1
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Begouen Demeaux C, Boss E, Tan J, Frouin R. Algorithms to retrieve the spectral diffuse attenuation coefficient of light in the ocean from remote sensing. Opt Express 2024; 32:2507-2526. [PMID: 38297778 DOI: 10.1364/oe.505497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024]
Abstract
We recently found a significant bias between spectral diffuse attenuation coefficient (Kd(λ)) retrievals by common ocean color algorithms and measurements from profiling floats [Remote. Sens.14, 4500 (2022)10.3390/rs14184500]. Here we show, using a multi-satellite match-up dataset, that the bias is markedly reduced by simple "tuning" of the algorithm's empirical coefficients. However, while the float dataset encompasses a larger proportion of the ocean's variability than previously used datasets, it does not cover the whole range of variability of observed remote sensing reflectance (Rrs). Thus, using algorithms tuned to this more comprehensive dataset may still result in a temporal and/or geographical bias in global application. To address this generalization issue, we evaluated a variety of analytical algorithms based on radiative transfer theory and settled on a specific one. This algorithm computes Kd(λ) from inherent optical properties (IOPs) obtained from an Rrs inversion and information about the angular distribution of the radiance transmitted through the air/ocean interface. The resulting Kd(λ) estimates at 412 and 490 nm were not appreciably biased against the float measurements. Evaluation using other in-situ datasets and radiative transfer simulations was also satisfactory. Statistical performance was good in both clear and turbid waters. Further work should be conducted to examine whether the tuned algorithms and/or the new analytical algorithm demonstrate adequate hyperspectral performance.
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2
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Bisson KM, Werdell PJ, Chase AP, Kramer SJ, Cael BB, Boss E, McKinna L, Behrenfeld MJ. Informing ocean color inversion products by seeding with ancillary observations. Opt Express 2023; 31:40557-40572. [PMID: 38041353 DOI: 10.1364/oe.503496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Ocean reflectance inversion algorithms provide many products used in ecological and biogeochemical models. While a number of different inversion approaches exist, they all use only spectral remote-sensing reflectances (Rrs(λ)) as input to derive inherent optical properties (IOPs) in optically deep oceanic waters. However, information content in Rrs(λ) is limited, so spectral inversion algorithms may benefit from additional inputs. Here, we test the simplest possible case of ingesting optical data ('seeding') within an inversion scheme (the Generalized Inherent Optical Property algorithm framework default configuration (GIOP-DC)) with both simulated and satellite datasets of an independently known or estimated IOP, the particulate backscattering coefficient at 532 nm (bbp(532)). We find that the seeded-inversion absorption products are substantially different and more accurate than those generated by the standard implementation. On global scales, seasonal patterns in seeded-inversion absorption products vary by more than 50% compared to absorption from the GIOP-DC. This study proposes one framework in which to consider the next generation of ocean color inversion schemes by highlighting the possibility of adding information collected with an independent sensor.
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3
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Kaneko H, Endo H, Henry N, Berney C, Mahé F, Poulain J, Labadie K, Beluche O, El Hourany R, Chaffron S, Wincker P, Nakamura R, Karp-Boss L, Boss E, Bowler C, de Vargas C, Tomii K, Ogata H. Predicting global distributions of eukaryotic plankton communities from satellite data. ISME Commun 2023; 3:101. [PMID: 37740029 PMCID: PMC10517053 DOI: 10.1038/s43705-023-00308-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic-subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.
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Affiliation(s)
- Hiroto Kaneko
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Nicolas Henry
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016, Paris, France
| | - Cédric Berney
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29680, Roscoff, France
| | - Frédéric Mahé
- CIRAD, UMR PHIM, F-34398, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Odette Beluche
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Roy El Hourany
- Univ. Littoral Côte d'Opale, Univ. Lille, CNRS, IRD, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 62930, Wimereux, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Ryosuke Nakamura
- Digital Architecture Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29680, Roscoff, France
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
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4
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Zhang K, Chen Y, Zhao H, Lee Z, Boss E, Stachlewska I, Dionisi D, Jamet C, Girolamo PD, Malinka A, Jiang C, Wu H, Wu L, Chen F, Zhu X, Wang N, Chen C, Liu Q, Wu L, Zhou Y, Chen W, Liu D. Comprehensive, Continuous, and Vertical Measurements of Seawater Constituents with Triple-Field-of-View High-Spectral-Resolution Lidar. Research (Wash D C) 2023; 6:0201. [PMID: 37475723 PMCID: PMC10355187 DOI: 10.34133/research.0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
Measuring the characteristics of seawater constituent is in great demand for studies of marine ecosystems and biogeochemistry. However, existing techniques based on remote sensing or in situ samplings present various tradeoffs with regard to the diversity, synchronism, temporal-spatial resolution, and depth-resolved capacity of their data products. Here, we demonstrate a novel oceanic triple-field-of-view (FOV) high-spectral-resolution lidar (HSRL) with an iterative retrieval approach. This technique provides, for the first time, comprehensive, continuous, and vertical measurements of seawater absorption coefficient, scattering coefficient, and slope of particle size distribution, which are validated by simulations and field experiments. Furthermore, it depicts valuable application potentials in the accuracy improvement of seawater classification and the continuous estimation of depth-resolved particulate organic carbon export. The triple-FOV HSRL with high performance could greatly increase the knowledge of seawater constituents and promote the understanding of marine ecosystems and biogeochemistry.
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Affiliation(s)
- Kai Zhang
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center,
Zhejiang University, Hangzhou 311200, China
| | - Yatong Chen
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
- Donghai Laboratory, Zhoushan 316021, China
| | - Hongkai Zhao
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Zhongping Lee
- State Key Lab of Marine Environmental Science, College of Ocean and Earth Sciences,
Xiamen University, Xiamen 361102, China
| | - Emmanuel Boss
- School of Marine Sciences,
University of Maine, Orono, ME 04469-5741, USA
| | | | - Davide Dionisi
- Institute of Marine Sciences,
Italian National Research Council, Rome 00133, Italy
| | - Cédric Jamet
- Université du Littoral Côte d'Opale, CNRS, Univ. Lille, IRD, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, Wimereux F-62930, France
| | - Paolo D. Girolamo
- Institute Scuola di Ingegneria,
Università della Basilicata, Potenza 85100, Italy
| | - Aleksey Malinka
- Institute of Physics,
National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Chengchong Jiang
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Hongda Wu
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Lingyun Wu
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Feitong Chen
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Xiaolei Zhu
- Key Laboratory of Space Laser Communication and Detection Technology, Shanghai Institute of Optics and Fine Mechanics,
Chinese Academy of Sciences, Shanghai 201800, China
| | - Nanchao Wang
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Chuxiao Chen
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Qun Liu
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Lan Wu
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Yudi Zhou
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
| | - Weibiao Chen
- Key Laboratory of Space Laser Communication and Detection Technology, Shanghai Institute of Optics and Fine Mechanics,
Chinese Academy of Sciences, Shanghai 201800, China
| | - Dong Liu
- Ningbo Research Institute, State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering,
Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center,
Zhejiang University, Hangzhou 311200, China
- Intelligent Optics & Photonics Research Center,
Jiaxing Research Institute Zhejiang University, Jiaxing 314000, China
- Jiaxing Key Laboratory of Photonic Sensing & Intelligent Imaging, Jiaxing 314000, China
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5
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Canesi M, Douville E, Montagna P, Taviani M, Stolarski J, Bordier L, Dapoigny A, Coulibaly GEH, Simon AC, Agelou M, Fin J, Metzl N, Iwankow G, Allemand D, Planes S, Moulin C, Lombard F, Bourdin G, Troublé R, Agostini S, Banaigs B, Boissin E, Boss E, Bowler C, de Vargas C, Flores M, Forcioli D, Furla P, Gilson E, Galand PE, Pesant S, Sunagawa S, Thomas OP, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, Reynaud S. Differences in carbonate chemistry up-regulation of long-lived reef-building corals. Sci Rep 2023; 13:11589. [PMID: 37463961 DOI: 10.1038/s41598-023-37598-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.
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Affiliation(s)
- Marine Canesi
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France.
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco.
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco.
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | - Paolo Montagna
- Institute of Polar Sciences (ISP), CNR, Via Gobetti 101, 40129, Bologna, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Marco Taviani
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
- Institute of Marine Sciences (ISMAR), CNR, Via Gobetti 101, 40129, Bologna, Italy
| | - Jarosław Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, 00818, Warsaw, Poland
| | - Louise Bordier
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | - Arnaud Dapoigny
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | - Gninwoyo Eric Hermann Coulibaly
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | | | | | - Jonathan Fin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, 75005, Paris, France
| | - Nicolas Metzl
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, 75005, Paris, France
| | - Guillaume Iwankow
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
| | - Serge Planes
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | | | - Fabien Lombard
- Institut de la Mer de Villefranche Sur Mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, 06230, Villefranche-sur-Mer, France
| | | | | | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | - Emilie Boissin
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Sorbonne Université, 29680, Roscoff, France
| | - Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
- Institute for Research on Cancer and Aging (IRCAN), Nice, France
| | - Paola Furla
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
- Institute for Research on Cancer and Aging (IRCAN), Nice, France
| | - Eric Gilson
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
- Institute for Research on Cancer and Aging (IRCAN), Nice, France
- Department of Medical Genetics, CHU, Nice, France
| | - Pierre E Galand
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Sorbonne Université, 66650, Banyuls sur Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, H91 TK33, Galway, Ireland
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
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6
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Knowles B, Bonachela JA, Cieslik N, Della Penna A, Diaz B, Baetge N, Behrenfeld MJ, Naumovitz K, Boss E, Graff JR, Halsey KH, Haramaty L, Karp-Boss L, Bidle KD. Altered growth and death in dilution-based viral predation assays. PLoS One 2023; 18:e0288114. [PMID: 37418487 DOI: 10.1371/journal.pone.0288114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Viral lysis of phytoplankton is one of the most common forms of death on Earth. Building on an assay used extensively to assess rates of phytoplankton loss to predation by grazers, lysis rates are increasingly quantified through dilution-based techniques. In this approach, dilution of viruses and hosts are expected to reduce infection rates and thus increase host net growth rates (i.e., accumulation rates). The difference between diluted and undiluted host growth rates is interpreted as a measurable proxy for the rate of viral lytic death. These assays are usually conducted in volumes ≥ 1 L. To increase throughput, we implemented a miniaturized, high-throughput, high-replication, flow cytometric microplate dilution assay to measure viral lysis in environmental samples sourced from a suburban pond and the North Atlantic Ocean. The most notable outcome we observed was a decline in phytoplankton densities that was exacerbated by dilution, instead of the increased growth rates expected from lowered virus-phytoplankton encounters. We sought to explain this counterintuitive outcome using theoretical, environmental, and experimental analyses. Our study shows that, while die-offs could be partly explained by a 'plate effect' due to small incubation volumes and cells adhering to walls, the declines in phytoplankton densities are not volume-dependent. Rather, they are driven by many density- and physiology-dependent effects of dilution on predation pressure, nutrient limitation, and growth, all of which violate the original assumptions of dilution assays. As these effects are volume-independent, these processes likely occur in all dilution assays that our analyses show to be remarkably sensitive to dilution-altered phytoplankton growth and insensitive to actual predation pressure. Incorporating altered growth as well as predation, we present a logical framework that categorizes locations by the relative dominance of these mechanisms, with general applicability to dilution-based assays.
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Affiliation(s)
- Ben Knowles
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, California, United States of America
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Juan A Bonachela
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nick Cieslik
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Alice Della Penna
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Ben Diaz
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nick Baetge
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Micheal J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Karen Naumovitz
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Jason R Graff
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kimberly H Halsey
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Liti Haramaty
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Kay D Bidle
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
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7
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Cael BB, Bisson K, Boss E, Dutkiewicz S, Henson S. Global climate-change trends detected in indicators of ocean ecology. Nature 2023; 619:551-554. [PMID: 37438519 PMCID: PMC10356596 DOI: 10.1038/s41586-023-06321-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Strong natural variability has been thought to mask possible climate-change-driven trends in phytoplankton populations from Earth-observing satellites. More than 30 years of continuous data were thought to be needed to detect a trend driven by climate change1. Here we show that climate-change trends emerge more rapidly in ocean colour (remote-sensing reflectance, Rrs), because Rrs is multivariate and some wavebands have low interannual variability. We analyse a 20-year Rrs time series from the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Aqua satellite, and find significant trends in Rrs for 56% of the global surface ocean, mainly equatorward of 40°. The climate-change signal in Rrs emerges after 20 years in similar regions covering a similar fraction of the ocean in a state-of-the-art ecosystem model2, which suggests that our observed trends indicate shifts in ocean colour-and, by extension, in surface-ocean ecosystems-that are driven by climate change. On the whole, low-latitude oceans have become greener in the past 20 years.
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Affiliation(s)
- B B Cael
- National Oceanography Centre, Southampton, UK.
| | - Kelsey Bisson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | | | - Stephanie Dutkiewicz
- Center for Global Change Science, Massachusetts Institute of Technology, Cambridge, MA, USA
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8
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O'Brien T, Boss E. Correction: O'Brien et al. Correction of Radiometry Data for Temperature Effect on Dark Current, with Application to Radiometers on Profiling Floats. Sensors 2022, 22, 6771. Sensors (Basel) 2023; 23:5700. [PMID: 37420939 DOI: 10.3390/s23125700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 07/09/2023]
Abstract
The authors wish to correct the following errors in the original paper [...].
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Affiliation(s)
- Terence O'Brien
- Institute for the Study of Earth, Ocean and Space, University of New Hampshire, Durham, NH 03824, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
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9
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Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz-García DA, Nugues MM, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nat Commun 2023; 14:3037. [PMID: 37264015 DOI: 10.1038/s41467-023-38502-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.
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Affiliation(s)
- Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | | | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany
| | - Barbara Porro
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Claudia Pogoreutz
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maggy M Nugues
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Paola Furla
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric Gilson
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Department of Medical Genetics, CHU Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, 8 rue de Prague, 75012, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
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10
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Rouan A, Pousse M, Djerbi N, Porro B, Bourdin G, Carradec Q, Hume BC, Poulain J, Lê-Hoang J, Armstrong E, Agostini S, Salazar G, Ruscheweyh HJ, Aury JM, Paz-García DA, McMinds R, Giraud-Panis MJ, Deshuraud R, Ottaviani A, Morini LD, Leone C, Wurzer L, Tran J, Zoccola D, Pey A, Moulin C, Boissin E, Iwankow G, Romac S, de Vargas C, Banaigs B, Boss E, Bowler C, Douville E, Flores M, Reynaud S, Thomas OP, Troublé R, Thurber RV, Planes S, Allemand D, Pesant S, Galand PE, Wincker P, Sunagawa S, Röttinger E, Furla P, Voolstra CR, Forcioli D, Lombard F, Gilson E. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals. Nat Commun 2023; 14:3038. [PMID: 37263999 DOI: 10.1038/s41467-023-38499-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.
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Affiliation(s)
- Alice Rouan
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France.
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France.
| | - Melanie Pousse
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Nadir Djerbi
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Barbara Porro
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | | | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Benjamin Cc Hume
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, La Paz, Baja California Sur, 23096, La Paz, México
| | - Ryan McMinds
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- University of South Florida Center for Global Health and Infectious Diseases Research, Tampa, FL, USA
- Maison de la Modélisation, de la Simulation et des Interactions (MSI),, Université Côte d'Azur, Nice, France
| | - Marie-Josèphe Giraud-Panis
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Romane Deshuraud
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Alexandre Ottaviani
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Lycia Die Morini
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Camille Leone
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Lia Wurzer
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Jessica Tran
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Alexis Pey
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Tara Ocean Foundation, 8 rue de Prague, 75012, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Guillaume Iwankow
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Bernard Banaigs
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth, and Planetary Sciences, 76100, Rehovot, Israel
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, H91TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Tara Ocean Foundation, 8 rue de Prague, 75012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Stephane Pesant
- European Bioinformatics Institute, Wellcome Genome Campus, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge CB10 1SD, UK, UK
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Eric Röttinger
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Paola Furla
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | | | - Didier Forcioli
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
- Institut Universitaire de France, Ministère chargé de l'enseignement supérieur, Paris, France
| | - Eric Gilson
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France.
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France.
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France.
- Department of Medical Genetics, CHU, Nice, France.
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11
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Lombard F, Bourdin G, Pesant S, Agostini S, Baudena A, Boissin E, Cassar N, Clampitt M, Conan P, Da Silva O, Dimier C, Douville E, Elineau A, Fin J, Flores JM, Ghiglione JF, Hume BCC, Jalabert L, John SG, Kelly RL, Koren I, Lin Y, Marie D, McMinds R, Mériguet Z, Metzl N, Paz-García DA, Pedrotti ML, Poulain J, Pujo-Pay M, Ras J, Reverdin G, Romac S, Rouan A, Röttinger E, Vardi A, Voolstra CR, Moulin C, Iwankow G, Banaigs B, Bowler C, de Vargas C, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Sullivan MB, Thomas OP, Troublé R, Thurber RV, Wincker P, Zoccola D, Allemand D, Planes S, Boss E, Gorsky G. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Sci Data 2023; 10:324. [PMID: 37264023 DOI: 10.1038/s41597-022-01757-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/10/2022] [Indexed: 06/03/2023] Open
Abstract
The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.
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Affiliation(s)
- Fabien Lombard
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
- Institut Universitaire de France, 75231, Paris, France.
| | - Guillaume Bourdin
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Alberto Baudena
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Nicolas Cassar
- Nicholas School of the Environment, Duke University, Durham, NC, USA
- Laboratoire des Sciences de l'Environnement Marin, UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer, Brest, France
| | - Megan Clampitt
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Pascal Conan
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
- Sorbonne Université, CNRS, OSU STAMAR - UAR2017, 75252 Paris, France
| | - Ophélie Da Silva
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Céline Dimier
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Amanda Elineau
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Jonathan Fin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - J Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Jean-François Ghiglione
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
| | | | - Laetitia Jalabert
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Rachel L Kelly
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Ilan Koren
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Yajuan Lin
- Nicholas School of the Environment, Duke University, Durham, NC, USA
- Laboratoire des Sciences de l'Environnement Marin, UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer, Brest, France
- Environmental Research Center, Duke Kunshan University, Kunshan, China
| | - Dominique Marie
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Ryan McMinds
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Maison de la Modélisation, de la Simulation et des Interactions (MSI), Nice, France
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Zoé Mériguet
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Nicolas Metzl
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maria Luiza Pedrotti
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Mireille Pujo-Pay
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
| | - Joséphine Ras
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Gilles Reverdin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Assaf Vardi
- Weizmann Institute of Science, Department of Plant and Environmental Science, Rehovot, Israel
| | | | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, UMR 8222, LECOB, Banyuls-sur-Mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Department of Medical Genetics, CHU, Nice, France
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Matthew B Sullivan
- Department of Microbiology and Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, Galway, Ireland
| | | | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Gaby Gorsky
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
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12
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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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13
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Galand PE, Ruscheweyh HJ, Salazar G, Hochart C, Henry N, Hume BCC, Oliveira PH, Perdereau A, Labadie K, Belser C, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Armstrong EJ, Paz-García DA, Ziegler M, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Zoccola D, Voolstra CR, Thurber RV, Sunagawa S, Wincker P, Allemand D, Planes S. Diversity of the Pacific Ocean coral reef microbiome. Nat Commun 2023; 14:3039. [PMID: 37264002 DOI: 10.1038/s41467-023-38500-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.
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Affiliation(s)
- Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France.
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Nicolas Henry
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | | | - Pedro H Oliveira
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Aude Perdereau
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | | | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, BCS, México
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
- Institut Universitaire de France, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Fondation Tara Océan, Paris, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
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14
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Belser C, Poulain J, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S, Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, Wincker P. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition. Sci Data 2023; 10:326. [PMID: 37264047 DOI: 10.1038/s41597-023-02204-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/14/2022] [Indexed: 06/03/2023] Open
Abstract
Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.
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Affiliation(s)
- Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Frederick Gavory
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Julie Guy
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Stefan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Paul Mielle
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 91000, Evry, France
| | - Aude Perdereau
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Gaelle Samson
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Shahinaz Gas
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | | | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls/Mer, France
| | - J Michel Flores
- Weizmann Institute of Science, Dept. Earth and Planetary Science, Rehovot, Israel
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Gabriela Perna
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, 8093, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - David A Paz García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, Col. Playa Palo de Santa Rita Sur, La Paz, 23096, Baja California Sur, México
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d' Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, 8093, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, 97331, Corvallis, OR, USA
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Claude Scarpelli
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - E' Krame Jacoby
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Pedro H Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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15
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Noel B, Denoeud F, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol 2023; 24:123. [PMID: 37264421 DOI: 10.1186/s13059-023-02960-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
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Affiliation(s)
- Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | | | - Laura Capasso
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
- Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Sylvie Tambutté
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | | | - Guillaume Iwankow
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Sarah Romac
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire Des Sciences du Climat Et de L'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-Sur-Yvette, 91191, France
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls Sur Mer, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de La Mer de Villefranche Sur Mer, Sorbonne Université, Laboratoire d'Océanographie de Villefranche, Villefranche-Sur-Mer, 06230, France
- Institut Universitaire de France, Paris, 75231, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Department of Human Genetics, CHU Nice, Nice, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France.
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16
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Armstrong EJ, Lê-Hoang J, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz-García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, Wincker P. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean. Nat Commun 2023; 14:3056. [PMID: 37264036 DOI: 10.1038/s41467-023-38610-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.
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Affiliation(s)
- Eric J Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, La Paz, Baja California Sur, 23096, México
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Emilie Boissin
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Guillaume Iwankow
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Department of Medical Genetics, CHU, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan institute, University of Galway, University Road H91TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, 97331, Corvallis, OR, USA
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860, Perpignan Cedex, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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17
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Dall'Olmo G, Bhaskar TVS U, Bittig H, Boss E, Brewster J, Claustre H, Donnelly M, Maurer T, Nicholson D, Paba V, Plant J, Poteau A, Sauzède R, Schallenberg C, Schmechtig C, Schmid C, Xing X. Real-time quality control of optical backscattering data from Biogeochemical-Argo floats. Open Res Eur 2023; 2:118. [PMID: 37645295 PMCID: PMC10446022 DOI: 10.12688/openreseurope.15047.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Biogeochemical-Argo floats are collecting an unprecedented number of profiles of optical backscattering measurements in the global ocean. Backscattering (BBP) data are crucial to understanding ocean particle dynamics and the biological carbon pump. Yet, so far, no procedures have been agreed upon to quality control BBP data in real time. METHODS Here, we present a new suite of real-time quality-control tests and apply them to the current global BBP Argo dataset. The tests were developed by expert BBP users and Argo data managers and have been implemented on a snapshot of the entire Argo dataset. RESULTS The new tests are able to automatically flag most of the "bad" BBP profiles from the raw dataset. CONCLUSIONS The proposed tests have been approved by the Biogeochemical-Argo Data Management Team and will be implemented by the Argo Data Assembly Centres to deliver real-time quality-controlled profiles of optical backscattering. Provided they reach a pressure of about 1000 dbar, these tests could also be applied to BBP profiles collected by other platforms.
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Affiliation(s)
- Giorgio Dall'Olmo
- Sezione di Oceanografia, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Borgo Grotta Gigante, Trieste, 34010, Italy
- Plymouth Marine Laboratory, Plymouth, PL1 3DH, UK
| | - Udaya Bhaskar TVS
- Indian National Centre for Ocean Information Services (INCOIS), Ministry of Earth Sciences (MoES), Ocean Valley, Pragathinagar (BO), Nizampet (SO), Hyderabad, 500090, India
| | - Henry Bittig
- Leibniz Institute for Baltic Sea Research Warnemünde, Rostock-Warnemünde, 18119, Germany
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, 04469-5706, USA
| | - Jodi Brewster
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL, USA
| | - Hervé Claustre
- Laboratoire d’Océanographie de Villefranche (LOV), CNRS & Sorbonne University, Villefranche-sur-Mer, 06230, France
| | - Matt Donnelly
- British Oceanographic Data Centre (BODC), National Oceanography Centre (NOC), Liverpool, UK
| | - Tanya Maurer
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA, 95039, USA
| | - David Nicholson
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02478, USA
| | - Violetta Paba
- British Oceanographic Data Centre (BODC), National Oceanography Centre (NOC), Liverpool, UK
| | - Josh Plant
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA, 95039, USA
| | - Antoine Poteau
- Laboratoire d’Océanographie de Villefranche (LOV), CNRS & Sorbonne University, Villefranche-sur-Mer, 06230, France
| | - Raphaëlle Sauzède
- Laboratoire d’Océanographie de Villefranche (LOV), CNRS & Sorbonne University, Villefranche-sur-Mer, 06230, France
| | - Christina Schallenberg
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | | | - Xiaogang Xing
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Hangzhou, China
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18
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Behrenfeld MJ, Bisson KM, Boss E, Gaube P, Karp-Boss L. Phytoplankton community structuring in the absence of resource-based competitive exclusion. PLoS One 2022; 17:e0274183. [PMID: 36112595 PMCID: PMC9481051 DOI: 10.1371/journal.pone.0274183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022] Open
Abstract
Under most natural marine conditions, phytoplankton cells suspended in the water column are too distantly spaced for direct competition for resources (i.e., overlapping cell boundary layers) to be a routine occurrence. Accordingly, resource-based competitive exclusion should be rare. In contrast, contemporary ecosystem models typically predict an exclusion of larger phytoplankton size classes under low-nutrient conditions, an outcome interpreted as reflecting the competitive advantage of small cells having much higher nutrient ‘affinities’ than larger cells. Here, we develop mechanistically-focused expressions for steady-state, nutrient-limited phytoplankton growth that are consistent with the discrete, distantly-spaced cells of natural populations. These expressions, when encompassed in a phytoplankton-zooplankton model, yield sustained diversity across all size classes over the full range in nutrient concentrations observed in the ocean. In other words, our model does not exhibit resource-based competitive exclusion between size classes previously associated with size-dependent differences in nutrient ‘affinities’.
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Affiliation(s)
- Michael J. Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
- * E-mail:
| | - Kelsey M. Bisson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, United States of America
| | - Peter Gaube
- Applied Physics Laboratory, University of Washington, Seattle, Washington, United States of America
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, United States of America
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19
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Pedrotti ML, Lombard F, Baudena A, Galgani F, Elineau A, Petit S, Henry M, Troublé R, Reverdin G, Ser-Giacomi E, Kedzierski M, Boss E, Gorsky G. An integrative assessment of the plastic debris load in the Mediterranean Sea. Sci Total Environ 2022; 838:155958. [PMID: 35580673 DOI: 10.1016/j.scitotenv.2022.155958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The Mediterranean Sea is recognized as one of the most polluted areas by floating plastics. During the Tara Mediterranean expedition, an extensive sampling of plastic debris was conducted in seven ecoregions, from Gibraltar to Lebanon with the aim of providing reliable estimates of regional differences in floating plastic loads and plastic characteristics. The abundance, size, surface, circularity and mass of 75,030 pieces were analyzed and classified in a standardized multi-parameter database. Their average abundance was 2.60 × 105 items km-2 (2.25 × 103 to 8.50 × 106 km-2) resulting in an estimate of about 650 billion plastic particles floating on the surface of the Mediterranean. This corresponds to an average of 660 metric tons of plastic, at the lower end of literature estimates. High concentrations of plastic were observed in the northwestern coastal regions, north of the Tyrrhenian Sea, but also off the western and central Mediterranean basins. The Levantine basin south of Cyprus had the lowest concentrations. A Lagrangian Plastic Pollution Index (LPPI) predicting the concentration of plastic debris was validated using the spatial resolution of the data. The advanced state of plastic degradation detected in the analyses led to the conclusion that stranding/fragmentation/resuspension is the key process in the dynamics of floating plastic in Mediterranean surface waters. This is supported by the significant correlation between pollution sources and areas of high plastic concentration obtained by the LPPI.
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Affiliation(s)
- Maria Luiza Pedrotti
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7093, LOV, Villefranche sur Mer, France.
| | - Fabien Lombard
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7093, LOV, Villefranche sur Mer, France
| | - Alberto Baudena
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7093, LOV, Villefranche sur Mer, France
| | | | - Amanda Elineau
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7093, LOV, Villefranche sur Mer, France
| | - Stephanie Petit
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7093, LOV, Villefranche sur Mer, France
| | | | | | - Gilles Reverdin
- Sorbonne Université CNRS/IRD/MNHN (LOCEAN/IPSL UMR 7159), Paris, France
| | - Enrico Ser-Giacomi
- Dept. of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology (MIT) Cambridge, MA, United States
| | - Mikaël Kedzierski
- Université Bretagne Sud, UMR CNRS 6027, IRDL, F-56100 Lorient, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, United States
| | - Gabriel Gorsky
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7093, LOV, Villefranche sur Mer, France
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20
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O’Brien T, Boss E. Correction of Radiometry Data for Temperature Effect on Dark Current, with Application to Radiometers on Profiling Floats. Sensors (Basel) 2022; 22:6771. [PMID: 36146125 PMCID: PMC9505084 DOI: 10.3390/s22186771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Measurements of daytime radiometry in the ocean are necessary to constrain processes such as photosynthesis, photo-chemistry and radiative heating. Profiles of downwelling irradiance provide a means to compute the concentration of a variety of in-water constituents. However, radiometers record a non-negligible signal when no light is available, and this signal is temperature dependent (called the dark current). Here, we devise and evaluate two consistent methods for correction of BGC-Argo radiometry measurements for dark current: one based on measurements during the day, the other based on night measurements. A daytime data correction is needed because some floats never measure at night. The corrections are based on modeling the temperature of the radiometer and show an average bias in the measured value of nearly 0.01 W m-2 nm-1, 3 orders of magnitude larger than the reported uncertainty of 2.5×10-5 W m-2 nm-1 for the sensors deployed on BGC-Argo floats (SeaBird scientific OCR504 radiometers). The methods are designed to be simple and robust, requiring pressure, temperature and irradiance data. The correction based on nighttime profiles is recommended as the primary method as it captures dark measurements with the largest dynamic range of temperature. Surprisingly, more than 28% of daytime profiles (130,674 in total) were found to record significant downwelling irradiance at 240-250 dbar. The correction is shown to be small relative to near-surface radiance and thus most useful for studies investigating light fields in the twilight zone and the impacts of radiance on deep organisms. Based on these findings, we recommend that BGC-Argo floats profile occasionally at night and to depths greater than 250 dbar. We provide codes to perform the dark corrections.
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Affiliation(s)
- Terence O’Brien
- Institute for the study of Earth, Ocean and Space, University of New Hampshire, Durham, NH 03824, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
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21
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Delmont TO, Gaia M, Hinsinger DD, Frémont P, Vanni C, Fernandez-Guerra A, Eren AM, Kourlaiev A, d'Agata L, Clayssen Q, Villar E, Labadie K, Cruaud C, Poulain J, Da Silva C, Wessner M, Noel B, Aury JM, de Vargas C, Bowler C, Karsenti E, Pelletier E, Wincker P, Jaillon O, Acinas SG, Bork P, Karsenti E, Bowler C, Sardet C, Stemmann L, de Vargas C, Wincker P, Lescot M, Babin M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Jaillon O, Kandels S, Iudicone D, Ogata H, Pesant S, Sullivan MB, Not F, Lee KB, Boss E, Cochrane G, Follows M, Poulton N, Raes J, Sieracki M, Speich S. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genom 2022; 2:100123. [PMID: 36778897 PMCID: PMC9903769 DOI: 10.1016/j.xgen.2022.100123] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 12/10/2021] [Accepted: 04/04/2022] [Indexed: 12/20/2022]
Abstract
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
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Affiliation(s)
- Tom O. Delmont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Corresponding author
| | - Morgan Gaia
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Damien D. Hinsinger
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Chiara Vanni
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity at Oldenburg, Germany
| | - Artem Kourlaiev
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Leo d'Agata
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Quentin Clayssen
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Emilie Villar
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Cruaud
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Marc Wessner
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Tara Oceans CoordinatorsSunagawaShinichi12AcinasSilvia G.13BorkPeer141516KarsentiEric171819BowlerChris1718SardetChristian1720StemmannLars1720de VargasColomban1721WinckerPatrick1722LescotMagali1723BabinMarcel1724GorskyGabriel1720GrimsleyNigel172526GuidiLionel1720HingampPascal1723JaillonOlivier1722KandelsStefanie1417IudiconeDaniele27OgataHiroyuki28PesantStéphane2930SullivanMatthew B.313233NotFabrice21LeeKarp-Boss34BossEmmanuel34CochraneGuy35FollowsMichael36PoultonNicole37RaesJeroen383940SierackiMike37SpeichSabrina4142Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, EtH Zürich, Zürich, SwitzerlandDepartment of Marine Biology and Oceanography, Institute of Marine Sciences–CsiC, Barcelona, SpainStructural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, GermanyMax Delbrück Center for Molecular Medicine, Berlin, GermanyDepartment of Bioinformatics, Biocenter, University of Würzburg, Würzburg, GermanyResearch Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOsee, Paris, FranceInstitut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, FranceDirectors’ Research, European Molecular Biology Laboratory, Heidelberg, GermanySorbonne Université, CNRS, Laboratoire D’Océanographie de Villefranche, Villefranche- sur- Mer, FranceSorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, FranceGénomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l’Énergie Atomique, CNrs, Université Evry, Université Paris- Saclay, Evry, FranceAix Marseille Universit/e, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, FranceDépartement de Biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)–CNRS (France), Université Laval, Quebec, QC, CanadaCNRS UMR 7232, Biologie Intégrative des Organismes Marins, Banyuls- sur- Mer, FranceSorbonne Universités Paris 06, OOB UPMC, Banyuls- sur- Mer, FranceStazione Zoologica Anton Dohrn, Naples, ItalyInstitute for Chemical Research, Kyoto University, Kyoto, JapanPaNGaea, University of Bremen, Bremen, GermanyMaruM, Center for Marine Environmental Sciences, University of Bremen, Bremen, GermanyDepartment of Microbiology, The Ohio State University, Columbus, OH, USADepartment of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USACenter for RNA Biology, The Ohio State University, Columbus, OH, USASchool of Marine Sciences, University of Maine, Orono, ME, USAEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UKDepartment of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USABigelow Laboratory for Ocean Sciences, East Boothbay, ME, USADepartment of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, BelgiumCenter for the Biology of Disease, VIB KU Leuven, Leuven, BelgiumDepartment of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, BelgiumDepartment of Geosciences, Laboratoire de Météorologie Dynamique, École Normale Supérieure, Paris, FranceOcean Physics Laboratory, University of Western Brittany, Brest, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Karsenti
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France,Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
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22
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Wang Y, Chen HH, Tang R, He D, Lee Z, Xue H, Wells M, Boss E, Chai F. Australian fire nourishes ocean phytoplankton bloom. Sci Total Environ 2022; 807:150775. [PMID: 34619187 DOI: 10.1016/j.scitotenv.2021.150775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
An unprecedented devastating forest fire occurred in Australia from September 2019 to March 2020. Satellite observations revealed that this rare fire event in Australia destroyed a record amount of more than 202,387 km2 of forest, including 56,471 km2 in eastern Australia, which is mostly composed of evergreen forest. The released aerosols contained essential nutrients for the growth of marine phytoplankton and were transported by westerly winds over the Southern Ocean, with rainfall-induced deposition to the ocean beneath. Here, we show that a prominent oceanic bloom, indicated by the rapid growth of phytoplankton, took place in the Southern Ocean along the trajectory of fire-born aerosols in response to atmospheric deposition. Calculations of carbon released during the fire versus carbon absorbed by the oceanic phytoplankton bloom suggest that they were nearly equal. This finding illustrates the critical role of the oceans in mitigating natural and anthropogenic carbon dioxide releases to the atmosphere, which are a primary driver of climate change.
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Affiliation(s)
- Yuntao Wang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Huan-Huan Chen
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China; Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Rui Tang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Ding He
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China; Organic Geochemistry Unit, School of Earth Sciences, Zhejiang University, Hangzhou 310027, China
| | - Zhongping Lee
- School for the Environment, University of Massachusetts Boston, Boston 02125, USA
| | - Huijie Xue
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Mark Wells
- School of Marine Sciences, University of Maine, Orono 04469, USA; State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono 04469, USA
| | - Fei Chai
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China; Ocean College, Zhejiang University, Zhoushan 316021, China.
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23
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Behrenfeld MJ, O'Malley R, Boss E, Karp-Boss L, Mundt C. Phytoplankton biodiversity and the inverted paradox. ISME COMMUN 2021; 1:52. [PMID: 36750580 PMCID: PMC9723737 DOI: 10.1038/s43705-021-00056-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/08/2022]
Abstract
Earth's aquatic food webs are overwhelmingly supported by planktonic microalgae that live in the sunlit water column where only a minimum number of physical niches are readily identifiable. Despite this paucity of environmental differentiation, these "phytoplankton" populations exhibit a rich biodiversity, an observation not easily reconciled with broadly accepted rules of resource-based competitive exclusion. This conundrum is referred to as the "Paradox of the Plankton". Consideration of physical distancing between nutrient depletion zones around individual phytoplankton, however, suggests a competition-neutral resource landscape. Application of neutral theory to the sheer number of phytoplankton in physically-mixed water masses yields a prediction of astronomical biodiversity, suggesting the inverted paradox: Why are there so few phytoplankton species? Here, we introduce a trophic constraint on phytoplankton that, when combined with stochastic principals of ecological drift, predicts only modest levels of diversity in an otherwise competition-neutral landscape. Our "trophic exclusion" principle predicts diversity to be independent of population size and yields a species richness across cell-size classes that is consistent with broad oceanographic survey observations.
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Affiliation(s)
- Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
| | - Robert O'Malley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Christopher Mundt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
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24
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Zhang X, Leymarie E, Boss E, Hu L. Deriving the angular response function for backscattering sensors. Appl Opt 2021; 60:8676-8687. [PMID: 34613093 DOI: 10.1364/ao.437735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
We derived the angular response function (WN) for scattering sensors that automatically satisfies the normalization criterion and its corresponding weight (WT). WN's, derived for two commercial sensors, HydroScat-6 (HOBI Labs) and ECO-BB (Sea-Bird Inc.), agrees well with the Monte Carlo simulation and direct measurements. The backscattering measured for microbeads of known sizes agrees better with Mie calculation when the derived WN was applied. We deduced that the reduction of WT with increasing attenuation coefficient is related to path length attenuation and showed that this theoretically derived correction factor performs better than the default methods for the two commercial backscattering sensors. The analysis conducted in this study also leads to an estimate of uncertainty budget for the two sensors. The major uncertainty for ECO-BB is associated with its angular response function because of its wide field of view, whereas the main uncertainty for the HydrScat-6 is due to attenuation correction because of its relatively long path length.
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25
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Bisson KM, Boss E, Werdell PJ, Ibrahim A, Frouin R, Behrenfeld MJ. Seasonal bias in global ocean color observations. Appl Opt 2021; 60:6978-6988. [PMID: 34613181 PMCID: PMC8500483 DOI: 10.1364/ao.426137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
In this study, we identify a seasonal bias in the ocean color satellite-derived remote sensing reflectances (Rrs(λ);sr-1) at the ocean color validation site, Marine Optical BuoY. The seasonal bias in Rrs(λ) is present to varying degrees in all ocean color satellites examined, including the Visible Infrared Imaging Radiometer Suite, Sea-Viewing Wide Field-of-View Sensor, and Moderate Resolution Imaging Spectrometer. The relative bias in Rrs has spectral dependence. Products derived from Rrs(λ) are affected by the bias to varying degrees, with particulate backscattering varying up to 50% over a year, chlorophyll varying up to 25% over a year, and absorption from phytoplankton or dissolved material varying by up to 15%. The propagation of Rrs(λ) bias into derived products is broadly confirmed on regional and global scales using Argo floats and data from the cloud-aerosol lidar with orthogonal polarization instrument aboard the cloud-aerosol lidar and infrared pathfinder satellite. The artifactual seasonality in ocean color is prominent in areas of low biomass (i.e., subtropical gyres) and is not easily discerned in areas of high biomass. While we have eliminated several candidates that could cause the biases in Rrs(λ), there are still outstanding questions regarding potential contributions from atmospheric corrections. Specifically, we provide evidence that the aquatic bidirectional reflectance distribution function may in part cause the observed seasonal bias, but this does not preclude an additional effect of the aerosol estimation. Our investigation highlights the contributions that atmospheric correction schemes can make in introducing biases in Rrs(λ), and we recommend more simulations to discern these influence Rrs(λ) biases. Community efforts are needed to find the root cause of the seasonal bias because all past, present, and future data are, or will be, affected until a solution is implemented.
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Affiliation(s)
- K. M. Bisson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - E. Boss
- School of Marine Sciences, University of Maine, Orono, Maine 04469, USA
| | - P. J. Werdell
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, USA
| | - A. Ibrahim
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, USA
| | - R. Frouin
- Scripps Institution of Oceanography, La Jolla, California 92093, USA
| | - M. J. Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
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26
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Affiliation(s)
- Michael J. Behrenfeld
- Department of Botany and Plant Pathology Oregon State University 4575 SW Research Way Corvallis Oregon 97333 USA
| | - Kimberly H. Halsey
- Department of Microbiology Oregon State University Nash Hall 226 Corvallis Oregon 97331 USA
| | - Emmanuel Boss
- School of Marine Sciences University of Maine 5706 Aubert Hall Orono Maine 04469‐5706 USA
| | - Lee Karp‐Boss
- School of Marine Sciences University of Maine 5706 Aubert Hall Orono Maine 04469‐5706 USA
| | - Allen J. Milligan
- Department of Botany and Plant Pathology Oregon State University 4575 SW Research Way Corvallis Oregon 97333 USA
| | - Graham Peers
- Department of Biology Colorado State University Biology Building, Room 111, 1878 Campus Delivery Fort Collins Colorado 80523‐1878 USA
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27
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Qiu G, Xing X, Boss E, Yan XH, Ren R, Xiao W, Wang H. Relationships between optical backscattering, particulate organic carbon, and phytoplankton carbon in the oligotrophic South China Sea basin. Opt Express 2021; 29:15159-15176. [PMID: 33985221 DOI: 10.1364/oe.422671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
The particulate backscattering coefficient (bbp) provides effective proxies for particulate organic carbon (POC) and phytoplankton carbon (Cphy); however, their bio-optical relationships in the oligotrophic ocean are rarely reported. In this work, based on the in-situ synchronous optical and biogeochemical measurements in the oligotrophic South China Sea (SCS) basin, we refined the regional relationships between POC (and Cphy) and bbp and investigated the impacts of phytoplankton community compositions and size classes on the bbp variability. The observations showed that: 1) POC and Cphy exhibited good linear relationships with bbp; 2) the relationship between Cphy and POC could also be fitted in a linear function with a positive POC intercept, and the POC contributed by phytoplankton-covarying non-algal particles was nearly two-fold of Cphy; and 3) the POC-specific bbp (b*bp) was positively correlated with the fraction of the phytoplankton groups haptophytes (Type 8) and diatoms to total Chla, but negatively correlated with the fraction of pico-phytoplankton to Chla (fpico). These findings suggest that in oligotrophic waters, the variability of b*bp was mainly determined by the variability in the relative contribution of large phytoplankton with complex structures.
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28
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Bisson KM, Boss E, Werdell PJ, Ibrahim A, Behrenfeld MJ. Particulate Backscattering in the Global Ocean: A Comparison of Independent Assessments. Geophys Res Lett 2021; 48:e2020GL090909. [PMID: 34531620 PMCID: PMC8442828 DOI: 10.1029/2020gl090909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/08/2020] [Indexed: 06/13/2023]
Abstract
How well do we know the particulate backscattering coefficient (bbp) in the global ocean? Satellite lidar bbp has never been validated globally and few studies have compared lidar bbp to bbp derived from reflectances (via ocean color) or in situ observations. Here, we validate lidar bbp with autonomous biogeochemical Argo floats using a decorrelation analysis to identify relevant spatiotemporal matchup scales inspired by geographical variability in the Rossby radius of deformation. We compare lidar, float, and ocean color bbp at the same locations and times to assess performance. Lidar bbp outperforms ocean color, with a median percent error of 18% compared to 24% in the best case and a relative bias of -11% compared to -21%, respectively. Phytoplankton carbon calculated from ocean color and lidar exhibits basin-scale differences that can reach ±50%.
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Affiliation(s)
- K. M. Bisson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - E. Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - P. J. Werdell
- NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Greenbelt, Maryland, USA
| | - A. Ibrahim
- NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Greenbelt, Maryland, USA
- Science Systems and Applications Inc., Lanham, MD, USA
| | - M. J. Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
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Houskeeper HF, Draper D, Kudela RM, Boss E. Chlorophyll absorption and phytoplankton size information inferred from hyperspectral particulate beam attenuation. Appl Opt 2020; 59:6765-6773. [PMID: 32749383 DOI: 10.1364/ao.396832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
Electromagnetic theory predicts spectral dependencies in extinction efficiency near a narrow absorption band for a particle with an index of refraction close to that of the medium in which it is immersed. These absorption band effects are anticipated in oceanographic beam-attenuation (beam-c) spectra, primarily due to the narrow red peak in absorption produced by the phytoplankton photopigment, chlorophyll a (Chl a). Here we present a method to obtain Chl a absorption and size information by analyzing an eigendecomposition of hyperspectral beam-c residuals measured in marine surface waters by an automatic underway system. We find that three principal modes capture more than 99% of the variance in beam-c residuals at wavelengths near the Chl a red absorption peak. The spectral shapes of the eigenvectors resemble extinction efficiency residuals attributed to the absorption band effects. Projection of the eigenvectors onto the beam-c residuals produces a time series of amplitude functions with absolute values that are strongly correlated to concurrent Chl a absorption line height (aLH) measurements (r values of 0.59 to 0.83) and hence provide a method to estimate Chl a absorption. Multiple linear regression of aLH on the amplitude functions enables an independent estimate of aLH, with RMSE of 3.19⋅10-3m-1 (3.3%) or log10-RMSE of 18.6%, and a raw-scale R2 value of 0.90 based on the Tara Oceans Expedition data. Relationships between the amplitude functions and the beam-c exponential slopes are in agreement with theory relating beam-c to the particle size distribution. Compared to multispectral analysis of beam-c slope, hyperspectral analysis of absorption band effects is anticipated to be relatively insensitive to the addition of nonpigmented particles and to monodispersion.
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Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 2020; 179:1084-1097.e21. [PMID: 31730851 PMCID: PMC6912166 DOI: 10.1016/j.cell.2019.10.008] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. Video Abstract
Most epipelagic planktonic groups exhibit a poleward decline of diversity No latitudinal diversity gradient was observed below the photic zone Temperature emerges as the best predictor of epipelagic plankton diversity Global warming may increase plankton diversity, particularly at high latitudes
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Affiliation(s)
- Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Manoela C Brandão
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Séverine Martini
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Hannah Byrne
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St., Cambridge, MA 02138, USA
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Université Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Dodji Soviadan
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Joannie Ferland
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Claudie Marec
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany; Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Céline Dimier
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 36 Nakhimovsky Prosp., 117997 Moscow, Russia
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Marcel Babin
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eric Pelletier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Laurent Bopp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; LMD/IPSL, ENS, PSL Research University, École Polytechnique, Sorbonne Université, CNRS, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
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Casey KA, Rousseaux CS, Gregg WW, Boss E, Chase AP, Craig SE, Mouw CB, Reynolds RA, Stramski D, Ackleson SG, Bricaud A, Schaeffer B, Lewis MR, Maritorena S. A global compilation of in situ aquatic high spectral resolution inherent and apparent optical property data for remote sensing applications. Earth Syst Sci Data 2020; 12:1123-1139. [PMID: 36419961 PMCID: PMC9680849 DOI: 10.5194/essd-12-1123-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Light emerging from natural water bodies and measured by radiometers contains information about the local type and concentrations of phytoplankton, non-algal particles and colored dissolved organic matter in the underlying waters. An increase in spectral resolution in forthcoming satellite and airborne remote sensing missions is expected to lead to new or improved capabilities for characterizing aquatic ecosystems. Such upcoming missions include NASA's Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission; the NASA Surface Biology and Geology designated observable mission; and NASA Airborne Visible/Infrared Imaging Spectrometer - Next Generation (AVIRIS-NG) airborne missions. In anticipation of these missions, we present an organized dataset of geographically diverse, quality-controlled, high spectral resolution inherent and apparent optical property (IOP-AOP) aquatic data. The data are intended to be of use to increase our understanding of aquatic optical properties, to develop aquatic remote sensing data product algorithms, and to perform calibration and validation activities for forthcoming aquatic-focused imaging spectrometry missions. The dataset is comprised of contributions from several investigators and investigating teams collected over a range of geographic areas and water types, including inland waters, estuaries, and oceans. Specific in situ measurements include remote-sensing reflectance, irradiance reflectance, and coefficients describing particulate absorption, particulate attenuation, non-algal particulate absorption, colored dissolved organic matter absorption, phytoplankton absorption, total absorption, total attenuation, particulate backscattering, and total backscattering. The dataset can be downloaded from https://doi.org/10.1594/PANGAEA.902230 (Casey et al., 2019).
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Affiliation(s)
- Kimberly A. Casey
- Earth Sciences Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
- U.S. Geological Survey, Reston, VA 20192, USA
| | - Cecile S. Rousseaux
- Earth Sciences Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
- Universities Space Research Association, Columbia, MD 20771, USA
| | - Watson W. Gregg
- Earth Sciences Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Alison P. Chase
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Susanne E. Craig
- Universities Space Research Association, Columbia, MD 20771, USA
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - Colleen B. Mouw
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Rick A. Reynolds
- Marine Physical Laboratory, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Dariusz Stramski
- Marine Physical Laboratory, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Annick Bricaud
- CNRS and Sorbonne Université, Laboratoire d’Océanographie de Villefranche (LOV), 06230 Villefranche-sur-mer, France
| | - Blake Schaeffer
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Marlon R. Lewis
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stéphane Maritorena
- Earth Research Institute, University of California, Santa Barbara, CA 93106, USA
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Cael BB, Chase A, Boss E. Information content of absorption spectra and implications for ocean color inversion. Appl Opt 2020; 59:3971-3984. [PMID: 32400669 DOI: 10.1364/ao.389189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
The increasing use of hyperspectral optical data in oceanography, both in situ and via remote sensing, holds the potential to significantly advance characterization of marine ecology and biogeochemistry because, in principle, hyperspectral data can provide much more detailed inferences of ecosystem properties via inversion. Effective inferences, however, require careful consideration of the close similarity of different signals of interest, and how these interplay with measurement error and uncertainty to reduce the degrees of freedom (DoF) of hyperspectral measurements. Here we discuss complementary approaches to quantify the DoF in hyperspectral measurements in the case of in situ particulate absorption measurements, though these approaches can also be used on other such data, e.g., ocean color remote sensing. Analyses suggest intermediate (${\sim}5 $∼5) DoF for our dataset of global hyperspectral particulate absorption spectra from the Tara Oceans expedition, meaning that these data can yield coarse community structure information. Empirically, chlorophyll is an effective first-order predictor of absorption spectra, meaning that error characteristics and the mathematics of inversion need to be carefully considered for hyperspectral data to provide information beyond that which chlorophyll provides. We also discuss other useful analytical tools that can be applied to this problem and place our results in the context of hyperspectral remote sensing.
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Haëntjens N, Della Penna A, Briggs N, Karp‐Boss L, Gaube P, Claustre H, Boss E. Detecting Mesopelagic Organisms Using Biogeochemical-Argo Floats. Geophys Res Lett 2020; 47:e2019GL086088. [PMID: 32713981 PMCID: PMC7375162 DOI: 10.1029/2019gl086088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/09/2020] [Accepted: 02/14/2020] [Indexed: 06/01/2023]
Abstract
During the North Atlantic Aerosols and Marine Ecosystems Study in the western North Atlantic, float-based profiles of fluorescent dissolved organic matter and backscattering exhibited distinct spike layers at ∼ 300 m. The locations of the spikes were at depths similar or shallower to where a ship-based scientific echo sounder identified layers of acoustic backscatter, an Underwater Vision Profiler detected elevated concentration of zooplankton, and mesopelagic fish were sampled by a mesopelagic net tow. The collocation of spike layers in bio-optical properties with mesopelagic organisms suggests that some can be detected with float-based bio-optical sensors. This opens the door to the investigation of such aggregations/layers in observations collected by the global biogeochemical-Argo array allowing the detection of mesopelagic organisms in remote locations of the open ocean under-sampled by traditional methods.
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Affiliation(s)
| | - Alice Della Penna
- Applied Physics LaboratoryUniversity of WashingtonSeattleWAUSA
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539CNRS‐Ifremer‐IRD‐UBO‐Institut Universitaire Européen de la Mer (IUEM)PlouzanéFrance
| | | | - Lee Karp‐Boss
- School of Marine SciencesUniversity of MaineOronoMEUSA
| | - Peter Gaube
- Applied Physics LaboratoryUniversity of WashingtonSeattleWAUSA
| | - Hervé Claustre
- Laboratoire d'Océanographie de Villefranche, UMR 7093CNRS et Sorbonne UniversitéVillefranche‐sur‐merFrance
| | - Emmanuel Boss
- School of Marine SciencesUniversity of MaineOronoMEUSA
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Fox J, Behrenfeld MJ, Haëntjens N, Chase A, Kramer SJ, Boss E, Karp-Boss L, Fisher NL, Penta WB, Westberry TK, Halsey KH. Phytoplankton Growth and Productivity in the Western North Atlantic: Observations of Regional Variability From the NAAMES Field Campaigns. Front Mar Sci 2020. [PMID: 0 DOI: 10.3389/fmars.2020.00024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The ability to quantify spatio-temporal variability in phytoplankton growth and productivity is essential to improving our understanding of global carbon dynamics and trophic energy flow. Satellite-based observations offered the first opportunity to estimate depth-integrated net primary production (NPP) at a global scale, but early modeling approaches could not effectively address variability in algal physiology, particularly the effects of photoacclimation on changes in cellular chlorophyll. Here, a previously developed photoacclimation model was used to derive depth-resolved estimates of phytoplankton division rate (μ) and NPP. The new approach predicts NPP values that closely match discrete measurements of 14C-based NPP and effectively captured both spatial and temporal variability observed during the four field campaigns of the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES). We observed favorable growth conditions for phytoplankton throughout the annual cycle in the subtropical western North Atlantic. As a result, high rates of μ are sustained year-round resulting in a strong coupling between growth and loss processes and a more moderate spring bloom compared to the high-latitude subarctic region. Considerable light limitation was observed in the subarctic province during the winter, which resulted in divergent growth dynamics, stronger decoupling from grazing pressure and a taxonomically distinct phytoplankton community. This study demonstrates how detailed knowledge of phytoplankton division rate furthers our understanding of global carbon cycling by providing insight into the resulting influence on phytoplankton taxonomy and the loss processes that dictate the fate of fixed carbon.
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Xue K, Boss E, Ma R, Shen M. Algorithm to derive inherent optical properties from remote sensing reflectance in turbid and eutrophic lakes. Appl Opt 2019; 58:8549-8564. [PMID: 31873359 DOI: 10.1364/ao.58.008549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Inherent optical properties play an important role in understanding the biogeochemical processes of lakes by providing proxies for a variety of biogeochemical quantities, including phytoplankton pigments. However, to date, it has been difficult to accurately derive the absorption coefficient of phytoplankton $[{a_{ph}}(\lambda )]$[aph(λ)] in turbid and eutrophic waters from remote sensing. A large dataset of remote sensing of reflectance $[{R_{rs}}(\lambda )]$[Rrs(λ)] and absorption coefficients was measured for samples collected from lakes in the middle and lower reaches of the Yangtze River and Huai River basin (MLYHR), China. In the process of scattering correction of spectrophotometric measurements, the particulate absorption coefficients $[{a_p}(\lambda )]$[ap(λ)] were first assumed to have no absorption in the near-infrared (NIR) wavelength. This assumption was corrected by estimating the particulate absorption coefficients at 750 nm $[{a_p}({750})]$[ap(750)] from the concentrations of chlorophyll-a (Chla) and suspended particulate matter, which was added to the ${a_p}(\lambda )$ap(λ) as a baseline. The resulting mean spectral mass-specific absorption coefficient of the nonalgal particles (NAPs) was consistent with previous work. A novel iterative IOP inversion model was then designed to retrieve the total nonwater absorption coefficients $[{a_{nw}}(\lambda )]$[anw(λ)] and backscattering coefficients of particulates $[{b_{bp}}(\lambda )]$[bbp(λ)], ${a_{ph}}(\lambda )$aph(λ), and ${a_{dg}}(\lambda )$adg(λ) [absorption coefficients of NAP and colored dissolved organic matter (CDOM)] from ${R_{rs}}(\lambda )$Rrs(λ) in turbid inland lakes. The proposed algorithm performed better than previously published models in deriving ${a_{nw}}(\lambda )$anw(λ) and ${b_{bp}}(\lambda )$bbp(λ) in this region. The proposed algorithm performed well in estimating the ${a_{ph}}(\lambda )$aph(λ) for wavelengths $ > {500}\;{\rm nm}$>500nm for the calibration dataset [${\rm N} = {285}$N=285, unbiased absolute percentage difference $({\rm UAPD}) = {55.22}\% $(UAPD)=55.22%, root mean square error $({\rm RMSE}) = {0.44}\;{{\rm m}^{ - 1}}$(RMSE)=0.44m-1] and for the validation dataset (${\rm N} = {57}$N=57, ${\rm UAPD} = {56.17}\% $UAPD=56.17%, ${\rm RMSE} = {0.71}\;{{\rm m}^{ - 1}}$RMSE=0.71m-1). This algorithm was then applied to Sentinel-3A Ocean and Land Color Instrument (OLCI) satellite data, and was validated with field data. This study provides an example of how to use local data to devise an algorithm to obtain IOPs, and in particular, ${a_{ph}}(\lambda )$aph(λ), using satellite ${R_{rs}}(\lambda )$Rrs(λ) data in turbid inland waters.
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Bisson KM, Boss E, Westberry TK, Behrenfeld MJ. Evaluating satellite estimates of particulate backscatter in the global open ocean using autonomous profiling floats. Opt Express 2019; 27:30191-30203. [PMID: 31684269 PMCID: PMC6839783 DOI: 10.1364/oe.27.030191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/02/2019] [Indexed: 05/26/2023]
Abstract
Satellite retrievals of particulate backscattering (bbp) are widely used in studies of ocean ecology and biogeochemistry, but have been historically difficult to validate due to the paucity of available ship-based comparative field measurements. Here we present a comparison of satellite and in situ bbp using observations from autonomous floats (n = 2,486 total matchups across three satellites), which provide bbp at 700 nm. With these data, we quantify how well the three inversion products currently distributed by NASA ocean color retrieve bbp. We find that the median ratio of satellite derived bbp to float bbp ranges from 0.77 to 1.60 and Spearman's rank correlations vary from r = 0.06 to r = 0.79, depending on which algorithm and sensor is used. Model skill degrades with increased spatial variability in remote sensing reflectance, which suggests that more rigorous matchup criteria and factors contributing to sensor noisiness may be useful to address in future work, and/or that we have built in biases in the current widely distributed inversion algorithms.
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Affiliation(s)
- K. M. Bisson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - E. Boss
- School of Marine Sciences, University of Maine, Orono, Maine 04469, USA
| | - T. K. Westberry
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - M. J. Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
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Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D. The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol 2019; 17:e3000483. [PMID: 31545807 PMCID: PMC6776362 DOI: 10.1371/journal.pbio.3000483] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/03/2019] [Indexed: 02/01/2023] Open
Abstract
Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
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Affiliation(s)
- Serge Planes
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- * E-mail:
| | - Denis Allemand
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
| | | | - Bernard Banaigs
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emilie Boissin
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - J. Michel Flores
- Weizmann Institute of Science, Dept. Earth and Planetary Science, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Paola Furla
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Pierre E. Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Jean-François Ghiglione
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université Laboratoire d’Océanographie Microbienne LOMIC, UMR 7621, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Stephane Pesant
- PANGEA, Data Publisher for Earth and Environment Science, Bremen, Germany
- MARUM—Center for Marine Environmental Sciences, Universität Bremen, Bremen, Germany
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | | | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, United States of America
| | - Shinichi Sunagawa
- Department of Biology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Olivier P. Thomas
- Marine Biodiscovery Laboratory, School of Chemistry and Ryan Institute, National University of Ireland, Galway (NUI Galway), Galway, Ireland
| | - Romain Troublé
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- La Fondation Tara Expéditions, “Base Tara” 11, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | | | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
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Frouin RJ, Franz BA, Ibrahim A, Knobelspiesse K, Ahmad Z, Cairns B, Chowdhary J, Dierssen HM, Tan J, Dubovik O, Huang X, Davis AB, Kalashnikova O, Thompson DR, Remer LA, Boss E, Coddington O, Deschamps PY, Gao BC, Gross L, Hasekamp O, Omar A, Pelletier B, Ramon D, Steinmetz F, Zhai PW. Atmospheric Correction of Satellite Ocean-Color Imagery During the PACE Era. Front Earth Sci (Lausanne) 2019; 7:10.3389/feart.2019.00145. [PMID: 32440515 PMCID: PMC7241613 DOI: 10.3389/feart.2019.00145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission will carry into space the Ocean Color Instrument (OCI), a spectrometer measuring at 5nm spectral resolution in the ultraviolet (UV) to near infrared (NIR) with additional spectral bands in the shortwave infrared (SWIR), and two multi-angle polarimeters that will overlap the OCI spectral range and spatial coverage, i. e., the Spectrometer for Planetary Exploration (SPEXone) and the Hyper-Angular Rainbow Polarimeter (HARP2). These instruments, especially when used in synergy, have great potential for improving estimates of water reflectance in the post Earth Observing System (EOS) era. Extending the top-of-atmosphere (TOA) observations to the UV, where aerosol absorption is effective, adding spectral bands in the SWIR, where even the most turbid waters are black and sensitivity to the aerosol coarse mode is higher than at shorter wavelengths, and measuring in the oxygen A-band to estimate aerosol altitude will enable greater accuracy in atmospheric correction for ocean color science. The multi-angular and polarized measurements, sensitive to aerosol properties (e.g., size distribution, index of refraction), can further help to identify or constrain the aerosol model, or to retrieve directly water reflectance. Algorithms that exploit the new capabilities are presented, and their ability to improve accuracy is discussed. They embrace a modern, adapted heritage two-step algorithm and alternative schemes (deterministic, statistical) that aim at inverting the TOA signal in a single step. These schemes, by the nature of their construction, their robustness, their generalization properties, and their ability to associate uncertainties, are expected to become the new standard in the future. A strategy for atmospheric correction is presented that ensures continuity and consistency with past and present ocean-color missions while enabling full exploitation of the new dimensions and possibilities. Despite the major improvements anticipated with the PACE instruments, gaps/issues remain to be filled/tackled. They include dealing properly with whitecaps, taking into account Earth-curvature effects, correcting for adjacency effects, accounting for the coupling between scattering and absorption, modeling accurately water reflectance, and acquiring a sufficiently representative dataset of water reflectance in the UV to SWIR. Dedicated efforts, experimental and theoretical, are in order to gather the necessary information and rectify inadequacies. Ideas and solutions are put forward to address the unresolved issues. Thanks to its design and characteristics, the PACE mission will mark the beginning of a new era of unprecedented accuracy in ocean-color radiometry from space.
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Affiliation(s)
- Robert J. Frouin
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Correspondence: Robert J. Frouin,
| | - Bryan A. Franz
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, United States
| | - Amir Ibrahim
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, United States
- Science Systems and Applications Inc., Lanham, MD, United States
| | - Kirk Knobelspiesse
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, United States
| | - Ziauddin Ahmad
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, United States
- Science Application International Corporation, McLean, VA, United States
| | - Brian Cairns
- NASA Goddard Institute for Space Studies, New York, NY, United States
| | - Jacek Chowdhary
- NASA Goddard Institute for Space Studies, New York, NY, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, United States
| | - Heidi M. Dierssen
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Jing Tan
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Oleg Dubovik
- Laboratoire d’Optique Atmosphérique, Université de Lille, Villeneuve d’Ascq, France
| | - Xin Huang
- Laboratoire d’Optique Atmosphérique, Université de Lille, Villeneuve d’Ascq, France
| | - Anthony B. Davis
- Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, United States
| | - Olga Kalashnikova
- Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, United States
| | - David R. Thompson
- Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, United States
| | - Lorraine A. Remer
- Joint Center for Earth System Technology, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, United States
| | - Odele Coddington
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO, United States
| | | | - Bo-Cai Gao
- Naval Research Laboratory, Washington, DC, United States
| | | | - Otto Hasekamp
- Earth Science Group, Netherlands Institute for Space Research, Utrecht, Netherlands
| | - Ali Omar
- Atmospheric Composition Branch, NASA Langley Research Center, Hampton, VA, United States
| | - Bruno Pelletier
- Institut de Recherche Mathématique, Université de Rennes, Rennes, Franc
| | | | | | - Peng-Wang Zhai
- Department of Physics, University of Maryland Baltimore County, Baltimore, MD, United States
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Talley LD, Rosso I, Kamenkovich I, Mazloff MR, Wang J, Boss E, Gray AR, Johnson KS, Key RM, Riser SC, Williams NL, Sarmiento JL. Southern Ocean Biogeochemical Float Deployment Strategy, With Example From the Greenwich Meridian Line (GO-SHIP A12). J Geophys Res Oceans 2019; 124:403-431. [PMID: 31007997 PMCID: PMC6472510 DOI: 10.1029/2018jc014059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 09/01/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Biogeochemical Argo floats, profiling to 2,000-m depth, are being deployed throughout the Southern Ocean by the Southern Ocean Carbon and Climate Observations and Modeling program (SOCCOM). The goal is 200 floats by 2020, to provide the first full set of annual cycles of carbon, oxygen, nitrate, and optical properties across multiple oceanographic regimes. Building from no prior coverage to a sparse array, deployments are based on prior knowledge of water mass properties, mean frontal locations, mean circulation and eddy variability, winds, air-sea heat/freshwater/carbon exchange, prior Argo trajectories, and float simulations in the Southern Ocean State Estimate and Hybrid Coordinate Ocean Model (HYCOM). Twelve floats deployed from the 2014-2015 Polarstern cruise from South Africa to Antarctica are used as a test case to evaluate the deployment strategy adopted for SOCCOM's 20 deployment cruises and 126 floats to date. After several years, these floats continue to represent the deployment zones targeted in advance: (1) Weddell Gyre sea ice zone, observing the Antarctic Slope Front, and a decadally-rare polynya over Maud Rise; (2) Antarctic Circumpolar Current (ACC) including the topographically steered Southern Zone chimney where upwelling carbon/nutrient-rich deep waters produce surprisingly large carbon dioxide outgassing; (3) Subantarctic and Subtropical zones between the ACC and Africa; and (4) Cape Basin. Argo floats and eddy-resolving HYCOM simulations were the best predictors of individual SOCCOM float pathways, with uncertainty after 2 years of order 1,000 km in the sea ice zone and more than double that in and north of the ACC.
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Affiliation(s)
- L. D. Talley
- Scripps Institution of OceanographyUniversity of California, San DiegoLa JollaCAUSA
| | - I. Rosso
- Scripps Institution of OceanographyUniversity of California, San DiegoLa JollaCAUSA
| | - I. Kamenkovich
- Rosenstiel School of Marine and Atmospheric SciencesUniversity of MiamiMiamiFLUSA
| | - M. R. Mazloff
- Scripps Institution of OceanographyUniversity of California, San DiegoLa JollaCAUSA
| | - J. Wang
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - E. Boss
- School of Marine SciencesUniversity of MaineOronoMEUSA
| | - A. R. Gray
- School of OceanographyUniversity of WashingtonSeattleWAUSA
| | - K. S. Johnson
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
| | - R. M. Key
- Program in Atmospheric and Oceanic SciencesPrinceton UniversityPrincetonNJUSA
| | - S. C. Riser
- School of OceanographyUniversity of WashingtonSeattleWAUSA
| | - N. L. Williams
- College of Earth, Ocean, and Atmospheric SciencesOregon State UniversityCorvallisORUSA
- Now at Pacific Marine Environmental LaboratoryNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - J. L. Sarmiento
- Program in Atmospheric and Oceanic SciencesPrinceton UniversityPrincetonNJUSA
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Organelli E, Dall'Olmo G, Brewin RJW, Tarran GA, Boss E, Bricaud A. The open-ocean missing backscattering is in the structural complexity of particles. Nat Commun 2018; 9:5439. [PMID: 30575718 PMCID: PMC6303329 DOI: 10.1038/s41467-018-07814-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/15/2018] [Indexed: 11/16/2022] Open
Abstract
Marine microscopic particles profoundly impact global biogeochemical cycles, but our understanding of their dynamics is hindered by lack of observations. To fill this gap, optical backscattering measured by satellite sensors and in-situ autonomous platforms can be exploited. Unfortunately, these observations remain critically limited by an incomplete mechanistic understanding of what particles generate the backscattering signal. To achieve this understanding, optical models are employed. The simplest of these models—the homogeneous sphere—severely underestimates the measured backscattering and the missing signal has been attributed to submicron particles. This issue is known as the missing backscattering enigma. Here we show that a slightly more complex optical model—the coated sphere—can predict the measured backscattering and suggests that most of the signal comes from particles >1 µm. These findings were confirmed by independent size-fractionation experiments. Our results demonstrate that the structural complexity of particles is critical to understand open-ocean backscattering and contribute to solving the enigma. Particulate optical backscattering is key to studying the oceanic carbon pump though it remains unclear what particles are detected. Here the authors show that complex particles larger than 1 µm help reproduce all the measured backscattering across the Atlantic Ocean and explain the majority of the signal.
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Affiliation(s)
- Emanuele Organelli
- Plymouth Marine Laboratory, Prospect Place, The Hoe, PL1 3DH, Plymouth, UK. .,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, France.
| | - Giorgio Dall'Olmo
- Plymouth Marine Laboratory, Prospect Place, The Hoe, PL1 3DH, Plymouth, UK.,National Centre for Earth Observation, Plymouth Marine Laboratory, Prospect Place, The Hoe, PL1 3DH, Plymouth, UK
| | - Robert J W Brewin
- Plymouth Marine Laboratory, Prospect Place, The Hoe, PL1 3DH, Plymouth, UK.,National Centre for Earth Observation, Plymouth Marine Laboratory, Prospect Place, The Hoe, PL1 3DH, Plymouth, UK
| | - Glen A Tarran
- Plymouth Marine Laboratory, Prospect Place, The Hoe, PL1 3DH, Plymouth, UK
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Annick Bricaud
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, France
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Xing X, Briggs N, Boss E, Claustre H. Improved correction for non-photochemical quenching of in situ chlorophyll fluorescence based on a synchronous irradiance profile. Opt Express 2018; 26:24734-24751. [PMID: 30469586 DOI: 10.1364/oe.26.024734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/20/2018] [Indexed: 05/26/2023]
Abstract
In situ chlorophyll fluorometers have been used to quantify the distribution of chlorophyll concentration in natural waters for decades. However, chlorophyll fluorescence is depressed during daylight hours due to non-photochemical quenching (NPQ). Corrections attempted to date have provided improvement but still remain unsatisfactory, often over-estimating the expected value. In this study, we examine the relationship between NPQ and instantaneous Photosynthetically Active Radiation (iPAR) using field data from BGC-Argo floats equipped with Chlorophyll-a fluorometers and radiometers. This analysis leads to an improved NPQ correction that incorporates both iPAR and mixed layer depth (MLD) and is validated against data collected at sunrise or sunset. The optimal NPQ light threshold is found to be iPAR = 15 μmol quanta m-2 s-1, and the proposed methods based on such a light threshold correct the NPQ effect more accurately than others, except in "shallow-mixing" waters (NPQ light threshold depth deeper than MLD). For these waters, an empirical-relationship-based method is proposed for improvement of NPQ correction using an iPAR profile. It is therefore recommended that, for optimal NPQ corrections, profiling floats measuring chlorophyll fluorescence in daytime be equipped with iPAR radiometers.
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Boss E, Haëntjens N, Westberry TK, Karp-Boss L, Slade WH. Validation of the particle size distribution obtained with the laser in-situ scattering and transmission (LISST) meter in flow-through mode. Opt Express 2018; 26:11125-11136. [PMID: 29716037 DOI: 10.1364/oe.26.011125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
High spatial and temporal resolution estimates of the particle size distribution (PSD) in the surface ocean can enable improved understanding of biogeochemistry and ecosystem dynamics. Oceanic PSD measurements remain rare due to the time-consuming, manual sampling methods of common particle sizing instruments. Here, we evaluate the utility of measuring particle size data at high spatial resolution with a commercially-available submersible laser diffraction particle sizer (LISST-100X, Sequoia Scientific), operating in an automated mode with continuously flowing seawater. The LISST PSD agreed reasonably well with discrete PSD measurements obtained with a Coulter Counter and data from the flow-through sampling Imaging Flow-Cytobot, validating our methodology. Total particulate area and Volume derived from the LISST PSD agreed well with beam-attenuation and particulate organic carbon respectively, further validating the LISST PSD. Furthermore, When compared to the measured spectral characteristics of particulate beam attenuation, we find a significant correlation. However, no significant relationship between the PSD and spectral particulate backscattering was found.
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Laber CP, Hunter JE, Carvalho F, Collins JR, Hunter EJ, Schieler BM, Boss E, More K, Frada M, Thamatrakoln K, Brown CM, Haramaty L, Ossolinski J, Fredricks H, Nissimov JI, Vandzura R, Sheyn U, Lehahn Y, Chant RJ, Martins AM, Coolen MJL, Vardi A, DiTullio GR, Van Mooy BAS, Bidle KD. Coccolithovirus facilitation of carbon export in the North Atlantic. Nat Microbiol 2018. [DOI: 10.1038/s41564-018-0128-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
NASA’s Plankton, Aerosol, Cloud, Ocean Ecosystem satellite mission, still in planning stages, operates with a framework that could serve as an example for science support of future missions.
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Werdell PJ, McKinna LI, Boss E, Ackleson SG, Craig SE, Gregg WW, Lee Z, Maritorena S, Roesler CS, Rousseaux CS, Stramski D, Sullivan JM, Twardowski MS, Tzortziou M, Zhang X. An overview of approaches and challenges for retrieving marine inherent optical properties from ocean color remote sensing. Prog Oceanogr 2018; 160:186-212. [PMID: 30573929 PMCID: PMC6296493 DOI: 10.1016/j.pocean.2018.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ocean color measured from satellites provides daily global, synoptic views of spectral waterleaving reflectances that can be used to generate estimates of marine inherent optical properties (IOPs). These reflectances, namely the ratio of spectral upwelled radiances to spectral downwelled irradiances, describe the light exiting a water mass that defines its color. IOPs are the spectral absorption and scattering characteristics of ocean water and its dissolved and particulate constituents. Because of their dependence on the concentration and composition of marine constituents, IOPs can be used to describe the contents of the upper ocean mixed layer. This information is critical to further our scientific understanding of biogeochemical oceanic processes, such as organic carbon production and export, phytoplankton dynamics, and responses to climatic disturbances. Given their importance, the international ocean color community has invested significant effort in improving the quality of satellite-derived IOP products, both regionally and globally. Recognizing the current influx of data products into the community and the need to improve current algorithms in anticipation of new satellite instruments (e.g., the global, hyperspectral spectroradiometer of the NASA Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission), we present a synopsis of the current state of the art in the retrieval of these core optical properties. Contemporary approaches for obtaining IOPs from satellite ocean color are reviewed and, for clarity, separated based their inversion methodology or the type of IOPs sought. Summaries of known uncertainties associated with each approach are provided, as well as common performance metrics used to evaluate them. We discuss current knowledge gaps and make recommendations for future investment for upcoming missions whose instrument characteristics diverge sufficiently from heritage and existing sensors to warrant reassessing current approaches.
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Affiliation(s)
| | - Lachlan I.W. McKinna
- NASA Goddard Space Flight Center, Code 616, Greenbelt, MD, USA
- Go2Q Pty Ltd, Sunshine Coast, QLD, Australia
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, USA
| | | | - Susanne E. Craig
- NASA Goddard Space Flight Center, Code 616, Greenbelt, MD, USA
- Universities Space Research Association, Columbia, MD, USA
| | - Watson W. Gregg
- NASA Global Modeling and Assimilation Office, Greenbelt, MD, USA
| | - Zhongping Lee
- School for the Environment, University of Massachusetts Boston, Boston, MA, USA
| | | | - Collin S. Roesler
- Department of Earth and Oceanographic Science, Bowdoin College, Brunswick, ME, USA
| | - Cécile S. Rousseaux
- Universities Space Research Association, Columbia, MD, USA
- NASA Global Modeling and Assimilation Office, Greenbelt, MD, USA
| | - Dariusz Stramski
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - James M. Sullivan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Michael S. Twardowski
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Maria Tzortziou
- Department of Earth and Atmospheric Science, The City College of New York, New York, NY, USA
- NASA Goddard Space Flight Center, Code 614, Greenbelt, MD, USA
| | - Xiaodong Zhang
- Department of Earth System Science and Policy, University of North Dakota, Grand Forks, ND, USA
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Dall'Olmo G, Brewin RJW, Nencioli F, Organelli E, Lefering I, McKee D, Röttgers R, Mitchell C, Boss E, Bricaud A, Tilstone G. Determination of the absorption coefficient of chromophoric dissolved organic matter from underway spectrophotometry. Opt Express 2017; 25:A1079-A1095. [PMID: 29220986 DOI: 10.1364/oe.25.0a1079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/24/2017] [Indexed: 05/27/2023]
Abstract
Measurements of the absorption coefficient of chromophoric dissolved organic matter (ay) are needed to validate existing ocean-color algorithms. In the surface open ocean, these measurements are challenging because of low ay values. Yet, existing global datasets demonstrate that ay could contribute between 30% to 50% of the total absorption budget in the 400-450 nm spectral range, thus making accurate measurement of ay essential to constrain these uncertainties. In this study, we present a simple way of determining ay using a commercially-available in-situ spectrophotometer operated in underway mode. The obtained ay values were validated using independent collocated measurements. The method is simple to implement, can provide measurements with very high spatio-temporal resolution, and has an accuracy of about 0.0004 m-1 and a precision of about 0.0025 m-1 when compared to independent data (at 440 nm). The only limitation for using this method at sea is that it relies on the availability of relatively large volumes of ultrapure water. Despite this limitation, the method can deliver the ay data needed for validating and assessing uncertainties in ocean-colour algorithms.
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47
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Cael BB, Boss E. Simplified model of spectral absorption by non-algal particles and dissolved organic materials in aquatic environments. Opt Express 2017; 25:25486-25491. [PMID: 29041215 DOI: 10.1364/oe.25.025486] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
Absorption by non-algal particles (NAP, ad) and colored dissolved organic matter (CDOM, ag) are frequently modeled by exponential functions of wavelength, either separately or as a sum. We present a new representation of NAP-plus-CDOM absorption adg based on the stretched exponential function adg(λ) = A exp{-[s(λ - λo)]β}, whose parameter β can be considered a measure of optical heterogeneity. A double exponential representation of adg can be fit extremely well by a stretched exponential for all plausible parameter combinations, despite having one fewer free parameter than a double exponential. Fitting two published compilations of in situ adg data - one at low spectral resolution (n = 5, λ = 412-555 nm) and one at high spectral resolution (n = 201, λ = 300-700 nm) - the stretched exponential outperforms the single exponential, double exponential, and a power law. We thereby conclude that the stretched exponential is the preferred model for adg absorption in circumstances when NAP and CDOM cannot be separated, such as in remote sensing inversions.
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48
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Zhai PW, Hu Y, Winker DM, Franz BA, Werdell J, Boss E. Vector radiative transfer model for coupled atmosphere and ocean systems including inelastic sources in ocean waters. Opt Express 2017; 25:A223-A239. [PMID: 28437917 PMCID: PMC7780532 DOI: 10.1364/oe.25.00a223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Inelastic scattering plays an important role in ocean optics. The main inelastic scattering mechanisms include Raman scattering, fluorescence by colored dissolved organic matter (FDOM), and fluorescence by chlorophyll. This paper reports an implementation of all three inelastic scattering mechanisms in the exact vector radiative transfer model for coupled atmosphere and ocean Systems (CAOS). Simulation shows that FDOM contributes to the water radiation field in the broad visible spectral region, while chlorophyll fluorescence is limited in a narrow band centered at 685 nm. This is consistent with previous findings in the literature. The fluorescence distribution as a function of depth and viewing angle is presented. The impacts of fluorescence to the degree of linear polarization (DoLP) and orientation of the polarization ellipse (OPE) are studied. The DoLP is strongly influenced by inelastic scattering at wavelengths with strong inelastic scattering contribution. The OPE is less affected by inelastic scattering but it has a noticeable impact, in terms of the angular region of positive polarization, in the backward direction. This effect is more apparent for deeper water depth.
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Affiliation(s)
- Peng-Wang Zhai
- Department of Physics, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Yongxiang Hu
- MS 475 NASA Langley Research Center, Hampton, VA 23681-2199, USA
| | - David M. Winker
- MS 475 NASA Langley Research Center, Hampton, VA 23681-2199, USA
| | - Bryan A. Franz
- NASA Goddard Space Flight Center, Code 616, Greenbelt, Maryland 20771, USA
| | - Jeremy Werdell
- NASA Goddard Space Flight Center, Code 616, Greenbelt, Maryland 20771, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine 04401, USA
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49
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Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G. Plankton networks driving carbon export in the oligotrophic ocean. Nature 2016; 532:465-470. [PMID: 26863193 PMCID: PMC4851848 DOI: 10.1038/nature16942] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 12/18/2015] [Indexed: 01/02/2023]
Abstract
The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterised. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria, alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of just a few bacterial and viral genes can predict most of the variability in carbon export in these regions.
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Affiliation(s)
- Lionel Guidi
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France.,Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.,Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium.,Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Lucie Bittner
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut de Biologie Paris-Seine (IBPS), Evolution Paris Seine, F-75005, Paris, France.,Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Damien Eveillard
- LINA UMR 6241, Université de Nantes, EMN, CNRS, 44322 Nantes, France
| | | | - Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Youssef Darzi
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.,Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium
| | - Stephane Audic
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Léo Berline
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
| | - Jennifer Brum
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | | | - Shruti Malviya
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Céline Dimier
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.,Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg Germany
| | - Marc Picheral
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
| | - Julie Poulain
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry France
| | - Sarah Searson
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France.,Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | | | - Lars Stemmann
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
| | - Fabrice Not
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Pascal Hingamp
- Aix Marseille Université CNRS IGS UMR 7256 13288 Marseille France
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond 75231 Paris Cedex 05 France
| | - Mick Follows
- Dept of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, USA
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Stephane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jean Weissenbach
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry France.,CNRS, UMR 8030, CP5706, Evry France.,Université d'Evry, UMR 8030, CP5706, Evry France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry France.,CNRS, UMR 8030, CP5706, Evry France.,Université d'Evry, UMR 8030, CP5706, Evry France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC Pg. Marítim de la Barceloneta 37-49 Barcelona E08003 Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.,Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium.,Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France.,Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg Germany
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
| | - Gabriel Gorsky
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
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50
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Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science 2015; 348:1261447. [PMID: 25999514 DOI: 10.1126/science.1261447] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.
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Affiliation(s)
- Emilie Villar
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France.
| | - Gregory K Farrant
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Michael Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laurence Garczarek
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Sabrina Speich
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France. Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD) UMR 8539, Ecole Normale Supérieure, 24 Rue Lhomond, 75231 Paris Cedex 05, France
| | - Stéphane Audic
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Lucie Bittner
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Bruno Blanke
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France
| | - Jennifer R Brum
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Alison Chase
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - John R Dolan
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Fabrizio d'Ortenzio
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Jean-Pierre Gattuso
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Nicolas Grima
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France
| | - Lionel Guidi
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Christopher N Hill
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oliver Jahn
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jean-Louis Jamet
- Université de Toulon, Laboratoire PROTEE-EBMA E.A. 3819, BP 20132, 83957 La Garde Cedex, France
| | - Hervé Le Goff
- CNRS, UMR 7159, Laboratoire d'Océanographie et du Climat LOCEAN, 4 Place Jussieu, 75005 Paris, France
| | - Cyrille Lepoivre
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Shruti Malviya
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Eric Pelletier
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Jean-Baptiste Romagnan
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sébastien Santini
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Atsuko Tanaka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Pierre Testor
- CNRS, UMR 7159, Laboratoire d'Océanographie et du Climat LOCEAN, 4 Place Jussieu, 75005 Paris, France
| | - Thomas Vannier
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Flora Vincent
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Céline Dimier
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Marc Picheral
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Sarah Searson
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France.
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
| | - Pascal Hingamp
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France.
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
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