Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event.

BACKGROUND: Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a short period and may have a significant impact on the entire land‒sea continuum. This study focused on the effect of river runoff across the southwest coral lagoon ecosystem of Grand Terre Island of New Caledonia (South Pacific) after a cyclonic event, which is considered a pulse disturbance at our study site. The variability of coastal microbiomes, studied by the metabarcoding of V4 18S (protists) and V4-V5 16S (bacteria) rDNA genes, after the cyclone passage was associated with key environmental parameters describing the runoff impact (salinity, organic matter proxies, terrestrial rock origin metals) and compared to community structures observed during the dry season. RESULTS: Microbiome biodiversity patterns of the dry season were destructured because of the runoff impact, and land-origin taxa were observed in the coastal areas. After the rainy event, different daily community dynamics were observed locally, with specific microbial taxa explaining these variabilities. Plume dispersal modeling revealed the extent of low salinity areas up to the coral reef area (16 km offshore), but a rapid (< 6 days) recovery to typical steady conditions of the lagoon's hydrology was observed. Conversely, during the same time, some biological components (microbial communities, Chl a) and biogeochemical components (particulate nickel, terrigenous organic matter) of the ecosystem did not recover to values observed during the dry season conditions. CONCLUSION: The ecosystem resilience of subtropical ecosystems must be evaluated from a multidisciplinary, holistic perspective and over the long term. This allows evaluating the risk associated with a potential continued and long-term disequilibrium of the ecosystem, triggered by the change in the frequency and intensity of extreme climatic events in the era of planetary climatic changes.

Biogeochemical model of nitrogen cycling in Ahe (French Polynesia), a South Pacific coral atoll with pearl farming.

A biogeochemical model (ECO3M-Atoll) was configured to simulate the lower food web in Ahe Atoll lagoon where phytoplankton is mostly nitrogen limited. Understanding the dynamics of phytoplankton - the main food source for oysters - is crucial for the management and the allocation of new pearl farming sites. After parametrizing the model with in situ observations, we tested different hypotheses about nitrogen cycling (benthic remineralization, atmospheric N fixation, etc.) and compared the results to a large observational dataset. Model results show that simulated (pico- and nano-) phytoplankton biomass and nitrogen concentrations are close to in situ data. The simulated biogeochemical processes (uptake and primary production) are also very similar to the observed values. In the model, primary production ranged from 1.00 to 2.00 mg C m-3 h-1 for pico- and 0.40 to 1.00 mg C m-3 h-1 for nanophytoplankton; mean N uptake was 2.02 µmol N m-3 h-1 for pico- and 1.25 µmol N m-3 h-1 for nanophytoplankton.

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.

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.