Lombard Fabien

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Lombard
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Fabien
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  • Article
    Machine learning techniques to characterize functional traits of plankton from image data
    (Association for the Sciences of Limnology and Oceanography, 2022-06-30) Orenstein, Eric C. ; Ayata, Sakina Dorothée ; Maps, Frédéric ; Becker, Érica C. ; Benedetti, Fabio ; Biard, Tristan ; de Garidel-Thoron, Thibault ; Ellen, Jeffrey S. ; Ferrario, Filippo ; Giering, Sarah L. C. ; Guy-Haim, Tamar ; Hoebeke, Laura ; Iversen, Morten H. ; Kiørboe, Thomas ; Lalonde, Jean-François ; Lana, Arancha ; Laviale, Martin ; Lombard, Fabien ; Lorimer, Tom ; Martini, Séverine ; Meyer, Albin ; Möller, Klas O. ; Niehoff, Barbara ; Ohman, Mark D. ; Pradalier, Cédric ; Romagnan, Jean-Baptiste ; Schröder, Simon-Martin ; Sonnet, Virginie ; Sosik, Heidi M. ; Stemmann, Lars ; Stock, Michiel ; Terbiyik-Kurt, Tuba ; Valcárcel-Pérez, Nerea ; Vilgrain, Laure ; Wacquet, Guillaume ; Waite, Anya M. ; Irisson, Jean-Olivier
    Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.
  • Article
    Expanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018)
    (Frontiers Media, 2019-12-11) Gorsky, Gabriel ; Bourdin, Guillaume ; Lombard, Fabien ; Pedrotti, Maria Luiza ; Audrain, Samuel ; Bin, Nicolas ; Boss, Emmanuel S. ; Bowler, Chris ; Cassar, Nicolas ; Caudan, Loic ; Chabot, Genevieve ; Cohen, Natalie R. ; Cron, Daniel ; De Vargas, Colomban ; Dolan, John R. ; Douville, Eric ; Elineau, Amanda ; Flores, J. Michel ; Ghiglione, Jean-Francois ; Haëntjens, Nils ; Hertau, Martin ; John, Seth G. ; Kelly, Rachel L. ; Koren, Ilan ; Lin, Yajuan ; Marie, Dominique ; Moulin, Clémentine ; Moucherie, Yohann ; Pesant, Stephane ; Picheral, Marc ; Poulain, Julie ; Pujo-Pay, Mireille ; Reverdin, Gilles ; Romac, Sarah ; Sullivan, Mathew B. ; Trainic, Miri ; Tressol, Marc ; Troublé, Romain ; Vardi, Assaf ; Voolstra, Christian R. ; Wincker, Patrick ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Gilson, Eric ; Reynaud, Stephanie ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Vega Thurber, Rebecca ; Zoccola, Didier ; Planes, Serge ; Allemand, Denis ; Karsenti, Eric
    Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions.
  • Article
    Globally consistent quantitative observations of planktonic ecosystems
    (Frontiers Media, 2019-04-25) Lombard, Fabien ; Boss, Emmanuel S. ; Waite, Anya M. ; Vogt, Meike ; Uitz, Julia ; Stemmann, Lars ; Sosik, Heidi M. ; Schulz, Jan ; Romagnan, Jean-Baptiste ; Picheral, Marc ; Pearlman, Jay ; Ohman, Mark D. ; Niehoff, Barbara ; Möller, Klas O. ; Miloslavich, Patricia ; Lara-Lpez, Ana ; Kudela, Raphael M. ; Lopes, Rubens M. ; Kiko, Rainer ; Karp-Boss, Lee ; Jaffe, Jules S. ; Iversen, Morten H. ; Irisson, Jean-Olivier ; Fennel, Katja ; Hauss, Helena ; Guidi, Lionel ; Gorsky, Gabriel ; Giering, Sarah L. C. ; Gaube, Peter ; Gallager, Scott M. ; Dubelaar, George ; Cowen, Robert K. ; Carlotti, François ; Briseño-Avena, Christian ; Berline, Leo ; Benoit-Bird, Kelly J. ; Bax, Nicholas ; Batten, Sonia ; Ayata, Sakina Dorothée ; Artigas, Luis Felipe ; Appeltans, Ward
    In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well as analysis using particle counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next 10 years to move toward our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there, ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries and carbon sequestration.
  • Article
    The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean
    (Public Library of Science, 2019-09-23) Planes, Serge ; Allemand, Denis ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Boss, Emmanuel S. ; Bourdin, Guillaume ; Bowler, Chris ; Douville, Eric ; Flores, J. Michel ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Ghiglione, Jean-Francois ; Gilson, Eric ; Lombard, Fabien ; Moulin, Clémentine ; Pesant, Stephane ; Poulain, Julie ; Reynaud, Stephanie ; Romac, Sarah ; Sullivan, Matthew B. ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Troublé, Romain ; de Vargas, Colomban ; Vega Thurber, Rebecca ; Voolstra, Christian R. ; Wincker, Patrick ; Tara Pacific Consortium
    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.
  • Article
    Editorial: Technological advances for measuring planktonic components of the pelagic ecosystem: an integrated approach to data collection and analysis
    (Frontiers Media, 2023-01-26) Pitois, Sophie G. ; Fileman, Elaine S. ; Benfield, Mark C. ; Wiebe, Peter H. ; Lombard, Fabien
    The traditional collection of plankton samples, often using nets followed by visual sorting and taxonomic analysis is a labour intensive, time-consuming, and ultimately expensive process. The increasing demand for pelagic data combined with ever reducing budgets for monitoring and the general problem of the taxonomic impediment have driven the development of new tools and techniques for the sampling and analysis of this key ecosystem component.