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International audience; Benthic exchanges of oxygen and nutrient at the sediment-water interface were investigated under light and dark conditions at 5 selected sites in a sub-tropical atoll. Mean oxygen fluxes were - 1316.5 ± 242.0 μmol m−2 h−1 and mean effluxes of oxygen under light conditions were 2231.7 ± 626.4 μmol m−2 h−1, presumably due to microphytobenthos present at the sediment-water interface. The consequences of this high related productivity was a systematic consumption of nutrients (DIN, PO4 and Si(OH)4) during almost all light incubations, contrasting with the effluxes of nutrients during dark incubations. Our results suggest that the sediments were net autotrophic and the oxygen balance in favor of microbenthic production when compared to community demand. Diurnal rates of gross benthic primary productivity were high (3423 ± 1192 μmol m−2 h−1) which emphasize the role of microphytobenthos in maintaining the oxygen reservoir in tropical lagoons.

This study reports the first measurements of nitrogen uptake and new data on carbon fixation (15N/13C incorporation) for two size-fractionated phytoplankton ( 2 μm), on organic matter, and phytoplankton stocks in Ahe lagoon. Data were collected between November and December 2017, during the hot season with prevailing trade winds. Ammonium and nitrate uptake data (7.58 to 39.81 and 1.80 to 21.43 μmol N m−3 h−1, respectively) suggest a rapid turn-over of N-nutrients in the water column and show that primary production was largely sustained by recycled nitrogen providing 68% of the pelagic N demand. These results highlight the spatial heterogeneity of the measured processes linked to the local hydrodynamics, exhibiting higher regenerated production in the more exploited southwestern part of the lagoon and a higher proportion of new production in the north. Intense nutrient recycling appears to promote nanophytoplankton production which is critical for pearl oyster growth.

International audience; In remote coral reef environments, lagoon and reef in situ measurements of temperature are scarce. Sea Surface Temperature (SST) measured by satellite has been frequently used as a proxy of the lagoon temperature experienced by coral reef organisms (TL) especially during coral bleaching events. However, the link between SST and TL is poorly characterized. First, we compared the correlation between various SST series and TL from 2012 to 2016 in three atolls and one island in the Central South Pacific Ocean. Simple linear correlation between SST and TLranged between 0.44 and 0.97 depending on lagoons, localities of sensors, and type of SST data. High-resolution-satellite-measurements of SST inside the lagoons did not outperform oceanic SST series, suggesting that SST products are not adapted for small lagoons. Second, we modelled the difference between oceanic SST and TL as a function of the drivers of lagoon water renewal and mixing, namely waves, tide, wind, and season. The multivariate models reduced significantly the bias between oceanic SST and T. In atoll lagoons, and probably in other hydrodynamically semi-open systems, a correction taking into account these factors is necessary when SST are used to characterize organisms’ thermal stress thresholds.

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- and zooplankton abundance and community structure across the atoll lagoon rim of Ahe (Tuamotu Archipelago, French Polynesia). Plankton and environmental variables were monitored in May 2013 (i) at several stations inside and outside the lagoon and (ii) during time-series corresponding to ebb-flood tidal cycles in the two types of channels connecting the lagoon to the ocean: at the passage (300 m long and about 11 m deep) and in hoa (i.e reef-flat less than 50 cm depth). Our results highlight tidally-driven selective plankton exchanges between the lagoon and external ocean. Phytoplankton (chlorophyll-a) and zooplankton biomass were respectively 4 times and 7 times higher in the lagoon than at stations outside the atoll lagoon. Copepoda was the dominant zooplankton group at the oceanic station (>75% abundance) whereas meroplankton (with bivalve larvae most common) was dominant at the lagoon stations (54%), in the passage (55–82%) and in hoa (>80%). These differences between sites suggest a loss of bivalve larvae through export to the ocean and retention and/or increased production of copepods in the lagoon. The daily export of bivalve larvae represents a low percentage of the lagoon stock, in agreement with previously published larval dispersal numerical models. The retention of copepods could constitute a significant input of nutrients and organic matter (through excretion, feces release, decomposition, and remineralization) into the lagoon.

International audience; > Abstract Bacterial abundance and bacterivorous protist abundance and activity were examined in ice-brine and water column communities of a cold temperate Japanese lagoon (Saroma-Ko Lagoon, Hokkaido, 44 degreesN, 144 degreesE), during the late winter phase of ice community development (February-March 1992). Bacterial abundance averaged 6 and 1 x 10(5) cells ml-1 in the ice-brine and plankton samples, respectively, and generally decreased during the sampling period. Bacterivorous protists, identified based on direct observation of short-term (

Metazooplankton abundance, biomass (500 mu m) and community structure in the Ahe atoll were studied together with their relationships with environmental factors (temperature, salinity, wind) and trophic factors (phytoplankton, bacteria, heterotrophic nanoflagellates (HNF) and ciliates) during three periods in 2008-2009. Meroplankton, mainly bivalve and gastropod larvae, was dominant. Holoplankton was dominated by copepods, the main species being Oithona spp., Paracalanus parvus, Clausocalanus spp., Corycaeus spp., Acartia fossae and Undinula vulgaris. The results suggest a clear wind influence on the structure and horizontal distribution of the zooplankton communities. The metazooplankton appeared to be controlled mainly by food resources, suggesting a bottom-up control. The low nanophytoplankton biomass in contrast to the high abundance of picophytoplankton, HNF and nano-particle grazers (mainly Oithona spp., Paracalanus and bivalve larvae) highlighted the importance of the microbial loop in the food web. (C) 2012 Elsevier Ltd. All rights reserved.

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, temperature effect and the relationship between length and biovolume of the larvae, were determined from experiments or taken from the literature. The interpretation of the values of these parameters allowed us to identify the underlying adaptive character trait: P. margaritifera larvae have a good capacity to exploit low food concentrations and a narrow range of thermal tolerance restricted to hydrobiological conditions found in the tropical oligotrophic waters of its distribution zone. Growth simulations show a good fit with the observations made on reared larvae under different conditions: fed on either cultured algae or natural plankton, and with growth data from a natural cohort. Finally, a first application of the model to a pearl-culture lagoon reveals the predominant effect of the vertical structure of trophic resources in determining spatial variation in larval growth. Research highlights ► We developed a DEB model for Pinctada margaritifera larvae. ► To our knowledge, it is the third application of a DEB model for bivalve larvae, but the first one for tropical bivalves. ► This model is used to give insight into the ecology of this species. ► Application for aquaculture purposes is also discussed.

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. cumingii, Linné 1758) larvae in a French Polynesian atoll lagoon (Ahe, Tuamotu archipelago). Rearing of the pearl oyster for the production of black pearls takes on a major social and economic place in French Polynesia. However, the supply of pearl oyster seed to the farms depends entirely on the natural collection of wild spat of the only one specie P. margaritifera, and spatial and temporal variability of spat yield on collectors is very high. Needs cannot always be locally fulfilled. In this context, the objective of the present thesis is to analyze the relationship existing between the environment and the growth and dispersal of the pearl oyster larvae, in order to bring understanding elements and tools allowing the improvement of the collecting strategies. This work is based on an in situ study, which describes environmental heterogeneity and brings a vision of the larvae dispersal dynamics in the Ahe lagoon. In parallel, we developed a more explanatory approach of the links between the environment and the larvae, by an experimental approach and the application of deterministic models of growth and dispersal. Ahe is a relatively rich atoll lagoon, with higher picophytoplankton concentrations than the average of Polynesian atolls, and very high bivalve larvae abundances throughout the year. The study of environmental heterogeneity points out the supremacy of small spatial (vertical) and temporal (weekly) scales variations, compared with large scales (lagoonal and seasonal). The short-term variations of the weather conditions, mainly of the wind, explain most of this variability. In addition, we could highlight the combined influence of physical factors such as the hydrodynamics, and biological such as the access to the trophic resource or the larval swimming behavior, on the determinism and the maintenance of observed structures, as much for the phytoplanktonic communities than for the bivalve larvae. The development and application of a bioenergetic growth model, based on the dynamic energy budget theory (DEB), enable us to identify the sensitivity of the pearl oyster larvae to the space-time variations of the trophic resource, measured in situ. The Ahe lagoon environment appears thus potentially limiting for the P. margaritifera larvae growth. An average of 3 % of the larvae would reach the pedi-veligerian stage after 30 days of development. The validation of a dispersal model, integrating an empirical model of the larval vertical migration, allowed outlining the larval dispersion, under the combined effect of hydrodynamics and larval behavior. In spite of the important dispersal capability of the larvae at the lagoon scale, the wind orientation seems to be a major element determining the concentration sectors, and in fine the preferential area of settlement. The seasonal variability of the larval dispersal capability would be thus prevalent at the Ahe lagoon scale. These results allow identifying key sectors for the collecting practices, and the opportunity to develop a sanctuary area, providing a great quantity of larvae in the farmers collecting sector., La compréhension des facteurs déterminant le développement et la dispersion larvaire des espèces bentho-pélagiques constitue un sujet d’étude majeur en écologie marine, notamment pour la compréhension de la structure et dynamique des populations adultes. Dans ce travail, nous explorons ce déterminisme sur le développement et la dispersion des larves de l’huître perlière (Pinctada margaritifera var. cumingii, Linné 1758) dans le lagon d’un atoll de Polynésie française (Ahe, archipel des Tuamotu). La culture de l’huître perlière pour la production de perles noires tient une place sociale et économique de première importance en Polynésie française. Or, l’ensemble de cette filière perlicole repose sur la collecte naturelle du naissain de la seule espèce P. margaritifera, et la variabilité des rendements de captage est importante. La demande n’est donc pas toujours satisfaite localement. Dans ce contexte, l’objectif général de cette thèse est d’analyser la relation existant entre l’environnement, physique et biologique, et la croissance et dispersion des larves de l’huître perlière, afin d’apporter des éléments de compréhension et des outils qui permettront d’optimiser les stratégies de captage. Ces travaux s’appuient sur une étude in situ qui décrit l’hétérogénéité environnementale et apporte une vision de la dynamique de dispersion des cohortes larvaires dans le lagon de l’atoll d’Ahe. En parallèle, nous développons une approche plus explicative du lien entre l’environnement et la larve, par une démarche expérimentale et l’application de modèles déterministes de croissance et de transport. Ahe apparaît comme un atoll relativement riche, avec en particulier des concentrations en picophytoplancton supérieures à la moyenne des atolls polynésiens et d’importantes concentrations en larves de bivalves, tout au long de l’année. L’étude de l’hétérogénéité environnementale permet d’identifier la prédominance des variations aux petites échelles spatiales (verticale) et temporelles (hebdomadaire) au regard des variations à grande échelle (lagonaire et saisonnière). Les variations à court terme des conditions météorologiques, et en particulier du vent, expliquent une grande partie de cette variabilité. D’autre part, nous avons pu mettre en évidence l’influence combinée de facteurs physiques tels que l’hydrodynamisme, et biologiques tels que l’accès à la ressource ou les capacités de déplacement, sur le déterminisme et le maintien des structures observées, autant pour les communautés phytoplanctoniques que pour les larves de bivalves. Le développement et l’application d’un modèle bioénergétique de croissance, répondant à la théorie du budget d’énergie dynamique (DEB), nous permet d’identifier la sensibilité des larves de l’huître perlière aux variations spatio-temporelles de la ressource trophique mesurées in situ. Le milieu lagonaire d’Ahe apparaît ainsi potentiellement limitant pour la croissance larvaire de P. margaritifera. En moyenne 3 % des larves atteindraient le stade pédi-véligère au bout de 30 jours de développement. La validation d’un modèle de transport larvaire, intégrant un modèle empirique de nage verticale des larves, permet par ailleurs d’identifier le fonctionnement schématique de la dispersion larvaire à l’échelle du lagon, sous l’influence combinée du courant et du comportement. Malgré l’importante capacité de dispersion des larves, identifiée à l’échelle du lagon, l’orientation du vent semble être un élément majeur déterminant les zones de concentration des larves, et à terme les zones de fixation privilégiées. La variabilité saisonnière des capacités de dispersion larvaire serait donc prédominante à l’échelle du lagon d’Ahe. Ces résultats permettent d’identifier des secteurs clé pour l’orientation des pratiques de captage, et l’opportunité de mise en place d’une zone sanctuaire, à même de fournir une grande quantité de larves dans un secteur privilégié par les perliculteurs.

Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella) caerulea from the Caribbean to Palmyra Atoll via Hawaiʻi using morphological characteristics and genetic analyses based on one nuclear (18s rDNA) and three mitochondrial (COI, the barcoding COI extension (COI ext.) and rnl rDNA) markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68%) between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawaiʻi and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawaiʻi remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms.

International audience; A coupled three-dimensional physical-biological model was developed in order to simulate the ecological functioning and potential impacts of land-derived inputs in the southwest lagoon of New Caledonia. This model considered pelagic biogeochemical cycling of organic matter, taking into account advection and diffusion processes driven mainly by local wind fields and freshwater discharges. Modeled phytoplankton dynamics were strongly correlated with both freshwater nutrient inputs and wind-driven hydrodynamic processes, the latter resulting in a large input of oceanic water from the southeast part of the lagoon under trade wind conditions. In situ data obtained during the summer (January 1998) under trade wind conditions supported predicted concentration gradients along several coast to reef transects and provided a validation of the coupled physical-biogeochemical model. An additional sensitivity analysis showed that the alteration of the biogeochemical parameters did not strongly affect the results of the model. Freshwater inputs of nutrients were simulated using a realistic scenario corresponding to the summer rainy season of 1997-1998 in New Caledonia. Despite occasional flooding events from the main rivers considered in these simulations, no significant meso-scale phytoplankton bloom was identified. Hydrodynamically driven dispersion and rapid uptake of nutrients by phytoplankton were sufficient to spatially constrain the impact of river inputs and maintain oligotrophic conditions. The fine spatial grid of our three-dimensional model demonstrated that eutrophication in the southwest lagoon of New Caledonia is confined to the most restricted coastal embayments, while most of the lagoon experiences sustained oligotrophic conditions.

Data concerning the planktonic food web and the farmed pearl oysters of the lagoon of Takapoto Atoll were assembled into a steady state model of carbon flows. A method of optimisation, using constraints from the literature, called 'inverse analysis' was chosen as the numerical tool for estimating the missing flow values. The resulting food web is characterised by: 1) high primary production, achieved by low phytoplankton biomass, 2) high production of non-living matter, especially as dissolved organic carbon, 3) low bacterial production, 4) zooplankton dominated by protozoa (biomass and processes) and mesozooplankton (processes), and 5) very low consumption of plankton by farmed bivalves compared to planktonic fluxes. When considering the whole lagoon, the farmed oysters (Pinctada margaritifera) and associated bivalves (Pinctada maculata) consume 0.24% of the planktonic gross primary production. In addition, the consumption by natural populations of the main benthic bivalves in this lagoon (Chama iostoma, Arca ventricosa, Pinctada margaritifera and Pinctada maculata) is also low compared to the high planktonic primary production (4.1%). The oyster farming in this lagoon is thus very far from being food-limited. © 2001 Ifremer/CNRS/Inra/IRD/Cemagref/Editions scientifiques et médicales Elsevier SAS.

Pearl oysters are farmed in oligotrophic tropical atoll lagoons where planktonic communities are dominated by production from cyanobacteria smaller than 2 pm. Paradoxically, the pearl oyster Pinctada margaritifera only retains particles larger than 2 Pm. In this study, we assess the relative contribution of hetero/mixotrophic microbiota to the available planktonic resource. In Takapoto Atoll, picocyanobacteria are the dominant biomass (20 mug C l(-1)). The carbon biomass of ciliates and dinoflagellates ranges from 1 to 24 and 0.5 to 5 mug C l(-1) respectively, with a mean of 6 mug C l(-1) for ciliates and 2 mug C l(-1) for dinoflagellates. The possible retention by P. margaritifera on a natural protist suspension was investigated. Due to its high clearance rates (ca 20 l h(-1) g(-1)) the pearl oyster retained 85 mug C h(-1) g(-1) from ciliates and 55 mug C h(-1) g(-1) from dinoflagellates. Conversely, cyanobacteria were not efficiently retained by the bivalve and did not efficiently contribute to its diet. From our experiments, we concluded that hetero/mixotrophic protists rapidly and efficiently process the picoplanktonic resource towards filter-feeders, particularly pearl oysters.

The planktonic food web of Takapoto Atoll lagoon was studied using network analysis. This analysis includes four types of indices dealing with bilateral interactions of compartments, the trophic structure, biochemical cycles, and the topology of the flows. We found numerous parallel carbon pathways of similar importance, indicating a highly complex system compared to other marine ecosystems. Other characteristics were trophic levels not ranked in the same order as the size classes, the domination of system activity by processes at the first trophic level (and especially by herbivory), and cycling processes that involve many pathways. This is the first use of network analysis to describe completely a planktonic food web, and also the first comprehensive description of the trophic structure of the planktonic system in an atoll lagoon.

A steady-state model of the planktonic food web of the lagoon of Takapoto Atoll (Tuamotu Archipelago, French Polynesia) was developed to assess the characteristics of that ecosystem. The planktonic food web was divided into 7 compartments, whose carbon biomasses and rates of exchange were determined from field data combined with inverse analysis, the latter being used to estimate missing rates. Results indicate that the system was characterized by high phytoplankton production and, in agreement with previous results, low bacterial production. Due to their high metabolism, metazoan zooplankton played a dominant role in the cycling of carbon. In contrast, the contribution of protozoa was small. The non-living particulate organic carbon compartment also played a key role, qualitatively and quantitatively, because detritus was directly consumed by all heterotrophic compartments.