Atolls of the world: A reappraisal from an optical remote sensing and global mapping perspective.

The Millennium Coral Reef Mapping Project (MCRMP) aimed to map coral reefs worldwide at geomorphological thematic scales using Landsat satellite images at 30 m spatial resolution. The 5-level hierarchical classification scheme implemented by MCRMP identified at Level 2 'Atolls' as one of the main types of coral reef complexes. In this review, the qualitative criteria used by MCRMP to identify atolls are presented. Then, we report on the global census of atolls, from which a consistent geomorphologic GIS database is provided. A total of 598 atolls are identified and mapped. The quantitative database provides surface areas for all geomorphologic units at Level 4 and 5 of the MCRMP classification scheme. It allows further work on atoll and coral reef classifications, regionally and globally, in order to identify geomorphic trends and outliers. It is also a convenient database to use in multivariate analyses with ancillary biodiversity, fishery, socio-economic or climate data.

The wave regimes of the Central Pacific Ocean with a focus on pearl farming atolls.

Pearl farming sustainability in South Central Pacific (SCP) atolls strongly depends on water quality and renewal. These factors are partly controlled by the wave conditions that impact the lagoon circulation. To characterize the wave conditions around 83 SCP atolls including those hosting pearl farming activities, we used 18 years of WaveWatchIII simulation with a grid refined from 50 to 5 km resolution. Three regional wave regimes are statistically identified: two associated with long distant swells originating from mid-latitude storms, and one with local trade winds. All regimes occur with a relatively high frequency (22-44%), but with a marked seasonality. Wave conditions are also strongly modified locally during their propagation between the archipelagoes. Western and southern isolated atolls generally have a single regime all around their rims. In contrast, central Tuamotu atolls experience different regimes depending on their levels of protection. These results help understanding atoll hydrodynamics, which has implications for their management.

Characterization of south central Pacific Ocean wind regimes in present and future climate for pearl farming application.

In the South Pacific (SP) pearl farming atolls, wind is the main driver of lagoon water circulation, affecting dispersal and survival of pearl oyster larvae. To characterize typical wind conditions in the SP, wind regime classifications are performed from regional climate simulations using the WRF model, for present-day and for the end of the 21st century under RCP8.5 scenario conditions. At the daily time-scale, 4 regimes are identified: a trade-wind, a north-easterly, and two easterly regimes. Their characteristics are driven by large-scale circulation and climate modes of variability. In future projection, all regimes are characterized by a ~15% wind speed increase, while directions and occurrence frequencies undergo marginal changes. At the monthly time-scale that corresponds to pearl oyster pelagic larval duration, nine wind regimes are determined including three regimes with wind reversals. These regimes can be used to model typical lagoon conditions during larval dispersal.

The lagoon geomorphology of pearl farming atolls in the Central Pacific Ocean revisited using detailed bathymetry data.

The lagoons of seven French Polynesia and Cook Islands pearl farming atolls (Raroia, Takume, Mopelia, Takapoto, Ahe, Takaroa and Manihiki) were surveyed using multibeam and mono-beam sounders. From the detailed bathymetry, morphometric variables (average and maximum depth, frequency-area of depth, lagoon area and volume) are computed and compared. Remarkable geomorphological structures highlighted by bathymetric variations include deep reticulated structures and pinnacles. The seven atolls appear very different in abundance, size and density of these entities. Considering them as markers of the geological, sedimentological and eustatic processes that shape atoll lagoons, they are discussed in the context of the general theory of atoll lagoon formations involving karstic dissolution during Pleistocene or earlier low sea-level stands. In terms of pearl farming management, accurate bathymetric maps help pearl oyster wild stock assessment, development of circulation and biogeochemical models, better lagoon zoning and strategy to remove pearl farming derelict gears.

Tidal flushing and wind driven circulation of Ahe atoll lagoon (Tuamotu Archipelago, French Polynesia) from in situ observations and numerical modelling.

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 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 250 days, 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.

Bivalve larvae transport and connectivity within the Ahe atoll lagoon (Tuamotu Archipelago), with application to pearl oyster aquaculture management.

Patterns of bivalve larvae dispersal in the deep Ahe atoll lagoon was studied by using a numerical 3D transport model (MARS3D) coupled with a vertical swimming sub-model, forced mainly by tide and wind-induced currents. The simulations were validated against observations of larval dispersal monitored several days throughout the lagoon. Connectivity matrices describing larval exchanges inside the lagoon were inferred. Larvae displayed a significant dispersal capacity at the lagoon scale, especially with dominant eastern winds. With southeastern winds, larvae mostly remained in their origin sector. The total export rate of the larvae, toward the ocean through the pass and shallow lagoon borders, was independent of the wind conditions, with 1% of the total concentration exported per day. However, the tide-driven currents efficiently flushed larvae in sectors close to the pass. Connectivity matrices suggest that the south and west sectors were more suitable for spat collecting and that central sectors would be efficient sanctuaries if genitors were accumulated.

Characterizing the diversity of coral reef habitats and fish communities found in a UNESCO World Heritage Site: the strategy developed for Lagoons of New Caledonia.

Since 1972, the UNESCO "World Heritage Convention" offers an international canvas for conservation and management that targets areas of high cultural and environmental significance. To support the designation of areas within the 36.000 km(2) of New Caledonia coral reefs and lagoons as a World Heritage Site, the natural value and diversity of the proposed zones needed to be demonstrated. To exhaustively identify each configuration of shallow habitats, high resolution remote sensing images were used to select the sampling sites. This optimal scheme resulted in the selection of nearly 1300 sampling sites, and was then simplified to render its application realistic. In the final sampling plan, only the most common or the most remarkable coral zones were selected. Following this selection, in situ habitat and fish surveys were conducted in 2006-2008 in five large areas spanning a 600 km-long latitudinal gradient. Habitats were described using line-intercept transects in parallel with underwater visual census of indicator and commercial coral reef fish species. We report here on the results achieved in terms of: (i) the actual diversity of coral habitats captured by the remote sensing based sampling strategy, (ii) the different reef fish communities captured from the different sites, and (iii) how well they represent New Caledonia diversity. We discuss the possible generalization of this scheme to other sites, in the context of World Heritage Site selection and for other large-scale conservation planning activities.

Circulation and suspended sediment transport in a coral reef lagoon: the south-west lagoon of New Caledonia.

The south-west lagoon of New Caledonia is a wide semi-open coral reef lagoon bounded by an intertidal barrier reef and bisected by numerous deep inlets. This paper synthesizes findings from the 2000-2008 French National Program EC2CO-PNEC relative to the circulation and the transport of suspended particles in this lagoon. Numerical model development (hydrodynamic, fine suspended sediment transport, wind-wave, small-scale atmospheric circulation) allowed the determination of circulation patterns in the lagoon and the charting of residence time, the later of which has been recently used in a series of ecological studies. Topical studies based on field measurements permitted the parameterisation of wave set-up induced by the swell breaking on the reef barrier and the validation of a wind-wave model in a fetch-limited environment. The analysis of spatial and temporal variability of suspended matter concentration over short and long time-scales, the measurement of grain size distribution and the density of suspended matter (1.27 kg l(-1)), and the estimation of erodibility of heterogeneous (sand/mud, terrigenous/biogenic) soft bottoms was also conducted. Aggregates were shown to be more abundant near or around reefs and a possible biological influence on this aggregation is discussed. Optical measurements enabled the quantification of suspended matter either in situ (monochromatic measurements) or remotely (surface spectral measurements and satellite observations) and provided indirect calibration and validation of a suspended sediment transport model. The processes that warrant further investigation in order to improve our knowledge of circulation and suspended sediment transport in the New Caledonia lagoon as well as in other coral reef areas are discussed, as are the relevance and reliability of the numerical models for this endeavour.

Review of solutions for 3D hydrodynamic modeling applied to aquaculture in South Pacific atoll lagoons.

A workshop organized in French Polynesia in November 2004 allowed reviewing the current methods to model the three-dimensional hydrodynamic circulation in semi-enclosed atoll lagoons for aquaculture applications. Mollusk (e.g. pearl oyster, clam) aquaculture is a major source of income for South Pacific countries such as French Polynesia or Cook Islands. This aquaculture now requires a better understanding of circulation patterns to improve the spatial use of the lagoons, especially to define the best area to set larvae collectors. The pelagic larval duration of the relevant species (<20 days) and the size of the semi-closed lagoons (few hundreds of km2) drive the specifications of the model in terms of the spatial and temporal scale. It is considered that, in contrast with fish, mollusk larvae movements are limited and that their cycle occurs completely in the lagoon, without an oceanic stage. Atolls where aquaculture is productive are generally well-bounded, or semi-closed, without significant large and deep openings to the ocean. Nevertheless part of the lagoon circulation is driven by oceanic water inputs through the rim, ocean swells, tides and winds. Therefore, boundary conditions of the lagoon system are defined by the spatial structure of a very shallow rim (exposition and number of hoas), the deep ocean swell climate, tides and wind regimes. To obtain a realistic 3D numerical model of lagoon circulation with adequate forcing, it is thus necessary to connect in an interdisciplinary way a variety of methods (models, remote sensing and in situ data collection) to accurately represent the different components of the lagoon system and its specific boundary conditions. We review here the current methods and tools used to address these different components for a hypothetical atoll of the Tuamotu Archipelago (French Polynesia), representative of the semi-closed lagoons of the South Pacific Ocean. We hope this paper will serve as a guide for similar studies elsewhere and we provide guidelines in terms of costs for all the different stages involved.

Physical, chemical, and microbiological characteristics of microbial mats (kopara) in the South Pacific atolls of French Polynesia.

Microbial mats that develop in shallow brackish and hyposaline ponds in the rims of two French polynesian atolls (Rangiroa and Tetiaroa) were intensively investigated during the past three years. Comparative assessment of these mats (called kopara in polynesian language) showed remarkable similarities in their composition and structure. Due to the lack of iron, the color of the cyanobacterial pigments produced remained visible through the entire depth of the mats (20-40 cm depth), with alternate green, purple, and pink layers. Profiles of oxygen, sulfide, pH, and redox showed the anoxia of all mats from a depth of 2-3 mm. Analyses of bacterial pigments and bacterial lipids showed that all mats consisted of stratified layers of cyanobacteria (mainly Phormidium, Schizothrix, Scytonema) and purple and green phototrophic bacteria. The purple and green phototrophic bacteria cohabit with sulfate reducers (Desulfovibrio and Desulfobacter) and other heterotrophic bacteria. The microscopic bacterial determination emphasized the influence of salinity on the bacterial diversity, with higher diversity at low salinity, mainly for purple nonsulfur bacteria. Analyses of organic material and of exopolymers were also undertaken. Difference and similarities between mats from geomorphological, microbiological, and chemical points of view are discussed to provide multicriteria of classification of mats.