The Pacific oyster (Crassostreae gigas) has been introduced from Asia to numerous countries throughout the world (Canada, USA, Australia, New-Zealand, Chile, Mexico, Argentina, South Africa, Namibia and in numerous European countries including France) during the 20th century. C. gigas is currently the main oyster species farmed in the world and represents more than 95% of world production. For decades, C. gigas has been suffering mortalities but the severity of these outbreaks has dramatically increased since 2008. They mainly affect juvenile stages, decimating up to 100% of young oysters in French farms. In recent years, this mortality syndrome, designated Pacific oyster mortality syndrome (POMS), has become panzootic and represents a threat for the oyster industry worldwide. Recently, the consortium of the DECICOMP project overcame a major step towards understanding POMS using a holistic molecular approach developed in mesocosm. We showed that the infection by the Ostreid herpesvirus (OsHV-1 µVar) was the initial step of the infectious process leading to an immune-compromised state, which evolved towards subsequent bacteraemia by opportunistic bacterial pathogens. Nevertheless, by elucidating the mechanisms of the pathogenesis, only a part of the POMS complexity was deciphered. Indeed, this multifactorial disease is tightly controlled by a series of host and environmental factors (temperature, oyster age and diet). However, we still ignore the mechanisms by which these key factors control disease expression. This knowledge is urgently needed to elucidate the whole complexity of the disease and ultimately assess the epidemiological risk. In this context, the first objective of the DECICOMP project is to determine how temperature, oyster age and diet control POMS expression. The second objective is to weight and evaluate the interactions between all the factors controlling POMS in real farming conditions. Finally, our third objective is to model the epidemiological risk of POMS in oyster farms by using the sum of data generated in the project. To address the objectives of the DECICOMP project, we will combine laboratory/field experiments and theoretical approaches. Our multidisciplinary approach (mesoscosm and rationalized infections, integrative omics including epigenomics and metatranscriptomics, physiological/histological/functional validation approaches, modelling) is unique, ambitious and, as we believe, highly original. To reach our objectives, we have put together a consortium of researchers with highly complementary expertises that makes possible the implementation of a multiscale approach for deciphering the functioning of such a complex pathosystem from the finest molecular level to farmed populations. We believe DECICOMP will not only open prospects for substantial scientific knowledge advancement on a complex multifactorial disease but will also help decision-making thanks to tools and applied innovations for a sustainable and integrated management of oyster aquaculture. Indeed, by modelling the epidemiological risk under the influence of the different factors influencing POMS, we will be able to quantify the benefits of different measures that could be conducted by oyster farmers to play on these factors and consequently provide some action-levers to reduce the impact of the disease in farms.

In coastal regions, seaweed biomass turnover influences ecosystem functions both at local and global scales. It largely relies on specialized bacteria able to breakdown intact algal tissues and release degradation products in the water column. The ALGAVOR project will explore the ecological and metabolic strategies of such poorly known specialized marine bacteria of the genus Zobellia. We will combine cultivation-dependent and 'omics approaches to (i) evaluate the biodiversity, distribution, abundance, activity and catabolic functions of Zobellia spp in marine environments, (ii) decipher which metabolic pathways they use to degrade fresh seaweed biomass and (iii) study their cooperative interactions with scavenger bacteria that can profit from degradation products. Altogether, ALGAVOR will unveil the strategies of crucial bacteria considered as a bottleneck controlling the fate of organic matter in coastal habitats.

Population genetics methods allow researchers to infer historical events in human and non-human populations, at time scales for which historical records provide no information. Coalescent-based methods have been developed to infer these events. These methods have been successfully applied to many populations, using classical population genetics markers (e.g. microsatellites, DNA sequences). They have allowed us for instance to determine whether populations have undergone events of growth or decline, of migration between surrounding populations, and if some populations result from admixture events between two or more populations. The parameters of these demographic phenomena (e.g. growth rates, migration rates, ancestral population sizes, admixture rates) could be estimated to some extent. The amount of data available on DNA polymorphism is increasing by several orders of magnitude through the recent development of new kind of polymorphism datasets: DNA chips datasets with several hundred of thousands or even a few millions of single nucleotide polymorphisms (SNPs) and full genome sequences. Some of the SNPs are in coding or regulatory regions and may thus be submitted to selection, but others are outside these regions and can thus be used for demographic processes inference. This strong increase in the amount of available data may lead to the logical conclusion that demographic events could be inferred much more precisely thanks to these new datasets. Based on the existing methods, the main problem is to develop new algorithms adapted to such data, as they differ from classical data both by the amount of available polymorphism and also by the occurrence in these datasets of many linked loci, which offers the possibility to use the level of linkage disequilibrium inside the estimation process. The aim of this study is to develop new coalescent-based approaches (ABC and MCMC) for these new data sets and to apply them to human and Drosophila melanogaster polymorphism datasets. The first step will be to develop a simulation program that will be able to generate such large datasets. In a second step, the simulation program will be then used directly to develop ABC methods, but also as a mean to test the validity of the different methods. For the MCMC method, we will focus on how to optimize these methods for large data sets and if a strategy of optimal sub-sampling can be designed to keep a reasonable computing time. In a third step, we will apply these methods to real data on human and Drosophila populations. Regarding humans, the first question will be whether we can infer different demographic history for populations that have been submitted to different lifestyles, namely agriculturalists, herders and hunter-gatherers. In particular do these differences in lifestyle influence their expansion rate? The second question will be whether we can infer the history of migration and admixture of populations in Central Asia. Are these populations the results of admixture events between the neighbouring European and Asian populations, or conversely are they one of the first areas colonised after the emergence of modern humans out of Africa, areas from which other Eurasian area were subsequently colonised? Finally, we will also investigate the possibility to infer a recombination map along the genome in the different population taking into account their demographic history. Regarding D. melanogaster, we will investigate its demographic history in Africa exploiting the data produced by the DPGP project. Two main issue will be tackled, namely the timing and mode of expansion in Africa (particularly the proposed division between East and West African populations) and the time of the out-of–Africa.

Coccolithophores and planktonic foraminifera produce more than 90% of pelagic carbonates, thus being major actors in the global carbon cycle. Calcification of these unicellular organisms is known to be influenced by carbonate ion concentration and calcite saturation state of seawater as well as by other physico-chemical parameters. Carbon dioxide produced by human activities since the industrial revolution has already induced a decrease of ocean pH by about 0.1 units. The objective of CALHIS is to undertake the first very high-resolution evaluation of the impact of this pH drop on pelagic carbonate production. To this end, we have selected 3 categories of oceanic zones covering a wide range of carbonate ion concentration, calcification types and trophic levels: (1) the Mediterranean and Caribbean seas with waters with high carbonate ion concentration, oligotrophy, and organisms with well calcified shells; (2) the north Papuan coast and Patagonian shelf with lower carbonate concentration, higher nutrient levels and lightly calcified shells; (3) the Eastern Pacific margin (Peru and Mexico) characterized by upwelled waters with high nutrient levels and such low carbonate ion concentration and pH that coccolithophores would be predicted to no longer calcify, although some in fact exhibit highly calcified shells. In each of these zones, we have privileged access to research vessels for sampling. We will lead or participate in mini-cruises in each of these coastal areas in order to retrieve surface sediment cores that record the history of sedimentation of the last centuries and to collect water samples from the photic zone to establish present-day relationships between calcification and carbonate chemistry, through genetic, morphological and physico-chemical analyses. A range of coccolithophore genotypes and morphotypes will be isolated into laboratory culture in order to quantify eco-physiological tolerances and calibrate specific biomarkers. From well-dated (14C/ 210Pb) sediments, we will establish records of the state of calcification of foraminifera and coccolithophores, temperature, d13C, concentrations of specific biomarkers, and relative abundance of coccolithophore morphotypes and, when possible, genotypes (i.e. in anoxic sediments). These data will enable accurate quantification of changes in pelagic carbonate production over the last 300 years and determination of whether changes are related to recent global ocean acidification. This project is the logical continuation of a study recently published in Nature by most of the proponents of the proposal.

Rapidly accumulating environmental sequencing data have revealed that eukaryotic microbes are far more diverse and complex than previously thought. However, meta-barcoding and meta-genomics surveys are severely limited by the fact that the majority of environmental sequences do not match a sequence with associated phenotypic/taxonomic information in reference databases. Phytoplankton, a polyphyletic group of single-celled photosynthetic organisms that play key roles in aquatic food webs and global biogeochemical cycles, comprise an important part of this undescribed diversity. PHENOMAP will address this major “phenotype gap” for marine phytoplankton by undertaking targeted phenotypic description of key cryptic lineages. The work plan integrates a suite of state of the art methods that will be applied to two outstanding existing resources: the Roscoff Culture Collection, which is the largest and most diverse service collection of living microalgal strains in the world, and the Tara protist sample collection that contains over 15,000 fixed plankton samples from the worldwide Tara Oceans expeditions (2009-2018). Additional targeted sampling at 3 French marine stations will complement these resources. Phenotypic analyses will include light, fluorescence and electron microscopy for both live and fixed samples, as well as photosynthetic pigment analysis for cultures. For fixed samples, fluorescent in-situ hybridisation will be used to target cells belonging to the most abundant cryptic environmental lineages. Genetic barcoding of morphologically identified single cells isolated from fixed and live samples will complete the experimental strategy. We aim to formally describe at least 100 new taxa (including many high taxonomic rank lineages) and link genotypic to phenotypic information for hundreds of additional existing species, adding significant value to integrated community databases (PR2, UniEuk, Ecotaxa) that are increasingly central to studies on phytoplankton biology, ecology and evolution. Widespread dissemination of scientific outputs and development of innovative educational and outreach resources is integral to the PHENOMAP approach.