This study quantifies benthic nutrient fluxes and sedimentation rates in the Ahe Atoll lagoon (French Polynesia), in two stations located under pearl oyster frames, and two control stations away from the pearl culture facility. Dissolved inorganic nitrogen fluxes ranged between 2 and 35μmolNm⁻²h⁻¹ and Soluble Reactive Phosphorus varied between −3 and 8.2μmolPm⁻²h⁻¹. Particulate sedimentation rates beneath the oysters were approximately five times higher than in the control zone and the percentage of small particles (⩽63μm) were about the twice. In contrast, sediment composition was similar under and outside the direct influence of oyster frames. In this ecosystem, where primary production is dependent on the available nitrogen, our study revealed that, while highly variable, benthic fluxes could sometimes contribute up to 28% of the nitrogen demand for primary production.

This study examined the distribution of virioplankton and bacterioplankton in two coral reef systems (Ahe and Takaroa atolls) in the Tuamotu Archipelago, in comparison with the surrounding oligotrophic ocean. Mean concentrations of 4.8×10⁵ and 6.2×10⁵cellsml⁻¹ for bacteria and 8.1×10⁶ and 4.3×10⁶VLP(virus-like particle) ml⁻¹ were recorded in Ahe and Takaroa lagoons, respectively. Chlorophyll-a concentrations and dissolved organic matter were higher in Ahe whereas ³H thymidine incorporation rates were higher in Takaroa. First data on lytic and lysogenic strategies of phages in coral reef environments were discussed in this paper. The fraction of visibly infected cells by viruses was negligible regardless of the lagoon station (mean=0.15%). However, the fraction of lysogenic cells ranged between 2.5% and 88.9%. Our results suggest that the distribution patterns of virioplankton are apparently not coupled to the spatial dynamics of the bacterioplankton communities.

Bivalve larvae and hydrographic parameters were sampled over a range of spatio-temporal scales in a deep atoll lagoon. Bivalve larvae abundances were very high throughout the year: 18,550m⁻³ in average. Larvae were (i) concentrated at mid-depth with nocturnal ascent and diurnal descent, (ii) heterogeneously dispersed at the lagoon scale, (iii) subject to day-to-day variation in abundance and (iv) transferred between different parts of the lagoon providing evidence of intra-lagoonal connectivity. The primacy of physical factors was seen on large spatial scale with the diluting effect of water renewal and transfers by hydrodynamics. On smaller spatial scale, the primacy of biological processes was recognised, with larval swimming activity leading to dial vertical migration correlated with food concentration. Variations in larval abundance were driven by bivalve reproductive activity correlated with meteorological conditions (i.e. windy periods). Finally, relationship between bivalve larvae patterns and pearl oyster (Pinctada margaritifera) settlement structuring is discussed.

The environmental characteristics of Ahe deep lagoon (Tuamotu Archipelago, French Polynesia) were studied over 3years with the aim of explaining the spatial and temporal variability of the natural food available for pearl oysters with a special focus on phytoplankton biomass and global photosynthesis/respiration ratio of the lagoon. Chlorophyll averaged 0.34±0.01μgL⁻¹ and our findings did not confirm increased phytoplankton biomass in deep lagoonal waters. Phytoplankton production appears to be limited firstly by nitrogen and respiratory processes overpass photosynthetic processes at least in the north-eastern edge of the atoll. Grazing by pearl oysters in culture seems to decrease the POC concentration but not the phytoplankton biomass. Oysters graze mainly on non chlorophyllian particles.

Hydrodynamic functioning and water circulation of the semi-closed deep lagoon of Ahe atoll (Tuamotu Archipelago, French Polynesia) were investigated using 1year of field data and a 3D hydrodynamical model. Tidal amplitude averaged less than 30cm, but tide generated very strong currents (2ms⁻¹) in the pass, creating a jet-like circulation that partitioned the lagoon into three residual circulation cells. The pass entirely flushed excess water brought by waves-induced radiation stress. Circulation patterns were computed for climatological meteorological conditions and summarized with stream function and flushing time. Lagoon hydrodynamics and general overturning circulation was driven by wind. Renewal time was 250days, whereas the e-flushing time yielded a lagoon-wide 80-days average. Tide-driven flush through the pass and wind-driven overturning circulation designate Ahe as a wind-driven, tidally and weakly wave-flushed deep lagoon. The 3D model allows studying pearl oyster larvae dispersal in both realistic and climatological conditions for aquaculture applications.

Metazooplankton abundance, biomass (<80μm, 200–500μm and >500μm) 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.

In atoll lagoons of French Polynesia, growth and reproduction of pearl oysters are mainly driven by plankton concentration. However, the actual diet of black-lip pearl oysters Pinctada margaritifera in these lagoons is poorly known. To fill this gap, we used the flow through chamber method to measure clearance rates of P. margaritifera in Ahe atoll lagoon (Tuamotu Archipelago, French Polynesia). We found: (i) that pearl oysters cleared plankton at a rate that was positively related to plankton biovolume, (ii) that nanoflagellates were the main source of carbon for the pearl oysters, and (iii) that the quantity and origin of carbon filtrated by pearl oysters was highly dependent on the concentration and composition of plankton. These results provide essential elements for the comprehension of growth and reproduction variability of pearl oysters in atoll lagoons of French Polynesia.

To implement a numerical model of atoll lagoon circulation, we characterized first the significant wave height (Hs) regime of the Western Tuamotu Archipelago and the local attenuation due to the protection offered by large atolls in the south Tuamotu. Altimetry satellite data and a WAVEWATCH III two-way nested wave model at 5km resolution from 2000 to 2010 were used. Correlation between altimetry and model was high (0.88) over the period. According to the wave model, the archipelago inner seas experienced attenuated Hs year-long with a yearly average Hs around 1.3m vs a minimum of 1.6m elsewhere. The island shadow effect is especially significant in the austral winter. In contrast with southern atolls, Western Tuamotu experienced only few days per year of Hs larger than 2.5m generated by very high Hs southern swell, transient western local storms, strong easterly winds, and during the passage of distant hurricanes.

Responses of biological indices and oxidative stress biomarkers were studied in the giant clam Tridacna maxima and in the fish Epinephelus merra collected from two sites differing by their level of contamination in the French Polynesian Moorea island. Higher levels of catalase (CAT), glutathione-S-transferases (GST) and thiobarbituric acid reactive substances (TBARs) were observed in the hepatopancreas of T. maxima and in the liver of E. merra compared to muscle. CAT and TBARs levels were significantly higher in the hepatopancreas of clams collected from the impacted site (Vaiare) compared to the reference site (bay of Cook). The same pattern was observed for TBARs levels in the liver of E. merra. These results indicate that both organisms from the impacted site were exposed to contaminants leading to an oxidative stress and demonstrate, for the first time, the usefulness of T. maxima and E. merra as sentinel species for biomonitoring reef environments.

The spatial variations of the picoplankton (photoautotrophic and heterotrophic microorganisms) in the Ahe atoll lagoon were studied in May and October 2008 to assess whether they were affected by human activities along the atoll. Spatial patterns were studied using 10 sampling stations chosen according to the location of the anthropogenic activities (pearl farming, harbor). Experiments were also carried out to determine whether bacterial growth, with or without predators, was limited by inorganic (N and P) substrates. The results showed that heterotrophic bacterioplankton abundance was superior to the photoautotrophic organisms, especially in May. Significant increases in bacterial abundance were observed in May after 24h incubation with +P and +N (but not in October). All samples complied with the quality levels for fecal indicator bacteria (FIB) defined by the European Union and there was no evidence that human sewage had any impact on picoplankton over the whole atoll.