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1. Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia)

Author

Didier Aurelle, Marine Pratlong, Nicolas Oury, Anne Haguenauer, Pauline Gélin, Hélène Magalon, Mehdi Adjeroud, Pascal Romans, Jeremie Vidal-Dupiol, Michel Claereboudt, Camille Noûs, Lauric Reynes, Eve Toulza, François Bonhomme, Guillaume Mitta, Pierre Pontarotti, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Ecologie Marine et BIOdiversité (EMBIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut Pythéas (OSU PYTHEAS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aix Marseille Université (AMU), Université de La Réunion (UR), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Universités (COMUE), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Sultan Qaboos University (SQU), Laboratoire Cogitamus, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-12-ADAP-0016,ADACNI,Processus adaptatifs chez les cnidaires: étude intégrative de la réponse au stress thermique et au changement climatique, des gènes aux populations(2012), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)

Subjects
Genetic Structures, species delineation, Sequence Analysis, DNA, Plant Science, General Medicine, RAD sequencing, Anthozoa, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Species Specificity, Insect Science, Genetics, genetic structure, Animals, Animal Science and Zoology, Metagenomics, Pocillopora, clonal reproduction, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, coral
Abstract

International audience; Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test for species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RADsequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e. PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.

Published
2022
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2. Population genomics of Pocillopora corals: insights from RAD-sequencing

Author

François Bonhomme, Marine Pratlong, Eve Toulza, Pauline Gélin, Didier Aurelle, Hélène Magalon, Guillaume Mitta, Michel R. Claereboudt, Pierre Pontarotti, Anne Haguenauer, Nicolas Oury, Mehdi Adjeroud, Lauric Reynes, Pascal Romans, Camille Noûs, Jeremie Vidal-Dupiol, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Université de la Nouvelle-Calédonie (UNC), Université de La Réunion (UR), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Sultan Qaboos University (SQU), Laboratoire Cogitamus, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-12-ADAP-0016,ADACNI,Processus adaptatifs chez les cnidaires: étude intégrative de la réponse au stress thermique et au changement climatique, des gènes aux populations(2012), ANR-10-LABX-0046,EGID,EGID Diabetes Pole(2010), ANR-10-EQPX-0007,LIGAN PM,Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mitochondrial DNA, Lineage (evolution), [SDV]Life Sciences [q-bio], Population, Biology, RAD sequencing, 010603 evolutionary biology, 01 natural sciences, Population genomics, 03 medical and health sciences, genetic structure, 14. Life underwater, Pocillopora, education, coral, 030304 developmental biology, 0303 health sciences, education.field_of_study, Genetic diversity, species limits, biology.organism_classification, Genetic marker, Evolutionary biology, Genetic structure
Abstract

Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.

Published
2021

3. Metabolomics Reveal That Octocrylene Accumulates in Pocillopora damicornis Tissues as Fatty Acid Conjugates and Triggers Coral Cell Mitochondrial Dysfunction

Author

Alice M. S. Rodrigues, Didier Stien, Rémi Pillot, Fanny Clergeaud, Philippe Lebaron, Sonja K. Fagervold, Karine Lebaron, Pascal Romans, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), PIERRE FABRE-EDF (EDF)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Coral, Cell, Pocillopora damicornis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010402 general chemistry, 01 natural sciences, Analytical Chemistry, chemistry.chemical_compound, Metabolomics, Tandem Mass Spectrometry, medicine, Animals, Chromatography, High Pressure Liquid, chemistry.chemical_classification, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, biology, Fatty acid metabolism, Molecular Structure, 010401 analytical chemistry, Fatty Acids, Fatty acid, biology.organism_classification, Anthozoa, 0104 chemical sciences, Mitochondria, Octocrylene, medicine.anatomical_structure, chemistry, Biochemistry, Acrylates, Toxicity
Abstract

International audience; Octocrylene (OC) is an ingredient used in many sunscreens and cosmetics worldwide. Our group evaluated the toxicity of OC in corals. Adult Pocillopora damicornis coral was treated with OC at concentrations of 5, 50, 300, and 1000 μg/L. Most polyps were closed at concentrations of 300 μg/L and higher. Further, metabolomic profiling provided crucial information regarding OC accumulation in coral tissues and OC toxicity. First, we demonstrated that OC was transformed into fatty acid conjugates via oxidation of the ethylhexyl chain, yielding very lipophilic OC analogues that accumulate in coral tissues. Second, the differential analysis of coral profiles revealed higher levels of 15 acylcarnitines, suggesting abnormal fatty acid metabolism related to mitochondrial dysfunction. The formation of OC analogues suggests that OC concentrations measured in the environment, and organisms may have been largely underestimated. Overall, these results call for an in-depth evaluation of OC toxicity and the reevaluation of the actual OC accumulation rate in the ocean’s food chain, including OC–fatty acid conjugates.

Published
2019
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4. Survival of tissue balls from the coral Pocillopora damicornis L. exposed to cryoprotectant solutions

Author

Patrick Masanet, Florent Engelmann, Lucie Martinez, Dominique Barthélémy, Pascal Romans, Isabelle Engelmann-Sylvestre, and Lionel Feuillassier

Subjects
Glycerol, Ethylene Glycol, Cryoprotectant, Coral, Pocillopora damicornis, Biology, General Biochemistry, Genetics and Molecular Biology, Cryopreservation, chemistry.chemical_compound, Cryoprotective Agents, Animals, Tissue ball, Dimethyl Sulfoxide, Chromatography, Dimethyl sulfoxide, Methanol, General Medicine, Anatomy, biology.organism_classification, Anthozoa, Propylene Glycol, chemistry, Toxicity, General Agricultural and Biological Sciences, Ethylene glycol
Abstract

In this study, the tolerance of tissue balls (TBs, 100–300 μm in diameter) from the coral Pocillopora damicornis produced using mechanical excision to exposure to cryoprotectant (CPA) solutions was tested. TBs were treated for 20 min at room temperature with solutions of ethylene glycol (EG), methanol (Met), glycerol (Gly) or dimethyl sulfoxide (Me2SO) at concentrations between 1.0 and 4.5 M. Two parameters were used to evaluate the survival of TBs following CPA treatment. The Undamaged Duration of Tissue Balls (expressed in h) corresponded to the time period during which the membrane surface of TBs remained smooth and their motility was preserved. Tissue Ball Regression (expressed in μm/h) corresponded to the size reduction of TBs over time. TBs tolerated exposure to all CPAs tested at the three lower concentrations employed (1.0 M, 1.5 M and 2.0 M). No survival was achieved following exposure to a 4.5 M CPA solution. At concentrations of 3.0 and 4.0 M, higher Undamaged Duration of Tissue Balls and lower Tissue Ball Regression were obtained following treatment with EG compared to the other three CPAs. Our experiments show that TBs constitute a good experimental material to evaluate CPA toxicity on corals using large numbers of samples. Performing preliminary experiments with TBs may allow reducing the number of tests carried out with less easily available coral forms such as planulae, thereby preserving larval stocks.

Published
2014

5. Tolerance of apexes of coral Pocillopora damicornis L. to cryoprotectant solutions

Author

Patrick Masanet, Dominique Barthélémy, Isabelle Engelmann-Sylvestre, Lionel Feuillassier, Pascal Romans, and Florent Engelmann

Subjects
Glycerol, Ethylene Glycol, Sucrose, Molar concentration, Cryoprotectant, Pocillopora damicornis, General Biochemistry, Genetics and Molecular Biology, chemistry.chemical_compound, Cryoprotective Agents, Osmotic Pressure, Botany, Animals, Dimethyl Sulfoxide, solutions, Cryopreservation, biology, Dimethyl sulfoxide, Methanol, Osmolar Concentration, Trehalose, General Medicine, biology.organism_classification, Anthozoa, Adaptation, Physiological, Propylene Glycol, chemistry, cardiovascular system, Coral, Apex, General Agricultural and Biological Sciences, Ethylene glycol, Nuclear chemistry
Abstract

In this study, we investigated the tolerance of Pocillopora damicornis apexes to treatments with solutions containing penetrating and non-penetrating cryoprotective agents (CPAs). CPAs were employed individually or in binary, tertiary or quaternary solutions. In some experiments apexes were treated successively with two CPA solutions with increasing total concentration. P. damicornis apexes withstood exposure for up to 30 min to solutions containing 0.6-0.8 M sucrose (Suc) or trehalose (Tre). When apexes were treated with binary cryoprotectant solutions containing Suc and ethylene glycol (EG), methanol (Meth), dimethyl sulfoxide (Me2SO) or glycerol (Gly), the CPAs employed in combination with Suc could be ranked in the following order of decreasing tolerance: EG > Meth > Me2SO > Gly. P. damicornis apexes tolerated exposure to complex CPA solutions containing Suc, Me2SO, EG and/or Meth with a total molarity of 2.45 M. In experiments where two successive CPA solutions were employed, apexes withstood treatment with the second, more concentrated solution at 0 degrees C for up to 10 min. These preliminary results pave the way to the development of a cryopreservation protocol for P. damicornis apexes.

Published
2014

6. Temporal changes in the growth of two Mediterranean cold-water coral species, in situ and in aquaria

Author

Nadine Le Bris, Simon Pareige, Pascal Romans, Elwyn de la Vega, Franck Lartaud, Marc de Rafélis, Erwan Peru, Lionel Feuillassier, Marjorie Bideau, Karine Nedoncelle, Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biominéralisations et environnements sédimentaires (BES), Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Canyon, Mediterranean climate, geography, geography.geographical_feature_category, biology, Coral, media_common.quotation_subject, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Oceanography, biology.organism_classification, Lophelia, Mediterranean sea, Ecosystem, 14. Life underwater, Reproduction, ComputingMilieux_MISCELLANEOUS, media_common, Madrepora oculata
Abstract

In situ growth patterns of two-species of reef-building cold-water corals were investigated for the first time at different temporal scales, based on the redeployment of coral nubbins in their natural environment. Lophelia pertusa and Madrepora oculata were collected in November 2010 and May 2011 from the Lacaze-Duthiers canyon in the northwestern Mediterranean Sea (520 m depth). Three in situ growth experiments were performed from November 2010 to May 2011, May to September 2011 and November 2010 to September 2011. For comparison, aquaria experiments over comparable lengths of time were conducted with coral colonies collected in November 2010. In the canyon, new polyps from M. oculata and L. pertusa displayed similar growth rates in summer (5.8±3.8 and 7.3±1.7 mm yr−1 respectively), but M. oculata growed significantly slower during winter/spring than L. pertusa (4.1±1.8 and 8.4±2.7 mm yr−1 respectively). Budding rates however (the rate of new polyp addition per mother polyp per year) were similar between both species in winter/spring (45±40% for M. oculata and 48±72% for L. pertusa), but were significantly lower in summer for M. oculata (14±19%) compared to L. pertusa (58±94%). This seasonal difference in the growth between L. pertusa and M. oculata might reflect differences in species-specific physiology (such as reproduction) or feeding strategy, or a higher sensitivity of M. oculata to the variability of food supply in the Lacaze-Duthiers canyon resulting from periodic cascading events. The comparison of in situ and aquaria growth experiments showed no significant differences for budding and new polyp growth rates, which supports the validity of aquaria experiments for these kinds of investigations. However the budding rates observed were consistently lower in coral maintained in aquaria than those in in situ conditions, a finding which is to be considered when extrapolating laboratory based investigation results to the naturally occurring coral ecosystem.

Published
2014
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