Yoann Thomas

French National Research Institute for Sustainable Development (IRD) · OCEANS - LEMAR

AimThe spread of non-indigenous species in marine ecosystems world-wide is one of today's most serious environmental concerns. Using mechanistic modelling, we investigated how global change relates to the invasion of European coasts by a non-native marine invertebrate, the Pacific oyster Crassostrea gigas. LocationBourgneuf Bay on the French Atlant...

Significance Plastics are a contaminant of emerging concern accumulating in marine ecosystems. Plastics tend to break down into small particles, called microplastics, which also enter the marine environment directly as fragments from a variety of sources, including cosmetics, clothing, and industrial processes. Given their ubiquitous nature and sma...

The black-lip pearl oyster (Pinctada margaritifera) is cultured extensively to produce black pearls, especially in French Polynesia atoll lagoons. This aquaculture relies on spat collection, a process that experiences spatial and temporal variability and needs to be optimized by understanding which factors influence recruitment. Here, we investigat...

Shrimp farming in New Caledonia typically uses a flow-through system with water exchange rates as a tool to maintain optimum hydrological and biological parameters for the crop. Moreover, the effluent shows hydrobiological characteristics (minerals, phytoplankton biomass and organic matter) significantly higher than that of the receiving environmen...

In this study, we used orthomosaics and a digital surface model (DSM) generated from drone surveys to (1) characterize the distribution of mussel (Mytilus galloprovincialis) aggregations at high resolution (centimeters), and (2) evaluate the role of topographic features, intertidal height, slope, and orientation angle in determining mussel distribu...

The pearl-farming industry depends mostly on the natural recruitment of pearl oysters. Little is known about the relative influence of different ecological processes on the natural recruitment of pearl oysters across biogeo-graphical scales. Spatio-temporal dynamics of bivalve larvae and spats were described at Ahe and Mangareva, 1500 km apart acro...

We present a reconstruction of human demography and shell fishing activity in the Sine-Saloum mangrove Delta (Senegal) in the past 6000 years using the summed probability density (SPD) of radiocarbon dates in archaeological shell middens. We explore how this local history relates to the climatic and political history of West Africa. We find that tr...

The combined use of satellite-derived environmental data and a dynamic energy budget (DEB) model to determine Pacific oyster growth potential was adapted for the South African marine environment. Study areas consisted of the West Coast (high-chlorophyll, low temperature) and the South Coast (variable chlorophyll, higher temperature) ecoregions. Chl...

The natural productivity of ecosystems, farming practices and mortality events drive the rearing density and growth of oysters in shellfish farming areas. The variability of these drivers, which can be of natural or anthropic origin, is therefore an important source of variation in the growth performance and production of shellfish. Knowledge of th...

Individual traits and population parameters can be used as proxies of processes taking place within a range of scales, thus improving the way we can evaluate species response to environmental variability. In intertidal rocky shores, patterns at the within-site scale, i.e., between centimeters to hundreds of meters, are important for understanding t...

The Canary Current is a potential hotspot for climate change impacts on the oceans where 63 million people depend upon marine resources for national economies and livelihoods. Their unique vulnerability highlights the key roles of climate services and capacity building in order to develop effective adaptation measures.

Connectivity affects species demography, (meta)population dynamics, evolution, phylogeny and biogeography. Various methodological approaches are applied to measure connectivity. Biophysical modelling can explore systematically the influence of atmospheric, oceanic and ecological forcing, while genetics measures connectivity patterns within the samp...

The present dataset includes diverse information on individual traits and population parameters from a mussel population in a bathymetric gradient and with monthly frequency (from March 2019 to February 2020) from two rocky shores at Le Petit Minou, France (lon: -4.615860; lat: 48.339118). Each of the two shores was at the East and West side of the...

Marine organisms are currently experiencing an unprecedented rate of climatic warming, which affects their biogeography and threatens marine ecosystem integrity. To understand how benthic species will respond to ongoing seawater warming, we assessed the relative importance of processes acting at different scales using an individual-based modelling...

The black-lipped pearl oyster (Pinctada margaritifera) is extensively farmed in French Polynesia to produce black pearls. For a sustainable management of marine resources, studying interactions between organisms and environment, and the associated factors and processes that will impact their life cycle and thus modulate population dynamics is a maj...

Diseases pose an ongoing threat to aquaculture, fisheries and conservation of marine species, and determination of risk factors of disease is crucial for management. Our objective was to decipher the effects of host, pathogen and environmental factors on disease-induced mortality of Pacific oysters (Crassostrea gigas) across a latitudinal gradient....

Oyster production has historically taken place in intertidal zones, and shellfish farms already occupy large extents of the French intertidal space. The expansion of French shellfish aquaculture within intertidal areas is therefore spatially limited, and moving production to the subtidal offshore environment is considered to be a possible solution...

Aquaculture increasingly contributes to global seafood production, requiring new farm sites for continued growth. In France, oyster cultivation has conventionally taken place in the intertidal zone, where there is little or no further room for expansion. Despite interest in moving production further offshore, more information is needed regarding th...

Case study for Western (Brazil) and Eastern (Cape Verde, Senegal) tropical Atlantic countries, information on marine and coastal natural resources and their use and exploitation status

The present paper deals with the stochastic modeling of bio-colonization for the computation of stochastic hydrodynamic loading on jacket-type offshore structures. It relies on a multidisciplinary study gathering biological and physical research fields that accounts for uncertainties at all the levels. Indeed, bio-colonization of offshore structure...

The present paper deals with the stochastic modeling of bio-colonization for the computation of stochastic hydrodynamic loading on jacket-type offshore structures. It relies on a multidisciplinary study gathering biological and physical research fields that accounts of uncertainties at all the levels. Indeed, bio-colonization of offshore structures...

In French Polynesia black pearl farming represents one of the dominant business sectors. However, it still entirely relies on unpredictable Pinctada margaritifera spat collection success, which is itself conditioned by larval development completion. To assess the relationship between larval development and recruitment success, we studied under cont...

The potential for and productivity of shellfish aquaculture is strongly influenced by sea surface temperature (SST), and the concentration and nature of suspended particulate matter (SPM), which can both be monitored from space to determine shellfish growth conditions. Phytoplankton is a main food source for suspension-feeding bivalves. In too high...

Beyond key ecological services, marine resources are crucial for human food security and socio-economical sustainability. Among them, shellfish aquaculture and fishing are of primary importance but become more vulnerable under anthropogenic pressure, as evidenced by reported mass mortality events linked to global changes such as ocean warming and a...

As other filter-feeders, Crassostrea gigas can concentrate paralytic shellfish toxins (PST) by consuming dinoflagellate phytoplankton species like Alexandrium minutum. Intake of PST in oyster tissues mainly results from feeding processes, i.e. clearance rate, pre-ingestive sorting and ingestion that are directly influenced by environmental conditio...

In Europe, oyster production has historically taken place in intertidal zones. Shellfish farms already occupy large extents of intertidal space, and sometimes have for more than a century. The possibility of expanding shellfish aquaculture in intertidal areas is therefore spatially limited, and is also constrained by carrying capacity, water qualit...

Climate change exposes benthic species populations in coastal ecosystems to a combination of different stressors (e.g. warming, acidification and eutrophication), threatening the sustainability of the ecological functions they provide. Thermal stress appears to be one of the strongest drivers impacting marine ecosystems, acting across a wide range...

Like many marine species around the globe, several stocks of Atlantic cod (Gadus morhua) live in increasingly hypoxic waters. In the Gulf of Saint Lawrence (GSL) in Canada, the deep channels traversing the semi-enclosed sea exhibit year-round hypoxia, identified as one of the limiting factor for the recovery of GSL cod in its northern part. While m...

Hypoxia is a decrease in dissolved oxygen that causes physiological disturbances in marine fishes and invertebrates, including reduced mobility, growth rate and reproductive success, altered phenology and increased vulnerability to diseases. Under pressure from global changes such as warming or eutrophication, ocean and coastal ecosystems worldwide...

Identifying the drivers that control the reproductive success of a population is vital to forecasting the consequences of climate change in terms of distribution shift and population dynamics. In the present study, we aimed to improve our understanding of the environmental conditions that allowed the colonization of the Pacific oyster, Crassostrea...

In atoll lagoons, plankton richness is highly dependent on water exchange with the ocean through the atoll rim. However, the dynamics of the physical and biological fluxes at the lagoon-ocean interface remain poorly characterized. Here, we studied the combined effects of lagoon-ocean water exchanges and local environmental conditions on the phyto-...

Studies on impacts of emerging contaminants are challenging, as is the case for studying the smallest sizes (<100 µm) of microplastics, mainly because there is no clear view of their actual concentration and characteristics in the natural environment (1). Major developments are required to establish standardized procedures for collecting, fractiona...

Overview of the DEBSe@ project

Feeding strategies and digestive capacities can have important implications for variation in energetic pathways associated with ecological and economically important traits, such as growth or reproduction in bivalve species. Here, we investigated the role of amylase in the digestive processes of Crassostrea gigas, using in vivo RNA interference. Th...

Pearl oyster aquaculture is a major activity in French Polynesia atoll lagoons. After the economic decline that characterized the last decade, concerns recently rose about discarded installations and materials that supported aquaculture practices and by facilities abandoned after they had to close their activities. In May 2013, a first inventory of...

Studying the larval dispersal of bottom-dwelling species is necessary to understand their population dynamics and optimize their management. The black-lip pearl oyster (Pinctada margaritifera) is cultured extensively to produce black pearls, especially in French Polynesia's atoll lagoons. This aquaculture relies on spat collection, a process that c...

Hydrodynamic functioning and water circulation of the semi-closed deep lagoon of Ahe atoll (Tuamotu Archipelago, French Polynesia) were investigated using 1 year of field data and a 3D hydrodynamical model. Tidal amplitude averaged less than 30 cm, but tide generated very strong currents (2 ms(-1)) in the pass, creating a jet-like circulation that...

We applied, for the first time, a dynamic energy budget (DEB) growth model to the larval phase in the pearl oyster Pinctada margaritifera var. cumingii (Linnaeus, 1758) to evaluate the impact of spatio-temporal variation in the atoll lagoon environment on its capacity for development. The specific parameters of the model, which represent ingestion,...

In French Polynesia, the black-lip pearl oyster Pinctada margaritifera has been farmed to produce pearls since the 1980s, forming the basis of a major industry. The sustainability of this activity relies on spat collection in the lagoons. However, pearl oyster spat can be difficult to identify for the evaluation of stock variations. It is especiall...

Spatial and temporal scales of variability in phyto- and bacterioplankton abundance were investigated in a deep atoll lagoon (Ahe, French Polynesia), Ahe Lagoon showed a classical phytoplankton composition, but its picophytoplankton (Prochlorococcus, Synechococcus and picoeukaryotes) concentrations are higher than the mean for Polynesian atoll lago...

Understanding key factors determining the bentho-pelagic species larval growth and dispersal remains one of the challenges of marine ecology, notably to understand the adult population structure and dynamics. In the present study, we explore this determinism on the development and dispersal of the black-lip pearl oyster (Pinctada margaritifera var....

Bivalves cultivation plays a crucial role in coastal ecosystems, not only from the direct socio-economical activity generated but also from ecological interactions between cultivated stocks and their environment. Bivalve production is usually vulnerable to environmental and natural food variability. For management purposes; it is therefore importan...

In the booming context of shrimp culture in French Caledonia, some research actions need to be considered in order (i) to make sure this production will not impact the quality and biodiversity of the coastal environment it is contingent upon (ii) for the field to highlight, based on objective bases, its good "environmental image", for an efficient...