Algal symbiont diversity in Acropora muricata from the extreme reef of Bouraké associated with resistance to coral bleaching.

Widespread coral bleaching has generally been linked to high water temperatures at larger geographic scales. However, the bleaching response can be highly variable among individual of the same species, between different species, and across localities; what causes this variability remains unresolved. Here, we tracked bleached and non-bleached colonies of Acropora muricata to see if they recovered or died following a stress event inside the semi-enclosed lagoon of Bouraké (New Caledonia), where corals are long-term acclimatized to extreme conditions of temperature, pH and dissolved oxygen, and at a nearby control reef where conditions are more benign. We describe Symbiodiniaceae community changes based on next-generation sequencing of the ITS2 marker, metabolic responses, and energetic reserve measures (12 physiological traits evaluated) during the La Niña warm and rainy summer in 2021. Widespread coral bleaching (score 1 and 2 on the coral colour health chart) was observed only in Bouraké, likely due to the combination of the high temperatures (up to 32°C) and heavy rain. All colonies (i.e., Bouraké and reference site) associated predominantly with Symbiodinaceae from the genera Cladocopium. Unbleached colonies in Bouraké had a specific ITS2-type profile (proxies for Symbiodiniaceae genotypes), while the bleached colonies in Bouraké had the same ITS2-type profile of the reef control colonies during the stress event. After four months, the few bleached colonies that survived in Bouraké (B2) acquired the same ITS2 type profiles of the unbleached colonies in Bouraké. In terms of physiological performances, all bleached corals showed metabolic depression (e.g., Pgross and Rdark). In contrast, unbleached colonies in Bouraké maintained higher metabolic rates and energetic reserves compared to control corals. Our study suggests that Acropora muricata enhanced their resistance to bleaching thanks to specific Symbiodiniaceae associations, while energetic reserves may increase their resilience after stress.

A new set of N isotopic reference values for monitoring Ulva green tides in coral reef ecosystems.

Green tides occurrence has increased in coral reefs, yet few reference values have been documented to support bloom management in these ecosystems. Here, we took advantage of recent Ulva green tides that occurred in New Caledonia to (i) identify the elements limiting the growth of Ulva spp. during these blooms; and (ii) validate the use of isotopic markers for identifying sources of nutrients that generated blooms. N/P ratios highlighted a stronger limitation of algae by phosphorus than by nitrogen on sites under oceanic influence, while the proportions of N and P were optimal for algal growth at sites where green tides occurred. Macroalgae highly exposed to sewage water was characterized by higher δ15N than macroalgae collected in areas exposed to synthetic inorganic fertilizers. From these results, we established a new set of threshold values for using δ15N in Ulva species as an indicator of nitrogen source type in coral reefs.

Sponge organic matter recycling: Reduced detritus production under extreme environmental conditions.

Sponges are a key component of coral reef ecosystems and play an important role in carbon and nutrient cycles. Many sponges are known to consume dissolved organic carbon and transform this into detritus, which moves through detrital food chains and eventually to higher trophic levels via what is known as the sponge loop. Despite the importance of this loop, little is known about how these cycles will be impacted by future environmental conditions. During two years (2018 and 2020), we measured the organic carbon, nutrient recycling, and photosynthetic activity of the massive HMA, photosymbiotic sponge Rhabdastrella globostellata at the natural laboratory of Bouraké in New Caledonia, where the physical and chemical composition of seawater regularly change according to the tide. We found that while sponges experienced acidification and low dissolved oxygen at low tide in both sampling years, a change in organic carbon recycling whereby sponges stopped producing detritus (i.e., the sponge loop) was only found when sponges also experienced higher temperature in 2020. Our findings provide new insights into how important trophic pathways may be affected by changing ocean conditions.

Holographic reconstruction enhancement via unpaired image-to-image translation.

Digital holographic microscopy is an imaging process that encodes the 3D information of a sample into a single 2D hologram. The holographic reconstruction that decodes the hologram is conventionally based on the diffraction formula and involves various iterative steps in order to recover the lost phase information of the hologram. In the past few years, the deep-learning-based model has shown great potential to perform holographic reconstruction directly on a single hologram. However, preparing a large and high-quality dataset to train the models remains a challenge, especially when the holographic reconstruction images that serve as ground truth are difficult to obtain and can have a deteriorated quality due to various interferences of the imaging device. A cycle generative adversarial network is first trained with unpaired brightfield microscope images to restore the visual quality of the holographic reconstructions. The enhanced holographic reconstructions then serve as ground truth for the supervised learning of a U-Net that performs the holographic reconstruction on a single hologram. The proposed method was evaluated on plankton images and could also be applied to achieve super-resolution or colorization of the holographic reconstructions.

Temporal variability of benthic-pelagic coupling in shallow enclosed environment: A case study with eutrophying shrimp ponds.

The evolution of benthic pelagic coupling was followed in two semi-intensive shrimp ponds in New Caledonia, with a special emphasis on the role of microphytobenthos (MPB). Three distinct periods could be identified. During the first period, MPB activity led to relative decoupling between the water column and the sediment, both compartments being autotrophic with low nutrients exchanges. During the second period, the sediment operated at the edge of a functional switch between autotrophy and heterotrophy. The amplitude of nutrient fluxes depended of the pool considered (DIN, DIP) and showed light dark variation. In the last period, sediment switched to heterotrophy with the establishment of benthic-pelagic coupling concomitantly to a massive sediment resuspension due to the shrimp activity. These findings should be considered for the management of aquaculture ponds and shallow enclosed water bodies.

Monitoring mangrove forests after aquaculture abandonment using time series of very high spatial resolution satellite images: A case study from the Perancak estuary, Bali, Indonesia.

Revegetation of abandoned aquaculture regions should be a priority for any integrated coastal zone management (ICZM). This paper examines the potential of a matchless time series of 20 very high spatial resolution (VHSR) optical satellite images acquired for mapping trends in the evolution of mangrove forests from 2001 to 2015 in an estuary fragmented into aquaculture ponds. Evolution of mangrove extent was quantified through robust multitemporal analysis based on supervised image classification. Results indicated that mangroves are expanding inside and outside ponds and over pond dykes. However, the yearly expansion rate of vegetation cover greatly varied between replanted ponds. Ground truthing showed that only Rhizophora species had been planted, whereas natural mangroves consist of Avicennia and Sonneratia species. In addition, the dense Rhizophora plantations present very low regeneration capabilities compared with natural mangroves. Time series of VHSR images provide comprehensive and intuitive level of information for the support of ICZM.

Surveying shrimp aquaculture pond activity using multitemporal VHSR satellite images - case study from the Perancak estuary, Bali, Indonesia.

From the 1980's, Indonesian shrimp production has continuously increased through a large expansion of cultured areas and an intensification of the production. As consequences of diseases and environmental degradations linked to this development, there are currently 250,000ha of abandoned ponds in Indonesia. To implement effective procedure to undertake appropriate aquaculture ecosystem assessment and monitoring, an integrated indicator based on four criteria using very high spatial optical satellite images, has been developed to discriminate active from abandoned ponds. These criteria were: presence of water, aerator, feeding bridge and vegetation. This indicator has then been applied to the Perancak estuary, a production area in decline, to highlight the abandonment dynamic between 2001 and 2015. Two risk factors that could contribute to explain dynamics of abandonment were identified: climate conditions and pond locations within the estuary, suggesting that a spatial approach should be integrated in planning processes to operationalize pond rehabilitation.

Dynamics of phytoplankton communities in eutrophying tropical shrimp ponds affected by vibriosis.

Tropical shrimp aquaculture systems in New Caledonia regularly face major crises resulting from outbreaks of Vibrio infections. Ponds are highly dynamic and challenging environments and display a wide range of trophic conditions. In farms affected by vibriosis, phytoplankton biomass and composition are highly variable. These conditions may promote the development of harmful algae increasing shrimp susceptibility to bacterial infections. Phytoplankton compartment before and during mortality outbreaks was monitored at a shrimp farm that has been regularly and highly impacted by these diseases. Combining information from flow cytometry, microscopy, pigment and phylogenetic analysis, the presence of Picocyanobacteria, Prasinophyceae and Diatomophyceae were detected as dominant phytoplankton groups and Cryptophyceae, Prymnesiophyceae and Dinophyceae as minor components. At the onset of the first shrimp mortalities, Bacillariophyceae increased while Cyanobacteria, Prymnesiophyceae and Dinophyceae decreased in the water column, followed by proliferation of Prasinophyceae. Several taxa were identified as potential harmful algae (Cyanobacteria, dinoflagellates and Phaeocystis).

Spatial and temporal extension of eutrophication associated with shrimp farm wastewater discharges in the New Caledonia lagoon.

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 environment. Separate surveys were carried out in a bay (CH Bay) with a medium-size intensive farm (30 ha) (PO) and in a mangrove-lined creek (TE Creek) near a larger semi-intensive farm (133 ha) (SO). Net loads of nitrogen exported from the semi-intensive farm and the intensive farm amounted to 0.68 and 1.36 kg ha(-1)day(-1), respectively. At CH Bay, discharge effects were spatially limited and clearly restricted to periods of effluent release. The high residence time at site TE favoured the installation of a feedback system in which organic matter was not exported. Mineralization of organic matter led to the release of nutrients, which in turn, caused in an increased eutrophication of this ecosystem. The study of the pico- and nanophytoplankton assemblages showed (i) a shift in composition from picophytoplankton to nanophytoplankton from offshore towards the coast and (ii) a shift within the picophytoplankton with the disappearance of Prochlorococcus and the increase of picoeucaryotes towards the shoreline. These community changes may partially be related to a nitrogen enrichment of the environment by shrimp farm discharges. Thus, in view of the recent addition of the New Caledonian lagoon to the UNESCO World Heritage list, the data presented here could be a first approach to quantify farm discharges and evaluate their impact on the lagoon.

Nutrient and microbial dynamics in eutrophying shrimp ponds affected or unaffected by vibriosis.

A field survey was conducted on two intensive shrimp farms using similar technical practices: one (DF) historically affected by a vibriosis, the other (HC) in which the pathogen has been observed although no mortality event has occurred. Because historical data suggest that eutrophication process may directly or indirectly play a role in the disease outbreak, we focussed our research on its dynamics. A higher variability of the phytoplanktonic compartment linked to an imbalance in the molar N:P ratio was observed in farm DF compared to farm HC, implying a modification on the linkage between the bacteria and phytoplankton compartments at DF. The beginning of the mortality outbreak at DF followed a shift from pico- to nanophytoplankton. The organic matter mineralization process at the water-sediment interface may explain the disturbance observed in the water column during eutrophication. The consequences of this disturbance on shrimps' health status and pathogen ecology are discussed.