Éditeur(s) : HAL CCSD
Résumé : During the course of their life cycle organisms are exposed to natural environment variations capable of inducing physiological, morphological and behaviour changes, thus a phenotypic plasticity. Phenotypic plasticity is the ability of a genotype to generate a new phenotype following exogeneous or endogeneous stress. Here, we investigated the phenotypic plasticity of the non-calcifying symbiotic cnidarian Anemonia viridis at multiple levels of structural complexity, in vivo and in vitro. In vivo, we determined the mechanisms behind the phenotypic plasticity under expected future climate change (i.e. ocean acidification and ocean warming). Our results show physiological changes in the inorganic carbon use of the sea anemone A. viridis exposed to high pCO2 during a long-term stress in natura or a short-term stress in controlled conditions. We then observed an equivalent decrease in carbonic anhydrase activity, a key enzyme of cnidarian carbon concentrating mechanisms. Also, we demonstrated that an increase in seawater temperature modified the response observed during a high pCO2 scenario. In vitro, we established a viable primary cell culture from regenerating tentacles of A. viridis. We determined the gastrodermal tissue origin of the cultivated cells and validated the use of this new tool to the in vitro study of stress response at the cellular level. The set-up of this powerful in vitro tool will open a multitude of perspectives for the study of cellular responses to exogeneous stress (as global change perturbations) and to endogeneous stress (as the symbiosis constraints experienced by symbiotic cnidarians)
Durant leur cycle de vie, les organismes sont exposés à des variations environnementales capables d'induire des changements physiologiques, morphologiques et comportementaux, résultant d’une plasticité phénotypique. La plasticité phénotypique est la capacité d'un génotype à générer un nouveau phénotype suite à un stress. Ici, nous avons étudié la plasticité phénotypique d’un Cnidaire symbiotique et non-calcifiant, l’anémone de mer Anemonia viridis, à de multiples niveaux de complexité structurale, in vivo et in vitro. In vivo, nous avons identifié les mécanismes sous-jacents de la plasticité phénotypique potentiellement induits par les futurs changements climatiques (acidification et réchauffement des océans). Nos résultats montrent des modifications dans l'utilisation du carbone inorganique par A. viridis exposée à une forte pCO2 lors d’un stress chronique in natura ou lors d’un stress court en conditions contrôlées. Nous avons ainsi observé une diminution des activités anhydrase carbonique, une enzyme clé des mécanismes de concentration du carbone chez les Cnidaires. Nous avons aussi démontré que l'augmentation concomittante de la température modifie la réponse observée lors d'une élévation seule de la pCO2. In vitro, nous avons établi une culture de cellules primaires viables issue de tentacules d’A. viridis en régénération. Nous avons déterminé l'origine gastrodermale des cellules cultivées et validé l'utilisation de ce nouvel outil pour l'étude de la réponse au stress au niveau cellulaire. Ce nouvel outil ouvre une multitude de perspectives pour l'étude des réponses cellulaires aux stress exogènes (changement climatique) et endogènes (contraintes dues à la symbiose)
https://tel.archives-ouvertes.fr/tel-01674220

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2016AZUR4136
tel-01674220
https://tel.archives-ouvertes.fr/tel-01674220
https://tel.archives-ouvertes.fr/tel-01674220/document
https://tel.archives-ouvertes.fr/tel-01674220/file/2016AZUR4136.pdf

Éditeur(s) : Elsevier Science Bv
Résumé : Mechanisms controlling the transfer and retention of silicon (Si) along continental margins are poorly understood, but play a major role in the functioning of coastal ecosystems and the oceanic biological pump of carbon. Deep-sea fans are well recognized as carbon sink spots, but we lack knowledge about the importance of the fans in the global Si cycle. Here, we provide a first estimate of the role played by the Congo deep-sea fan, one of the biggest in the world, in the Si cycle. Sediment cores sampled in the deep-sea fan were analyzed to build a Si mass balance. An exceptionally high accumulation rate of amorphous silica aSiO(2) (2.29 +/- 0.58 mol Si m(-2) y(-1)) was found, due to a high sedimentation rate and the presence of aluminum in the sediments. Although favored by bioirrigation, recycling fluxes remained low (0.3 mol Si m(-2) y(-1)) and reconstructed input fluxes could only be explained by lateral inputs coming from the canyon. Preliminary calculations show that the rapid transport of aSiO(2) through the canyon and the excellent preservation efficiency in the sediments imply that 50% of aSiO(2) river inputs from the Congo River accumulate annually in the deep-sea fan. Si:C ratios in deep-sea fan sediments were very low (0.2) and only three times as high as those measured in the river itself, which suggests that material from the river and the continental shelf was delivered directly through the canyon, with very little time for Si and C cycle decoupling to take place.
Journal Of Marine Systems (0924-7963) (Elsevier Science Bv), 2015-01 , Vol. 141 , P. 71-79

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00251/36242/35797.pdf
DOI:10.1016/j.jmarsys.2014.07.010
http://archimer.ifremer.fr/doc/00251/36242/

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : Université Paul Sabatier, Toulouse III
Résumé : The marine phytoplankton in the ocean represents only less than 1% of global biomass. Phytoplankton performs half of all photosynthesis. This autotrophic biomass in ocean is then an essential element in the climate regulation through processes as carbon dioxide absorption during the photosynthesis. Therefore, we need to estimate precisely this biomass as well as the processes which affect it. Using remotely sensed data (altimetry and ocean colour) and a coupled physical/biogeochemical model (MERCATOR-OPA/NPZDDON), Rossby waves and their influence on phytoplankton biomass are specifically studied in the North Atlantic Ocean. Their features and their influences on surface chlorophyll concentrations were analysed. Through the different mechanisms identified, we estimated that these waves can induce local increases from 60% to 150% of the estimated primary production.
Même si l'océan ne représente que moins de 1% de la biomasse liée aux plantes sur la terre, il est responsable de près de la moitié de la photosynthèse nette de la biosphère. Cette biomasse est par conséquent un élément essentiel dans la régulation du climat à travers par exemple le cycle océanique du carbone. Il est donc nécessaire d'estimer correctement cette biomasse ainsi que les processus qui l'affectent. A l'aide de données satellites altimétriques et couleur de l'eau et d'un modèle couplé physique/biogéochimie (MERCATOR-OPA / NPZDDON), les ondes de Rossby et leur influence sur cette biomasse sont spécifiquement étudiées dans l'océan Atlantique Nord. Leurs propriétés et leur influence sur les concentrations en chlorophylle de surface sont analysées. Au travers des mécanismes mis en jeu identifiés, nous estimons que ces ondes peuvent entraîner une augmentation locale comprise entre 60% et 150% de la production primaire estimée.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2005/these-2454.pdf
http://archimer.ifremer.fr/doc/00000/2454/

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : Deep-sea bivalves found at hydrothermal vents, cold seeps and organic falls are sustained by chemosynthetic bacteria which ensure part or all of their carbon nutrition. These symbioses are of prime importance for the functioning of the ecosystems. Similar symbioses occur in other bivalve species living in shallow and coastal reduced habitats worldwide. In recent years, several deep-sea species have been investigated from continental margins around Europe, West Africa, East America, the Gulf of Mexico, and from hydrothermal vents on the Mid-Atlantic Ridge. In parallel, numerous more easily accessible shallow marine species were studied. We here provide a summary of the current knowledge available on chemosymbiotic bivalves in the area ranging west-to-east from the Gulf of Mexico to Marmara Sea, and north-to-south from the Arctic to the Gulf of Guinea. Characteristics of symbioses in 51 species from the area are summarized for each of the five bivalve families documented to harbor chemosynthetic symbionts (Mytilidae, Vesicomyidae, Solemyidae, Thyasiridae and Lucinidae), and compared among families with special emphasis on ecology, life cycle, and connectivity. Chemosynthetic symbioses are a major adaptation to ecosystems and habitats exposed to reducing conditions, yet relatively little is known regarding their diversity and functioning apart from a few "model species" on which effort has focused over the last 30 yr. In the context of increasing concern about biodiversity and ecosystems, and increasing anthropogenic pressure on Oceans, we advocate for a better assessment of bivalve symbioses diversity in order to evaluate the capacities of these remarkable ecological and evolutionary units to withstand environmental change
Biogeosciences (1726-4170) (Copernicus Gesellschaft Mbh), 2013 , Vol. 10 , N. 5 , P. 3241-3267

Droits : Author(s) 2012. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00133/24417/22431.pdf
DOI:10.5194/bg-10-3241-2013
http://archimer.ifremer.fr/doc/00133/24417/

Éditeur(s) : HAL CCSD
Résumé : International audience
Pollen records, marine faunal associations and stable isotope compositions of sediments from Rhodes, Greece, have been determined to track environmental changes in the eastern Mediterranean during the Early and Middle Pleistocene. A detailed chronostratigraphic curve, based on magnetostratigraphic data, was obtained by correlating pollen spectra with the Mediterranean oxygen isotopic curve of Ocean Drilling Program Site 975. Five sedimentary sequences that correspond to marine oxygen isotope stage (MIS) 31–27 and to MIS 20–17 have been investigated in the confined Tsampika microbasin. High-amplitude Pinus variations confirm glacio-eustatic changes deduced from changes in marine faunal associations and sedimentary depositional environments. Reflecting climatic cycles identified in the marine carbonate oxygen isotope record, eight vegetation successions (characterized by the dominance first of mesothermic elements, then of mid- and high-altitude elements with Pinus, and ending with maxima in herb and steppe elements) have been documented. Most of them were probably driven by changes in insolation occurring in high northern latitudes (obliquity impact) during the late Early Pleistocene and early Middle Pleistocene.
Journal of the Geological Society, London

hal-00470360
https://hal.archives-ouvertes.fr/hal-00470360