, Sauzède, Raphaëlle, Claustre, Hervé, Fommervault, Orens, Gattuso, Jean-Pierre, Legendre, Louis, Johnson, Kenneth S, 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), 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 Recherche pour le Développement (IRD [Polynésie]), Centro de Investigacion Cientifica y de Education Superior de Ensenada [Mexico] (CICESE), Monterey Bay Aquarium Research Institute (MBARI), and Monterey Bay Aquarium Research Institute
Subjects: [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience
Published: 2017

32. Choanoflagellates alongside diverse uncultured predatory protists consume the abundant open-ocean cyanobacterium Prochlorococcus

Author: Wilken, Susanne, Yung, Charmaine C. M., Poirier, Camille, Massana, Ramon, Jimenez-Thamm, Valeria, Worden, Alexandra Z., Monterey Bay Aquarium Research Institute, Gordon and Betty Moore Foundation, European Commission, Simons Foundation, and Agencia Estatal de Investigación (España)
Subjects: Choanoflagellates, Heterotrophic nanoflagellates, Picocyanobacteria, Trophic transfer, Microbial food webs, Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Abstract: 3 pages, 2 figures, supporting information https://doi.org/10.1073/pnas.2302388120.-- Data, Materials, and Software Availability: Amplicons have been deposited in Sequence Read Archive (SRA) under bioproject PRJNA972531. All other data are included in the article and/or supporting information, Prochlorococcus is a key member of open-ocean primary producer communities. Despite its importance, little is known about the predators that consume this cyanobacterium and make its biomass available to higher trophic levels. We identify potential predators along a gradient wherein Prochlorococcus abundance increased from near detection limits (coastal California) to >200,000 cells mL−1 (subtropical North Pacific Gyre). A replicated RNA-Stable Isotope Probing experiment involving the in situ community, and labeled Prochlorococcus as prey, revealed choanoflagellates as the most active predators of Prochlorococcus, alongside a radiolarian, chrysophytes, dictyochophytes, and specific MAST lineages. These predators were not appropriately highlighted in multiyear conventional 18S rRNA gene amplicon surveys where dinoflagellates and other taxa had highest relative amplicon abundances across the gradient. In identifying direct consumers of Prochlorococcus, we reveal food-web linkages of individual protistan taxa and resolve routes of carbon transfer from the base of marine food webs, Funding came from Monterey Bay Aquarium Research Institute, Gordon and Betty Moore Foundation Grant 3788 (to A.Z.W.), and EC’s FP7 Marie Skłodowska-Curie grant 626182 (to S.W.). V.J. was funded partially by BIOS-SCOPE (Simons Foundation International), With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2023

33. Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition: Incorporation of diverse mixotrophic strategies

Author: Mitra, Aditee, Flynn, Kevin J., Tillmann, Urban, Raven, John A., Caron, David, Stoecker, Diane K., Not, Fabrice, Hansen, Per J., Hallegraeff, Gustaaf, Sanders, Robert, Wilken, Susanne, McManus, George, Johnson, Mathew, Pitta, Paraskevi, Våge, Selina, Berge, Terje, Calbet, Albert, Thingstad, Frede, Jeong, Hae Jin, Burkholder, JoAnn, Glibert, Patricia M., Granéli, Edna, Lundgren, Veronica, Swansea University, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Division of Plant Sciences, College of Life Sciences, University of Dundee, Department of Biological Sciences, University of Southern California (USC), University of Maryland Center for Environmental Science, Horn Point Laboratory, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre for Ocean Life, University of Copenhagen = Københavns Universitet (KU), Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), Department of Biology, Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Marine Sciences, University of Connecticut (UCONN), Woods Hole Oceanographic Institution (WHOI), Hellenic Centre for Marine Research (HCMR), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of Biological Sciences [Bergen] (BIO / UiB), University of Bergen (UiB), School of Earth and Environmental Sciences [Seoul] (SEES), Seoul National University [Seoul] (SNU), Center for Applied Aquatic Ecology, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Lund University, Department of Biology and Environmental Sciences, Linnaeus University, University of Copenhagen = Københavns Universitet (UCPH), Institute for Marine and Antarctic Studies [Hobart] (IMAS), and Lund University [Lund]
Subjects: phagotroph, phototroph, Food Chain, Plankton functional types (PFTs), Eukaryota, Microbiology, Zooplankton, Phototrophic Processes, mixotroph, microzooplankton, Phytoplankton, Animals, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Energy Metabolism, Phylogeny
Abstract: International audience; Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic “phytoplankton” and phagotrophic “microzooplankton”. However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an eco-physiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks.
Published: 2016

34. Picophytoplankton biomass distribution in the global ocean

Author: Diego Macías, Lisa Campbell, Osvaldo Ulloa, Stéphan Jacquet, Michael W. Lomas, George B. McManus, François Lantoine, Francisco P. Chavez, Michael R. Landry, William K. W. Li, Michel Gosselin, Erik T. Buitenhuis, David M. Karl, Frédéric Partensky, Daniel Vaulot, Tyndall Centre for Climate Change Research and School of Environmental Sciences, University of East Anglia [Norwich] (UEA), Fisheries and Oceans Canada, Bedford Institute of Oceanography, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Bermuda Institute of Ocean Sciences (BIOS), Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Department of Oceanography, University of Hawaii, Departmento de Oceanografía & Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental, Universidad de Concepción - University of Concepcion [Chile], Department of Oceanography [College Station], Texas A&M University [College Station], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Department of Coastal Ecology and Management, Institute of Marine Sciences of Andalusia, Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Department of Marine sciences, University of Connecticut (UCONN), U (CarboChange) 264879, Networks of Centres of Excellence of Canada-ArcticNet, Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Scripps Institution of Oceanography (SIO), University of California-University of California, MArine Phototrophic Prokaryotes (MAPP), Universidad de Concepción [Chile], and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Biodiversité et Ecologie, Distribution (economics), picophytoplancton, 01 natural sciences, Cell size, Biodiversity and Ecology, Abundance (ecology), Phytoplankton, 14. Life underwater, biomasse microbienne, lcsh:Environmental sciences, 0105 earth and related environmental sciences, lcsh:GE1-350, Biomass (ecology), océan, biology, business.industry, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Synechococcus, biology.organism_classification, Biomass carbon, lcsh:Geology, analyse par flux cytométrique, Oceanography, General Earth and Planetary Sciences, Environmental science, Prochlorococcus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: Buitenhuis, Erik et al., The smallest marine phytoplankton, collectively termed picophytoplankton, have been routinely enumerated by flow cytometry since the late 1980s during cruises throughout most of the world ocean. We compiled a database of 40 946 data points, with separate abundance entries for Prochlorococcus, Synechococcus and picoeukaryotes. We use average conversion factors for each of the three groups to convert the abundance data to carbon biomass. After gridding with 1° spacing, the database covers 2.4% of the ocean surface area, with the best data coverage in the North Atlantic, the South Pacific and North Indian basins, and at least some data in all other basins. The average picophytoplankton biomass is 12 ± 22 μg C l−1 or 1.9 g C m−2. We estimate a total global picophytoplankton biomass of 0.53–1.32 Pg C (17–39% Prochlorococcus, 12–15% Synechococcus and 49–69% picoeukaryotes), with an intermediate/best estimate of 0.74 Pg C. Future efforts in this area of research should focus on reporting calibrated cell size and collecting data in undersampled regions., We thank Claude Belzile, Jacques Neveux and Genevieve Tremblay for their comments on a draft manuscript, the EU (CarboChange, contract 264879) for financial support to ETB, and the Networks of Centres of Excellence of Canada-ArcticNet for financial support to MG.
Published: 2012

35. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Author: Robert Otillar, Olivier Panaud, Aaron Poliakov, Ian T. Paulsen, Eve Toulza, Steven Robbens, Heidrun Gundlach, Pedro M. Coutinho, E. Virginia Armbrust, Jill E. Gready, Klaus F. X. Mayer, Jasmyn Pangilinan, Kemin Zhou, Igor V. Grigoriev, Wenche Eikrem, Marie L. Cuvelier, Elif Demir, Ursula Goodenough, Jonathan H. Badger, Hervé Moreau, Susan Lucas, Peter von Dassow, Yves Van de Peer, Evelyne Derelle, Pierre Rouzé, Andrew E. Allen, Erika Lindquist, Uwe John, Elodie Foulon, Jeremy Schmutz, Fabrice Not, William Lanier, Meredith V. Everett, Alex N. Zelensky, Sarah M. McDonald, Benoît Piégu, Jane Grimwood, Tania Wyss, Chelle L. Gentemann, Aasf Salamov, Micaela S. Parker, Stephane Rombauts, Alexandra Z. Worden, Carolyn A. Napoli, Thomas Mock, Bernard Henrissat, Jae-Hyeok Lee, Inna Dubchak, Melinda P. Simmons, Andrea Aerts, Debashish Bhattacharya, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, School of Oceanography [Seattle], University of Washington [Seattle], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Biology Institute, University of Arizona, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, Stanford University School of Medicine [Stanford], Stanford University [Stanford], and Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, MESH: Sequence Analysis, DNA, RNA, Untranslated, MESH: Oceans and Seas, MESH: Introns, MESH: Plants, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, 18S ribosomal RNA, Bathycoccus, MESH: Chlorophyta, MESH: RNA, Untranslated, Chlorophyta, MESH: Ecosystem, MESH: Genetic Variation, Photosynthesis, MESH: Phylogeny, Clade, Phylogeny, MESH: Photosynthesis, Plant evolution, 0303 health sciences, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], MESH: Transcription Factors, Plants, Adaptation, Physiological, Biological Evolution, MESH: Gene Expression Regulation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Genes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Meiosis, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MESH: DNA Transposable Elements, Oceans and Seas, Molecular Sequence Data, MESH: Biological Evolution, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Ecosystem, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, Micromonas, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Repetitive Sequences, Nucleic Acid, MESH: Molecular Sequence Data, Genetic Variation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Sequence Analysis, DNA, biology.organism_classification, MESH: Adaptation, Physiological, Introns, MESH: Meiosis, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Gene Expression Regulation, Genes, Phytoplankton, DNA Transposable Elements, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Transcription Factors, MESH: Phytoplankton, 010606 plant biology & botany
Abstract: Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18 S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
Published: 2009

36. Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

Author: Richard Cooke, Adam Monier, Alexandra Z. Worden, Hervé Moreau, Nigel Grimsley, Evelyne Derelle, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Exeter, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, and Canadian Institute for Advanced Research (CIFAR)
Subjects: [SDV]Life Sciences [q-bio], Molecular Sequence Data, Immunology, Biodiversity, Sequence Homology, Genome, Viral, Viral Plaque Assay, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Synteny, Microbiology, Genome, Ostreococcus, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Chlorophyta, Phylogenetics, Virology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene Order, Mediterranean Sea, Cluster Analysis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Seawater, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Atlantic Ocean, Phylogeny, [SDV.GEN]Life Sciences [q-bio]/Genetics, Pacific Ocean, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Ecology, Host (biology), Strain (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Sequence Analysis, DNA, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Genetic Diversity and Evolution, Genetic distance, Evolutionary biology, Insect Science, Viruses
Abstract: The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus , which is found in coastal and mesotrophic systems, and O. tauri , which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri . Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. IMPORTANCE Marine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus . This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.
Published: 2015

37. Submarine landslides in the Santa Barbara Channel as potential tsunami sources

Author: Norm Maher, H. G. Greene, Philip Watts, C. E. Paull, Peter Eichhubl, Michael Fisher, L. Y. Murai, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Moss Landing Marine Laboratories, 8272 Moss Landing Road, Applied Fluids Engineering, Inc., AOA Geophysics, inc., United States Geological Survey [Reston] (USGS), Department of Geological Sciences [Stanford] (GS), Stanford EARTH, Stanford University-Stanford University, and EGU, Publication
Subjects: 010504 meteorology & atmospheric sciences, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010502 geochemistry & geophysics, Fault scarp, 01 natural sciences, lcsh:TD1-1066, Head (geology), Bathymetry, 14. Life underwater, lcsh:Environmental technology. Sanitary engineering, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Geomorphology, lcsh:Environmental sciences, 0105 earth and related environmental sciences, Colluvium, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, lcsh:GE1-350, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, lcsh:QE1-996.5, lcsh:Geography. Anthropology. Recreation, Landslide, Debris, [SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces, environment, Seafloor spreading, lcsh:Geology, lcsh:G, [SDU.STU] Sciences of the Universe [physics]/Earth Sciences, General Earth and Planetary Sciences, Seismology, Geology, Submarine landslide
Abstract: International audience; Recent investigations using the Monterey Bay Aquarium Research Institutes (MBARI) Remotely Operated Vehicles (ROVs) "Ventana" and "Tiburon" and interpretation of MBARI's EM 300 30 kHz multibeam bathymetric data show that the northern flank of the Santa Barbara Basin has experienced massive slope failures. Of particular concern is the large (130 km2) Goleta landslide complex located off Coal Oil Point near the town of Goleta, that measures 14.6-km long extending from a depth of 90 m to nearly 574 m deep and is 10.5 km wide. We estimate that approximately 1.75 km3 has been displaced by this slide during the Holocene. This feature is a complex compound submarine landslide that contains both surfical slump blocks and mud flows in three distinct segments. Each segment is composed of a distinct head scarp, down-dropped head block and a slide debris lobe. The debris lobes exhibit hummocky topography in the central areas that appear to result from compression during down slope movement. The toes of the western and eastern lobes are well defined in the multibeam image, whereas the toe of the central lobe is less distinct. Continuous seismic reflection profiles show that many buried slide debris lobes exist and comparison of the deformed reflectors with ODP Drill Site 149, Hole 893 suggest that at least 200 000 years of failure have occurred in the area (Fisher et al., 2005a). Based on our interpretation of the multibeam bathymetry and seismic reflection profiles we modeled the potential tsunami that may have been produced from one of the three surfical lobes of the Goleta slide. This model shows that a 10 m high wave could have run ashore along the cliffs of the Goleta shoreline. Several other smaller (2 km2 and 4 km2) slides are located on the northern flank of the Santa Barbara Basin, both to the west and east of Goleta slide and on the Conception fan along the western flank of the basin. One slide, named the Gaviota slide, is 3.8 km2, 2.6 km long and 1.7 km wide. A distinct narrow scar extends from near the eastern head wall of this slide for over 2km eastward toward the Goleta slide and may represent either an incipient failure or a remnant of a previous failure. Push cores collected within the main head scar of this slide consisted of hydrogen sulfide bearing mud, possibly suggesting active fluid seepage and a vibra-core penetrated ~50 cm of recent sediment overlying colluvium or landslide debris confirming the age of ~300 years as proposed by Lee et al. (2004). However, no seeps or indications of recent movement were observed during our ROV investigation within this narrow head scar indicating that seafloor in the scar is draped with mud.
Published: 2006

38. Protein quality control at the inner nuclear membrane

Author: Ewa Blaszczak, Marina Pantazopoulou, Matthias Meurer, Per O. Ljungdahl, Deike J. Omnus, Gwénaël Rabut, Audrey Brossard, Joseph Barry, Bernd Fischer, Daniel Kirrmaier, Wolfgang Huber, Anton Khmelinskii, Gaëlle Le Dez, Charles Boone, Alexander Gunnarsson, Michael Knop, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Anatomy and Cell Biology, Martin Luther University, Faculty of Medicine, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, European Molecular Biology Laboratory [Heidelberg] (EMBL), and Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
Subjects: Vesicle-associated membrane protein 8, Saccharomyces cerevisiae Proteins, Nuclear Envelope, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, Biology, Ubiquitin-conjugating enzyme, Article, 03 medical and health sciences, 0302 clinical medicine, Inner membrane, Integral membrane protein, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Membrane Proteins, Endoplasmic Reticulum-Associated Degradation, Transport protein, Ubiquitin ligase, Cell biology, Protein Transport, Membrane protein, Proteolysis, Ubiquitin-Conjugating Enzymes, biology.protein, Asi complex, 030217 neurology & neurosurgery
Abstract: International audience; The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm. The inner nuclear membrane (INM) functions in essential nuclear processes including chromatin organization and regulation of gene expression. The outer nuclear membrane is continuous with the endoplasmic reticulum and is the site of membrane protein synthesis. Protein homeostasis in this compartment is ensured by endoplasmic-reticulum-associated protein degradation (ERAD) pathways that in yeast involve the integral membrane E3 ubiquitin ligases Hrd1 and Doa10 operating with the E2 ubiquitin-conjugating enzymes Ubc6 and Ubc7 (refs 2, 3). However, little is known about protein quality control at the INM. Here we describe a protein degradation pathway at the INM in yeast (Saccharomyces cerevisiae) mediated by the Asi complex consisting of the RING domain proteins Asi1 and Asi3 (ref. 4). We report that the Asi complex functions together with the ubiquitin-conjugating enzymes Ubc6 and Ubc7 to degrade soluble and integral membrane proteins. Genetic evidence suggests that the Asi ubiquitin ligase defines a pathway distinct from, but complementary to, ERAD. Using unbiased screening with a novel genome-wide yeast library based on a tandem fluorescent protein timer, we identify more than 50 substrates of the Asi, Hrd1 and Doa10 E3 ubiquitin ligases. We show that the Asi ubiquitin ligase is involved in degradation of mislocalized integral membrane proteins, thus acting to maintain and safeguard the identity of the INM.
Published: 2014

39. Antepartum Dalteparin Versus no Antepartum Dalteparin for the Prevention of Pregnancy Complications in Pregnant Women With Thrombophilia (TIPPS)

Author: Graeme N. Smith, Ian A. Greer, Anne Marie Clement, James Dwyer, Mark Walker, Anne McLeod, Evelyne Rey, Kim Hinshaw, Suzette Coat, Joanne M Said, William M. Hague, John Kingdom, Alan Karovitch, Christine Demers, Susan R. Kahn, Robert M. Silver, Michael J. Kovacs, Susan Solymoss, Grégoire Le Gal, Jill Newstead-Angel, Mathew Sermer, Erin Keely, Wee-Shian Chan, Sarah D. McDonald, Rshmi Khurana, Philip S. Wells, Marc A. Rodger, Susan A. Robinson, Meena Khandelwal, Karen Rosene-Montella, Haematology, University of Ottawa [Ottawa], Clinical Epidemiology Program (PSW), The Ottawa Health Research Institute, Thrombosis Program, Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Hydrologie et de Géochimie de Strasbourg (LHyGeS), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Ecole et Observatoire des Sciences de la Terre (EOST), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamique des écosystèmes Caraïbe et biologie des espèces associées (DYNECAR EA 926), Université des Antilles et de la Guyane (UAG), Université Grenoble Alpes - UFR de Langues étrangères (LLCE et LEA) (UGA UFR LLCE LEA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Empirica ( Empirica Gesellschaft fuer Kommunikations und Technologieforschung MBH), GRAP, École d'architecture de l'Université Laval, Québec, Canada, Department of Medicine (LONDON ONTARIO - Med), University of Western Ontario (UWO), Department of Medecine [Montréal], McGill University = Université McGill [Montréal, Canada], University of Gloucestershire, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, European Southern Observatory (ESO), Department of Neuroscience, Physiology and Pharmacology, University College of London [London] (UCL), Groupe d'Etude de la Thrombose de Bretagne Occidentale (GETBO), Université de Brest (UBO)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO), Service d'angiologie et d'hémostase (MR), Hôpital Universitaire de Genève, Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), and Hôpital Universitaire de Genève = University Hospitals of Geneva (HUG)
Subjects: Dalteparin, medicine.medical_specialty, Antepartum, [SDV]Life Sciences [q-bio], 030204 cardiovascular system & hematology, [SDV.MHEP.GEO]Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, Thrombophilia, law.invention, 03 medical and health sciences, 0302 clinical medicine, Randomized controlled trial, law, Recurrent miscarriage, medicine, Stroke, Gynecology, Pregnancy, 030219 obstetrics & reproductive medicine, Placental abruption, Obstetrics, business.industry, Pregnant women, Prevention, Incidence (epidemiology), Absolute risk reduction, Obstetrics and Gynecology, Gestational age, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, General Medicine, 16. Peace & justice, medicine.disease, 3. Good health, Gestation, Open label, business, Fibrinolytic agent
Abstract: International audience; BACKGROUND: Thrombophilias are common disorders that increase the risk of pregnancy-associated venous thromboembolism and pregnancy loss and can also increase the risk of placenta-mediated pregnancy complications (severe pre-eclampsia, small-for-gestational-age infants, and placental abruption). We postulated that antepartum dalteparin would reduce these complications in pregnant women with thrombophilia. METHODS: In this open-label randomised trial undertaken in 36 tertiary care centres in five countries, we enrolled consenting pregnant women with thrombophilia at increased risk of venous thromboembolism or with previous placenta-mediated pregnancy complications. Eligible participants were randomly allocated in a 1:1 ratio to either antepartum prophylactic dose dalteparin (5000 international units once daily up to 20 weeks' gestation, and twice daily thereafter until at least 37 weeks' gestation) or to no antepartum dalteparin (control group). Randomisation was done by a web-based randomisation system, and was stratified by country and gestational age at randomisation day with a permuted block design (block sizes 4 and 8). At randomisation, site pharmacists (or delegates) received a randomisation number and treatment allocation (by fax and/or e-mail) from the central web randomisation system and then dispensed study drug to the local coordinator. Patients and study personnel were not masked to treatment assignment, but the outcome adjudicators were masked. The primary composite outcome was independently adjudicated severe or early-onset pre-eclampsia, small-for-gestational-age infant (birthweight
Published: 2015

40. Ka'ena Volcano--A precursor volcano of the island of O'ahu, Hawai'i

Author: Mary Tardona, Iris van der Zander, David A. Clague, Hervé Guillou, Douglas G. Pyle, Deborah E. Eason, John J. Mahoney, John M. Sinton, University of Hawai'i [Honolulu] (UH), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Paléocéanographie (PALEOCEAN), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, Dike, geography.geographical_feature_category, Lava, Geochemistry, Geology, Crust, Volcano, 13. Climate action, Ridge, Pumice, 14. Life underwater, Rift zone, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Submarine volcano, Geomorphology, ComputingMilieux_MISCELLANEOUS
Abstract: Ka‘ena and Wai‘alu Ridges form prominent submarine ridges NW of the island of O‘ahu, Hawai‘i. We evaluate whether or not either one of these ridges represents a submarine extension of Wai‘anae Volcano on O‘ahu using new bottom observations, geophysical surveys, and geochemical data acquired on new samples from the region. Wai‘alu Ridge has the morphology of a submarine rift zone but is too shallow for its distance from the O‘ahu shoreline; Ka‘ena Ridge also is unusually shallow and is surmounted by two topographic shields. Ka‘ena and Wai‘alu Ridges have similar magmatic and volcanic evolutionary histories, beginning ca. 5 Ma with a submarine, shield phase of volcanism that produced high-SiO 2 , low-FeO* tholeiites with higher 208 Pb/ 204 Pb than in the adjacent Wai‘anae Volcano. Late-shield volcanism included transitional and alkalic rock types, with lower SiO 2 and enrichment in incompatible elements, especially P 2 O 5 , Nb, Zr, Ti, and light rare earth elements. The transition from shield to late-shield stage occurred as the edifice was beginning to emerge from the sea. Geological observations and K/Ar ages indicate that Ka‘ena emerged above sea level ca. 3.5 Ma, reaching a maximum height of ∼4000 m above the abyssal ocean floor and 1000 m above sea level. Relatively weak gravity anomalies, topographic lineaments, and the orientation of dike complexes indicate a volcanic structure that is independent of Wai‘anae Volcano. Thus, volcanic structure, geochemistry, and age all indicate a precursor volcano to the island of O‘ahu, which we call Ka‘ena Volcano. After emergence, Ka‘ena Volcano tilted ∼2° to the south. We estimate a total volume of 20–27 × 10 3 km 3 for Ka‘ena Volcano, taking into account overlapping geometry of concurrently active volcanoes. Sample compositions from the Ka‘ena landslide deposit are entirely consistent with derivation from Ka‘ena, whereas most samples from the Wai‘anae slump are likely derived from Wai‘anae Volcano. Uniformly oriented dikes in the Wai‘anae NW rift zone likely reflect buttressing by a preexisting Ka‘ena Volcano. Unusual isotopic compositions of some Wai‘anae samples, including unique hydrous silicic lavas, probably reflect interaction with underlying Ka‘ena crust. A newly recognized lava flow field on the southern flank of Ka‘ena Ridge extends the previously known distribution of secondary volcanism in the Kaua‘i Channel. Putative submarine volcanic activity in the region in 1956 cannot have built a large edifice and is unlikely to have produced pumice that was found on O‘ahu shores. This eruptive activity therefore remains unconfirmed.
Published: 2014

41. Free-ocean CO 2 enrichment (FOCE) systems: present status and future developments

Author: Gattuso, Jean-Pierre, Kirkwood, W, Barry, J.P, Cox, E, Gazeau, Frédéric, Hansson, L, Hendriks, I, Kline, D.I., Mahacek, P, Martin, Sophie, Mcelhany, P., Peltzer, E.T., Reeve, J, Roberts, D, Saderne, V, Tait, K, Widdicombe, S, Brewer, P.G., Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, 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), Ocean Acidification International Coordination Centre, Global Change Department (IMEDEA (CSIC-UIB)), Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de las Islas Baleares (UIB)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de las Islas Baleares (UIB), Scripps Institute of Oceanography, University of California [San Diego] (UC San Diego), University of California-University of California, Ecogéochimie et Fonctionnement des Ecosystèmes Benthiques (EFEB), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Conservation Biology Division [Seattle], Northwest Fisheries Science Center (NWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Department of the environment, Channel Highway, Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Benthic Ecology group (GEOMAR), Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, 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)-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), Scripps Institution of Oceanography (SIO - UC San Diego), and University of California (UC)-University of California (UC)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry
Abstract: International audience; Free-ocean CO2 enrichment (FOCE) systems are designed to assess the impact of ocean acidification on biological communities in situ for extended periods of time (weeks to months). They overcome some of the drawbacks of laboratory experiments and field observations by enabling (1) precise control of CO2 enrichment by monitoring pH as an offset of ambient pH, (2) consideration of indirect effects such as those mediated through interspecific relationships and food webs, and (3) relatively long experiments with intact communities. Bringing perturbation experiments from the laboratory to the field is, however, extremely challenging. The main goal of this paper is to provide guidelines on the general design, engineering, and sensor options required to conduct FOCE experiments. Another goal is to introduce xFOCE, a community-led initiative to promote awareness, provide resources for in situ perturbation experiments, and build a user community. Present and existing FOCE systems are briefly described and examples of data collected presented. Future developments are also addressed as it is anticipated that the next generation of FOCE systems will include, in addition to pH, options for oxygen and/or temperature control. FOCE systems should become an important experimental approach for projecting the future response of marine ecosystems to environmental change.
Published: 2014

42. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

Author: Mary Ann Moran, Ronald P. Kiene, Matthew D. Johnson, Jennifer L. Jacobi, Gwenael Piganeau, Kjetill S. Jakobsen, Simon K. Davy, Edward C. Theriot, Uwe John, Alexander Kudryavtsev, Sarah R. Smith, Bente Edvardsen, Cristina Miceli, Adrian Marchetti, Karin Rengefors, Tatiana A. Rynearson, John M. Archibald, Matthew C. Posewitz, Brian Palenik, Alexandra Z. Worden, Pooja E. Umale, Boris Wawrik, Laura A. Katz, Satoshi Nagai, Anja Kamp, Lisa Campbell, Kathryn J. Coyne, Thomas Mock, E. Virginia Armbrust, Fabien Burki, Adriana Zingone, Sonya T. Dyhrman, Mary E. Rumpho, Bank Beszteri, Giovanna Romano, Declan C. Schroeder, Callum J. Bell, Yan Xu, Bassem Allam, Kay D. Bidle, Bethany D. Jenkins, Kelly B. Schilling, Giulio Petroni, David Roy Smith, Aurora M. Nedelcu, Arvind K. Bharti, Connie Lovejoy, Stephanie Guida, Spencer J. Greenwood, Peter Stief, David A. Caron, Senjie Lin, Marina Montresor, Denis H. Lynn, Patrick J. Keeling, Glen L. Wheeler, Linda A. Amaral-Zettler, Daniel Vaulot, Jan Pawlowski, Ruth D. Gates, Brian S. Leander, Heather M. Wilcox, Andrew R. Juhl, Govind Nadathur, Erick R. James, Rose Ann Cattolico, Alastair G. B. Simpson, Susanne Menden-Deuer, G. Jason Smith, George B. McManus, Christopher J. Gobler, Heidi M. Sosik, Connor Cameron, Jackie L. Collier, Shauna A. Murray, Scott N. Twary, William H. Wilson, Claudio H. Slamovits, Peter B. Ngam, Phillipe Deschamps, Eric E. Allen, Roberts, Roland G, Canadian Institute for Advanced Research (CIFAR), Department of Botany, University of British Columbia [Vancouver], Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Marine Biology Research Division, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), The Josephine Bay Paul Center for comparative molecular biology and evolution, Department of Geological Sciences [Providence], Brown University, School of Oceanography [Seattle], University of Washington [Seattle], Department of biochemistry & molecular biology, Dalhousie University [Halifax], National center for genome resources (NCGR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Institute of Marine and Coastal Science, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Department of Oceanography [College Station], Texas A&M University [College Station], Department of biology, University of Southern California (USC), University of Delaware [Newark], School of biological sciences, Victoria University of Wellington, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Department of earth and environmental sciences and the Lamont-Doherty earth observatory, Columbia University [New York], Department of Molecular Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Hawai'i Institute of Marine Biology, Hawai'i Institute of Marine Biology (HIMB), Department of biomedical sciences, University of Prince Edward Island, Graduate School of Oceanography [Narragansett], University of Rhode Island (URI), Department of cell and molecular biology, University of Rhode Island, University of Rhode Island (URI)-University of Rhode Island (URI), Woods Hole Oceanographic Institution (WHOI), Jacobs University [Bremen], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Department of biological sciences, Smith College [Northampton], University of South Alabama, Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University (SPSPU)-Saint Petersburg State Polytechnical University (SPSPU), Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Department of Marine sciences, University of Connecticut (UCONN), département de biologie, Université Laval [Québec] (ULaval), Department of Integrative Biology, University of Guelph, Department of zoology, University of British Columbia (UBC), Department of Marine, Earth, and Atmospheric Sciences [NCSU] (MEAS), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of New Brunswick (UNB), School of biosciences and biotechnology, Università degli Studi di Camerino = University of Camerino (UNICAM), School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Stazione Zoologica Anton Dohrn (SZN), Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney (UTS), Department of Marrine sciences, University of Puerto Rico (UPR), National Research Institute of Fisheries Science, University of Pisa - Università di Pisa, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry and Geochemistry, Colorado School of Mines, department of biology, Lund University [Lund], Department of molecular and cell biology, Marine Biological Association of the UK, University of Western Ontario (UWO), Moss Landing Marine Laboratories, Section of Integrative Biology, University of Texas at Austin [Austin], Los Alamos National Laboratory (LANL), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), department of microbiology and plant biology, University of Oklahoma (OU), Plymouth Marine Laboratory (PML), Bigelow Laboratory for Ocean Sciences, Princeton University, University of Britsh Columbia [Vancouver], University of California-University of California, University of Geneva [Switzerland], Università degli Studi di Camerino (UNICAM), Plymouth Marine Laboratory, and Roberts, Roland G.
Subjects: Genetics and Molecular Biology (all), Databases, Factual, animal genomics, Immunology and Microbiology (all), Biochemistry, Medical and Health Sciences, Transcriptome, transcriptome analysis, Community Page, sequence databases, Environmental Microbiology, Biology (General), Molecular Sequence Data, Sequence Analysis, Biodiversity, Eukaryota, Oceans and Seas, Agricultural and Biological Sciences (all), Biochemistry, Genetics and Molecular Biology (all), Neuroscience (all), Medicine (all), Genetics, General Neuroscience, marine ecology, Biological Sciences, genome sequencing, General Agricultural and Biological Sciences, Biologie, QH301-705.5, Sequence analysis, Ecology (disciplines), Marine Biology, Genomics, Biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Databases, Microbial ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 14. Life underwater, Life Below Water, Factual, Comparative genomics, Marine biology, Evolutionary Biology, General Immunology and Microbiology, Agricultural and Veterinary Sciences, Ecology and Environmental Sciences, Human Genome, Biology and Life Sciences, 15. Life on land, Evolutionary biology, plant genomics, Generic health relevance, genomic library construction, Genomic databases, Developmental Biology
Abstract: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes [1]. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics [2]. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases [3],[4], raising the question as to whether this is fit for purpose.
Published: 2014

43. Projected pH reductions by 2100 might put deep North Atlantic biodiversity at risk

Author: James P. Barry, Joachim Segschneider, Tilla Roy, Laurent Bopp, Raphael Roth, John P. Dunne, Jerry Tjiputra, Marion Gehlen, Roland Séférian, James C. Orr, Christoph Heinze, Scott C. Doney, Fortunat Joos, Daniel O.B. Jones, Laure Resplandy, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Modelling the Earth Response to Multiple Anthropogenic Interactions and Dynamics (MERMAID), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Groupe d'étude de l'atmosphère météorologique (CNRM-GAME), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS), National Oceanography Centre [Southampton] (NOC), University of Southampton, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), 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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), 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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Climate and Environmental Physics [Bern] (CEP), Physikalisches Institut [Bern], Universität Bern [Bern]-Universität Bern [Bern], Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Department of Marine Chemistry and Geochemistry (WHOI), Woods Hole Oceanographic Institution (WHOI), NOAA Geophysical Fluid Dynamics Laboratory (GFDL), National Oceanic and Atmospheric Administration (NOAA), Bjerknes Centre for Climate Research (BCCR), Department of Biological Sciences [Bergen] (BIO / UiB), University of Bergen (UiB)-University of Bergen (UiB), Geophysical Institute [Bergen] (GFI / BiU), University of Bergen (UiB), Uni Research Climate, Uni Research Ltd, Max Planck Institute for Meteorology (MPI-M), Max-Planck-Gesellschaft, ANR-10-LABX-0018,L-IPSL,LabEx Institut Pierre Simon Laplace (IPSL): Understand climate and anticipate future changes(2010), European Project: 211384,EC:FP7:ENV,FP7-ENV-2007-1,EPOCA(2008), European Project: 264879,EC:FP7:ENV,FP7-ENV-2010,CARBOCHANGE(2011), European Project: 312979,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2012-1,IS-ENES2(2013), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), and Universität Bern [Bern] (UNIBE)-Universität Bern [Bern] (UNIBE)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, 530 Physics, Seamount, Matematikk og naturvitenskap: 400::Geofag: 450::Oseanografi: 452 [VDP], lcsh:Life, Biodiversity, Climate change, 01 natural sciences, Mathematics and natural scienses: 400::Geosciences: 450::Oceanography: 452 [VDP], lcsh:QH540-549.5, Ecosystem, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 550 Earth sciences & geology, 0105 earth and related environmental sciences, Earth-Surface Processes, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Biota, Ocean acidification, 15. Life on land, lcsh:Geology, lcsh:QH501-531, Oceanography, 13. Climate action, Benthic zone, Marine protected area, lcsh:Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Geology
Abstract: International audience; This study aims to evaluate the potential for impacts of ocean acidification on North Atlantic deep-sea ecosystems in response to IPCC AR5 Representative Concentration Pathways (RCPs). Deep-sea biota is likely highly vulnerable to changes in seawater chemistry and sensitive to moderate excursions in pH. Here we show, from seven fully coupled Earth system models, that for three out of four RCPs over 17 % of the seafloor area below 500 m depth in the North Atlantic sector will experience pH reductions exceeding −0.2 units by 2100. Increased stratification in response to climate change partially alleviates the impact of ocean acidification on deep benthic environments. We report on major pH reductions over the deep North Atlantic seafloor (depth > 500 m) and at important deep-sea features, such as seamounts and canyons. By 2100, and under the high CO 2 scenario RCP8.5, pH reductions exceeding −0.2 (−0.3) units are projected in close to 23 % (∼ 15 %) of North Atlantic deep-sea canyons and ∼ 8 % (3 %) of seamounts-including seamounts proposed as sites of marine protected areas. The spatial pattern of impacts reflects the depth of the pH perturbation and does not scale linearly with atmospheric CO 2 concentration. Impacts may cause negative changes of the same magnitude or exceeding the current target of 10 % of preservation of marine biomes set by the convention on biological diversity, implying that ocean acidification may offset benefits from conservation/management strategies relying on the regulation of resource exploitation.
Published: 2014

44. An update to the surface ocean CO2 atlas (SOCAT version 2)

Author: Abdirahman M Omar, Jacqueline Boutin, T. Suzuki, Sara Jutterström, Aida F. Ríos, Reiner Schlitzer, Tobias Steinhoff, Arne Körtzinger, Ansley Manke, Nathalie Lefèvre, Nick J. Hardman-Mountford, H. Sun, S. van Heuven, J. Akl, T. Ichikawa, Ingunn Skjelvan, Andrew J. Watson, Leticia Barbero, Denis Pierrot, K. O'Brien, Z. Gao, Kevin Sullivan, Richard A. Feely, Rainer Sieger, R. D. Castle, Mario Hoppema, Aki Murata, Peter Landschützer, Truls Johannessen, Dorothee C. E. Bakker, Nobuo Tsurushima, Liliane Merlivat, Melissa Chierici, Alex Kozyr, Tsuneo Ono, H. J. W. de Baar, C. Cosca, Douglas W.R. Wallace, Betty Huss, Francisco P. Chavez, Christopher W. Hunt, Wiley Evans, K. Smith, Nicolas Metzl, Wei-Jen Huang, Agneta Fransson, Adrienne J. Sutton, Chisato Wada, K. Paterson, Kim I. Currie, Liqi Chen, Elizabeth M. Jones, Geun-Ha Park, Doug Vandemark, Penny Vlahos, Jerry Tjiputra, Taro Takahashi, Are Olsen, Siv K. Lauvset, Rik Wanninkhof, Wei-Jun Cai, Vassilis Kitidis, Nicholas R. Bates, Ute Schuster, Timothy Newberger, Colm Sweeney, V. V. S. S. Sarma, Bronte Tilbrook, S. Harasawa, Jeremy T. Mathis, S. Saito, Benjamin Pfeil, Maciej Telszewski, Steve D Jones, Burke Hales, Simone R. Alin, Joe Salisbury, Yukihiro Nojiri, Christopher L. Sabine, Yann Bozec, S. Hankin, University of East Anglia [Norwich] (UEA), Geophysical Institute [Bergen] (GFI / BiU), University of Bergen (UiB), Bjerknes Centre for Climate Research (BCCR), Department of Biological Sciences [Bergen] (BIO / UiB), University of Bergen (UiB)-University of Bergen (UiB), National Oceanic and Atmospheric Administration (NOAA), Joint Institute for the Study of the Atmosphere and Ocean (JISAO), University of Washington [Seattle], Institute of Cancer Epidemiology, Danish Cancer Society, NOAA Pacific Marine Environmental Laboratory [Seattle] (PMEL), National Institute for Environmental Studies (NIES), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), College of Life and Environmental Sciences [Exeter], University of Exeter, International Ocean Carbon Coordination Project, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami [Coral Gables], Bermuda Institute of Ocean Sciences (BIOS), Interactions et Processus au sein de la couche de Surface Océanique (IPSO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), 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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), 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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHImie Marine (CHIM), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Delaware [Newark], NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, University of Berlin, Marine Chemistry, Department of Chemistry, National Institute of Water and Atmospheric Research [Wellington] (NIWA), Royal Netherlands Institute for Sea Research (NIOZ), Computer Science Department (UBC-Computer Science), University of British Columbia (UBC), Norwegian Polar Institute, School of Mathematical Sciences, School of Mathematical Sciences, Beijing Normal University, Key Laboratory of Mathematics and Complex Systems, College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), Oceans and Atmosphere Flagship (CSIRO), CSIRO Oceans and Atmosphere Flagship, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Centre de Sciences Nucléaires et de Sciences de la Matière (CSNSM SNO), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Saclay-Univ. Paris-Sud, Ocean Process Analysis Laboratory (OPAL), University of New Hampshire (UNH), National Research Institute for Fisheries Science, Tyndall Centre for Climate Change Research and School of Environmental Sciences, IVL Swedish Environmental Research Institute Ltd, Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Institute of Biogeochemistry and Pollutant Dynamics [ETH Zürich] (IBP), Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Austral, Boréal et Carbone (ABC), Équipe CO2 (E-CO2), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado [Boulder]-National Oceanic and Atmospheric Administration (NOAA), National Institute of Advanced Industrial Science and Technology (AIST), Chemistry Department [Massachusetts Institute of Technology], Massachusetts Institute of Technology (MIT), Department of Computer Science [Royal Holloway], Royal Holloway [University of London] (RHUL), Cooperative Institute for Marine and Atmospheric Studies (CIMAS), University of Miami [Coral Gables]-University of Miami [Coral Gables], Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Japan Meteorological Agency (JMA), National Institute of Oceanography (CSIR), CSIR National Institute of Oceanography [India] (NIO), Department of chemistry and Biochemistry (DCB), Brigham Young University (BYU), École normale supérieure - Lyon (ENS Lyon), Marine Information Research Center, Instituto de Investigaciones Marinas de Vigo, Department of Mechanical Science and Engineering, Nagoya University, Centre for Isotope Research [Groningen] (CIO), University of Groningen [Groningen], Ocean Process Analysis Laboratory, Department of Marine Sciences, University of Connecticut (UCONN), Department of Oceanography [Halifax] (DO), Dalhousie University [Halifax], Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Swedish Environmental Research Institute (IVL), École normale supérieure de Lyon (ENS de Lyon), Ocean Ecosystems, and Isotope Research
Subjects: 0106 biological sciences, WATER FCO(2), PACIFIC, 010504 meteorology & atmospheric sciences, Data products, Meteorology, Surface ocean, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], 7. Clean energy, 01 natural sciences, Set (abstract data type), CARBON-DIOXIDE, Data acquisition, CAVITY RINGDOWN SPECTROSCOPY, AIR-SEA FLUX, PCO(2) VARIABILITY, 14. Life underwater, ATMOSPHERIC CO2, SOUTHERN-OCEAN, lcsh:Environmental sciences, 0105 earth and related environmental sciences, lcsh:GE1-350, Data processing, Atlas (topology), 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Carbon sink, Metadata, lcsh:Geology, NORTH-ATLANTIC-OCEAN, ANTARCTIC PENINSULA, 13. Climate action, Climatology, General Earth and Planetary Sciences, Environmental science
Abstract: 22 páginas, 9 figuras, 10 tablas.-- D. C. E. Bakker ... et al.-- This work is distributed under the Creative Commons Attribution 3.0 License.-- Proyecto Carbochange, The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO2 values) and extended data coverage (from 1968–2007 to 1968–2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models, Support for SOCAT has been received from the University of East Anglia (UK), the Bjerknes Centre for Climate Research, the Geophysical Institute at the University of Bergen (Norway), the Climate Observation Division of the Climate Program Office of the US National Oceanic and Atmospheric Administration, the University of Washington, Oak Ridge National Laboratory (USA), PANGAEA ® Data Publisher for Earth and Environmental Data (Germany), the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Germany), the National Institute for Environmental Studies (Japan), the Korean Institute of Ocean Science and Technology, the European Union projects CarboChange (FP7 264879) and GEO- CARBON (FP7 283080), the UK Ocean Acidification Research Programme (NE/H017046/1; funded by the Natural Environment Research Council, the Department for Energy and Climate Change and the Department for Environment, Food and Rural Affairs), the Research Council of Norway (CARBON-HEAT), the Scientific Committee on Oceanic Research (SCOR, US, OCE-0938349), the US National Science Foundation (OCE-1068958), Swedish Research Council projects (2009–2994; 2008–6228; 2009–2994) and the Swedish National Space Board (RESCUE project; REmote Sensing ocean Carbon UptakE).
Published: 2014

45. Physical-biological synchrony in the global ocean associated with recent variability in the central and western equatorial Pacific

Author: Messié, Monique, Chavez, Francisco, Monterey Bay Aquarium Research Institute (MBARI), and Monterey Bay Aquarium Research Institute
Subjects: ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience
Published: 2013

46. A global analysis of ENSO synchrony: The oceans' biological response to physical forcing

Author: Messié, Monique, Chavez, Francisco, Monterey Bay Aquarium Research Institute (MBARI), and Monterey Bay Aquarium Research Institute
Subjects: ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience
Published: 2012

47. Oxygen: A Fundamental Property Regulating Pelagic Ecosystem Structure in the Coastal Southeastern Tropical Pacific

Author: Arnaud Bertrand, Jesus Ledesma, Francisco P. Chavez, Michelle Graco, Alexis Chaigneau, Salvador Peraltilla, Florian Monetti, UMR 212 EME 'écosystèmes marins exploités' (EME), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD), Instituto del Mar del Peru (IMARPE), Echanges Côte-Large (ECOLA), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), and 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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, lcsh:Medicine, Marine Biology, Biology, Oceanography, 01 natural sciences, Abundance (ecology), Anchovy, Oceans, Animals, Marine ecosystem, Ecosystem, 14. Life underwater, lcsh:Science, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Tropical Climate, Multidisciplinary, Pacific Ocean, Ecology, 010604 marine biology & hydrobiology, lcsh:R, Sardine, Marine Ecology, Fishes, Pelagic zone, Biogeochemistry, biology.organism_classification, Marine Environments, Marine and aquatic sciences, Oxygen, Earth sciences, Community Ecology, Forage fish, Upwelling, lcsh:Q, Ocean Properties, Zoology, Ichthyology, Research Article, Ecological Environments
Abstract: Background: In the southeastern tropical Pacific anchovy (Engraulis ringens) and sardine (Sardinops sagax) abundance have recently fluctuated on multidecadal scales and food and temperature have been proposed as the key parameters explaining these changes. However, ecological and paleoecological studies, and the fact that anchovies and sardines are favored differently in other regions, raise questions about the role of temperature. Here we investigate the role of oxygen in structuring fish populations in the Peruvian upwelling ecosystem that has evolved over anoxic conditions and is one of the world's most productive ecosystems in terms of forage fish. This study is particularly relevant given that the distribution of oxygen in the ocean is changing with uncertain consequences. Methodology/Principal Findings: A comprehensive data set is used to show how oxygen concentration and oxycline depth affect the abundance and distribution of pelagic fish. We show that the effects of oxygen on anchovy and sardine are opposite. Anchovy flourishes under relatively low oxygen conditions while sardine avoid periods/areas with low oxygen concentration and restricted habitat. Oxygen consumption, trophic structure and habitat compression play a fundamental role in fish dynamics in this important ecosystem. Conclusions/Significance: For the ocean off Peru we suggest that a key process, the need to breathe, has been neglected previously. Inclusion of this missing piece allows the development of a comprehensive conceptual model of pelagic fish populations and change in an ocean ecosystem impacted by low oxygen. Should current trends in oxygen in the ocean continue similar effects may be evident in other coastal upwelling ecosystems.
Published: 2011

48. Rapid reorganization in ocean biogeochemistry off Peru towards the end of the Little Ice Age

Author: Hugues Boucher, Mohammed Boussafir, M. Mandeng-Yogo, Tim R. Baumgartner, Dimitri Gutiérrez, A. Campusano, Jean-Louis Reyss, Federico Velazco, Pedro M. Tapia, Renato Salvatteci, Francisco P. Chavez, Vicente Ferreira, A. Sifeddine, Luc Ortlieb, M. Garcia, Gabriel Vargas, M. C. Morales, Jorge Valdés, David B. Field, Direccion de Investigaciones Oceanograficas, Instituto del Mar del Peru (IMARPE), Paléo-environnements tropicaux et variabilité climatique (PALEOTROPIQUE), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Departamento de Geología, Universidad de Chile = University of Chile [Santiago] (UCHILE), Centro de Investigacion Científica y de Educacion Superior de Ensenada, Laboratorio de Palinologia y Paleobotanica, Universidad Peruana Cayetano Heredia (UPCH), Facultad de Recursos del Mar, Universidad de Antofagasta, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Océan et Interfaces (OCEANIS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut des Sciences de la Terre d'Orléans (ISTO), Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Petroproduccion, Petroecuador, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Biogeochemical cycle, 010504 meteorology & atmospheric sciences, lcsh:Life, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Present day, 010502 geochemistry & geophysics, 01 natural sciences, lcsh:QH540-549.5, Subtropical ridge, Regime shift, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Earth-Surface Processes, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 010604 marine biology & hydrobiology, Intertropical Convergence Zone, lcsh:QE1-996.5, Biogeochemistry, Pelagic zone, lcsh:Geology, lcsh:QH501-531, Oceanography, 13. Climate action, Walker circulation, lcsh:Ecology, Geology
Abstract: Climate and ocean ecosystem variability has been well recognized during the twentieth century but it is unclear if modern ocean biogeochemistry is susceptible to the large, abrupt shifts that characterized the Late Quaternary. Time series from marine sediments off Peru show an abrupt centennial-scale biogeochemical regime shift in the early nineteenth century, of much greater magnitude and duration than present day multi-decadal variability. A rapid expansion of the subsurface nutrient-rich, oxygen-depleted waters resulted in the present-day higher biological productivity, including pelagic fish. The shift was likely driven by a northward migration of the Intertropical Convergence Zone and the South Pacific Subtropical High to their present day locations, coupled with a strengthening of Walker circulation, towards the end of the Little Ice Age. These findings reveal the potential for large reorganizations in tropical Pacific climate with immediate effects on ocean biogeochemical cycling and ecosystem structure.
Published: 2009

49. Development, implementation and evaluation of a data-assimilative ocean forecasting system off the central California coast

Author: Patrick Marchesiello, James D. Doyle, James C. McWilliams, John D. Farrara, Russ E. Davis, Yi Chao, Jei-Kook Choi, Francisco P. Chavez, James G. Bellingham, Steve Ramp, Jeffrey D. Paduan, Mark A. Moline, David M. Fratantoni, Zhijin Li, Peggy Li, Xavier Capet, Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Raytheon ITSS, University of California, University of California [Los Angeles] (UCLA), University of California-University of California, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Naval Oceanographic Office, Scripps Institute of Oceanography, University of California [San Diego] (UC San Diego), Naval Research Laboratory (NRL), Woods Hole Oceanographic Institution (WHOI), Echanges Côte-Large (ECOLA), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), and Naval Postgraduate School (NPS)
Subjects: 010504 meteorology & atmospheric sciences, Meteorology, 010505 oceanography, Ocean current, Coastal ocean, Glider, Temperature salinity diagrams, Ocean modeling, Forecast skill, Reanalysis, Regional Ocean Modeling System, Oceanography, 01 natural sciences, Adaptive sampling, Nested set model, Data assimilation, Climatology, Environmental science, 14. Life underwater, Predictability, Ocean forecast, 0105 earth and related environmental sciences
Abstract: The development and implementation of a real-time ocean forecast system based on the Regional Ocean Modeling System (ROMS) off the coast of central California are described. The ROMS configuration consists of three nested modeling domains with increasing spatial resolutions: the US West coastal ocean at 15-km resolution, the central California coastal ocean at 5 km, and the Monterey Bay region at 1.5 km. All three nested models have 32 vertical sigma (or terrain-following) layers and were integrated in conj. unction with a three-dimensional variational data assimilation algorithm (3DVAR) to produce snapshots of the ocean state every 6 h (the reanalysis) and 48-h forecasts once a day. This ROMS forecast system was operated in real time during the field experiment known as the Autonomous Ocean Sampling Network (AOSN-II) in August 2003. After the field experiment, a number of improvements were made to the ROMS forecast system: more data were added in the reanalysis with more careful quality control procedures, improvements were made in the data assimilation scheme, as well as model surface and side boundary conditions. The results from the ROMS reanalysis are presented here. The ROMS reanalysis is first compared with the assimilated data as a consistency check. An evaluation of the ROMS reanalysis against the independent measurements that are not assimilated into the model is then presented. This evaluation shows the mean differences in temperature and salinity between reanalysis and observations to be less than 1 degrees C and 0.2 psu (practical salinity unit), respectively, with root-mean-square (RMS) differences of less than 1.5 degrees C and 0.25 psu. Qualitative agreement is found between independent current measurements and the ROMS reanalysis. The agreement is particularly good for the vertically integrated current along the offshore glider tracks: the ROMS reanalysis can realistically reproduce the poleward California Undercurrent. Reasonably good agreement is found in the spatial patterns of the surface current as measured by high-frequency (HF) radars. Preliminary results concerning the ROMS forecast skill and predictability are also presented. Future plans to improve the ROMS forecast system with a particular focus on assimilation of HF radar current measurements are discussed. Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration (NASA) Office of Naval Research (ONR) through a subcontract from MBARI to Raytheon ONR’s program element 0601153N for J. Doyle Computational resources for COAMPS were supported in part by the FNMOC.
Published: 2009

50. Early Gene Duplication within Chloroplastida and its correspondence with Relocation of Starch Metabolism to Chloroplasts

Author: Steven G. Ball, David Dauvillée, Hervé Moreau, Alexandra Z. Worden, Philippe Deschamps, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie biologique de Banyuls (LOBB), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Chloroplasts, Chlamydomonas reinhardtii, Oligosaccharides, Investigations, 01 natural sciences, Ostreococcus, 03 medical and health sciences, Volvox, Gene Duplication, Genetics, Glaucophyta, Plastid, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Endosymbiosis, Archaeplastida, Eukaryota, Membrane Transport Proteins, food and beverages, Starch, biology.organism_classification, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Chloroplast, Adenosine Diphosphate, Isoenzymes, Glucose, Biochemistry, 010606 plant biology & botany
Abstract: The endosymbiosis event resulting in the plastid of photosynthetic eukaryotes was accompanied by the appearance of a novel form of storage polysaccharide in Rhodophyceae, Glaucophyta, and Chloroplastida. Previous analyses indicated that starch synthesis resulted from the merging of the cyanobacterial and the eukaryotic storage polysaccharide metabolism pathways. We performed a comparative bioinformatic analysis of six algal genome sequences to investigate this merger. Specifically, we analyzed two Chlorophyceae, Chlamydomonas reinhardtii and Volvox carterii, and four Prasinophytae, two Ostreococcus strains and two Micromonas pusilla strains. Our analyses revealed a complex metabolic pathway whose intricacies and function seem conserved throughout the green lineage. Comparison of this pathway to that recently proposed for the Rhodophyceae suggests that the complexity that we observed is unique to the green lineage and was generated when the latter diverged from the red algae. This finding corresponds well with the plastidial location of starch metabolism in Chloroplastidae. In contrast, Rhodophyceae and Glaucophyta produce and store starch in the cytoplasm and have a lower complexity pathway. Cytoplasmic starch synthesis is currently hypothesized to represent the ancestral state of storage polysaccharide metabolism in Archaeplastida. The retargeting of components of the cytoplasmic pathway to plastids likely required a complex stepwise process involving several rounds of gene duplications. We propose that this relocation of glucan synthesis to the plastid facilitated evolution of chlorophyll-containing light-harvesting complex antennae by playing a protective role within the chloroplast.
Published: 2008

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