The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean

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

Adaptation d'Eunicella singularis en milieu perturbé (symbiose et structuration génétique)

La symbiose entre Cnidaires et Symbiodinium (Dinobionte photosynthétique) est relativement souple. Les Cnidaires généralistes sont capables de s adapter à un changement environnemental en modifiant leur population symbiotique. Les hôtes spécialistes, a priori privés d un tel mécanisme d adaptation, peuvent-ils malgré tout faire face aux modifications environnementales ? C est dans ce cadre que nous avons étudié la symbiose chez un hôte spécialiste en milieu variable : la gorgone méditerranéenne Eunicella singularis. En effet, la diversité symbiotique se limite à un seul clade ribosomique de Symbiodinium en Méditerranée. Des études de génétiques réalisées à l aide de microsatellites sur le bassin Méditerranéen Nord-Occidental ont révélé une diversité symbiotique intra-clade. Nous avons montré que les symbiotes se distribuent indépendamment de leurs hôtes et de la profondeur. Un échantillonnage des mêmes populations naturelles à 6 ans intervalle a mis en évidence des acquisitions horizontales massives de symbiotes chez des hôtes adultes. Des transplantations réciproques ainsi qu un suivi de colonies maintenues en aquarium semblent indiquer que de telles modifications nécessitent une variation environnementale forte. Par ailleurs, nous avons étudié le comportement de l association en absence d apport autotrophe et/ou hétérotrophe. Il en ressort que l hôte semble contrôler l association et qu il apparaît prioritaire quant au partage des ressources. Même chez un hôte dit spécialiste, l association avec Symbiodinium peut donc se révéler dynamique. Cela pourrait faciliter l adaptation de ces spécialistes, pour peu qu à la diversité génétique symbiotique corresponde une diversité fonctionnelle.The symbiosis between Cnidaria and Symbiodinium (photosynthetic Dinoflagelate) is relatively flexible. Generalist Cnidaria are able to adapt themselves to environmental variations by modifying their symbiont population. Are specialists hosts, a priori lacking this adaptive mechanism, able to confront environmental changes ? In this context, we studied the symbiosis n a specialist host : the Mediterranean sea whip Eunicella singularis. Indeed, symbiont diversity is limited to a single Symbiodinium ribosomal clade in Mediterranean Sea. Genetic studies based on microsatellites loci revealed a with-in independently from their host and from depth. A re-sampling of natural populations brought to light massive horizontal acquisitions of symbionts in adult colonies. Reciprocal transplants and monitoring of colonies maintained in aquarium seems to indicate that strong environmental variations are required for such modifications of symbiont populations. In addition we studied the behavior of this association when deprived of autotrophic and/or heterotrophic resources. We conclude that the host seems able to control the association and that he appears to have priority in resources sharing. Therefore, even for a specialist host, association with Symbiodinium can be a dynamic. This could make adaptation easier for this specialist, but only of genetic diversity is correlate with a functional diversity.NICE-BU Sciences (060882101) / SudocSudocFranceF

Development of microsatellite loci from a Mediterranean symbiotic gorgonian, Eunicella singularis (Cnidaria, Anthozoa), and its temperate-A Symbiodinium.

International audienc

Population assignments

File with population assignments for the samples: a two column text file with the sample ids in the first column and the ids of the populations in the second column

Data from: Next-generation phylogeography of the cockle Cerastoderma glaucum: highly heterogeneous genetic differentiation in a lagoon species

Aim. Coastal lagoons form an intriguing example of fragmented marine habitats. Restricted gene flow among isolated populations of lagoon species may promote their genetic divergence, and may thus provide a first step towards speciation. In the present study, the population genetic structure of the lagoon cockle Cerastoderma glaucum has been investigated to clarify the complex phylogeographic pattern found in previous studies, to localize major genetic breaks and to discuss their origin and maintenance. Location. The Atlantic and Mediterranean coasts, including the Baltic, North Sea and Black Sea. Methods. 204 C. glaucum individuals from 14 populations were genotyped using restriction-site associated DNA-sequencing (RADseq). The genetic diversity, divergence and structure were analyzed using genome-wide Single Nucleotide Polymorphisms (SNPs). Phylogenetic relationships were inferred under a coalescent model using SVDquartets. Results. The RADseq approach allowed inferring phylogeogeaphic relationships with an unprecedented resolution. Three deeply divergent lineages were identified within C. glaucum that are separated by many genetic barriers: one lineage in the Aegean-Black Sea region, one in the Ionian Sea, and the last one widely distributed from the Western Mediterranean to the Baltic Sea. The nested branching pattern displayed on the species tree largely agrees with the likely scenario of C. glaucum post-glacial expansion from the Mediterranean to the Baltic Sea. Main conclusion. The genetic differentiations between geographically separated lagoons proved to be strong, highlighting the evolutionary influence of these naturally fragmented habitats. The post-glacial expansion created complex patterns of spatial segregation of genetic diversity with allele frequency gradients in many outlier loci, but also discrepancies between the nuclear and mitochondrial genetic markers that probably arose from genetic surfing of mitochondrial variation

Matrix of RAD loci from pyRAD analysis

NEXUS file used for SVDquartet analysi

Assessing population genetic structure of sorghum landraces from North-western Morocco using allozyme and microsatellite markers

The level of genetic diversity and the population genetic structure of sorghum landraces from North-western Morocco have been investigated based on direct field-sampling using both allozyme and microsatellite markers. As expected, microsatellite markers showed a much higher degree of polymorphism than allozymes, but relative measures of genetic structure such as Wright's inbreeding coefficient F(IS) and Nei's coefficient of genetic differentiation G(ST) were similar for the two sets of markers. Substantial inbreeding was found to occur within fields, which confirms that sorghum is predominantly selfing under cultivation. Most of the genetic diversity in Moroccan landraces occurs within fields (more than 85%), as opposed to among fields or among regions, a result which contrasts to those of studies based on accessions from germplasm collections. It is suggested that individual fields of sorghum constitute valuable units of conservation in the context of in situ conservation practices.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Thermal threshold and sensitivity of the only symbiotic Mediterranean gorgonian Eunicella singularis by morphometric and genotypic analyses

International audienceThe only symbiotic Mediterranean gorgonian, Eunicella singularis, has faced several mortality events connected to abnormal high temperatures. Since thermotolerance data remain scarce, heat-induced necrosis was monitored in aquarium by morphometric analysis. Gorgonian tips were sampled at two sites: Medes (Spain) and Riou (France) Islands, and at two depths: 15 m and-35 m. Although coming from contrasting thermal regimes, seawater above 28 degrees C led to rapid and complete tissue necrosis for all four populations. However, at 27 degrees C, the time length leading to 50% tissue necrosis allowed us to classify samples within three classes of thermal sensitivity. Irrespectively of the depth, Medes specimens were either very sensitive or resistant, while Riou fragments presented a medium sensitivity. Microsatellite analysis revealed that host and symbiont were genetically differentiated between sites, but not between depths. Finally, these genetic differentiations were not directly correlated to a specific thermal sensitivity whose molecular bases remain to be discovered

First characterization of eight polymorphic microsatellites for Cystoseira amentacea var. stricta (Fucales, Sargassaceae)

First characterization of eight polymorphic microsatellites for Cystoseira amentacea var. stricta (Fucales, Sargassaceae

Strong genetic structuring of the cockle Cerastoderma glaucum across Europe: new insights from an intronic marker and multivariate analysis

International audienceThe distribution of the lagoon cockle Cerastoderma glaucum is strongly fragmented and usually restricted to isolated, shallow and nontidal lagoons. A high level of genetic structuring was found among the European populations of this species based on mtDNA (COI) sequences, as well as allozymic and microsatellite markers. However, the strengths and geographic locations of the major divisions differed among markers. In the present study we characterized the diversity of a new, potentially universal exon-primed intron-crossing marker, i34, for 17 C. glaucum populations. Allele frequency data at the i34 locus were informative and relevant with respect to geography. Multivariate analyses of new data together with previously published microsatellites confirmed the divergent character of the Ionian Sea and the Aegean-Ponto-Caspian populations, but also revealed the existence of a genetic cline from the Bay of Biscay to the Baltic Sea. Some noncongruent patterns among loci were detected, which may reflect either differential introgression along the genome at the hypothetical contact zone, or selective sweeps. This strong genetic differentiation, and the occurrence of private alleles, may hint at the presence of cryptic species within C. glaucum