In this study, we conducted a 14-month investigation in Daya Bay, southern China to understand the effects of oyster farming on phytoplankton community and biomass by using size-fractionated phytopigments. Results proved the filtering effects of oysters on phytoplankton biomass. During the oyster culture period, the average concentration of total chlorophyll a (sum of size-fractionated Chl a) within the farming area was approximately 60% lower than that at the reference site. Phytoplankton depletion in the aquaculture zone mainly occurred in micro-sized fractions (>20 μm) of Chl a, fucoxanthin, and peridinin. The influence of oyster filtration on nano-sized (2.7–20 μm) pigments seemed less than that on micro-sized ones. The depletion of peridinin and 19′-hex-fucoxanthin in aquaculture zone was higher than those of the other pigments, which indicated that flagellated cells might be selectively filtered by oysters and could be more easily influenced by oyster aquaculture. The pico-sized Chl a (<2.7 μm) comprised 24% of total Chl a on the average in the aquaculture zone during the cultural period compared to 6% in the reference site. Picoeukaryote abundance, which was determined via flow cytometry, was significantly higher in the aquaculture zone than in the non-aquaculture areas. The abundance of picoeukaryote is significantly and positively correlated with the concentrations of pico-sized prasinoxanthin, violaxanthin, and neoxanthin, indicating that picoeukaryote is dominated by those in prasinophyte. The results suggest that oyster aquaculture might stimulate the growth of prasinophyte, although the seasonal variations are mainly controlled by the water temperature in the study area. This research highlights the successful use of size-fractionated phytopigments to estimate size-specific phytoplankton biomass and community, which can be applied as a routine method to monitor the environmental effect and food resources of bivalve aquaculture.

Pharmaceuticals and personal care products in wastewater discharge can be stressors to estuarine species. We transplanted juvenile Pacific oysters at varying distances within sites near wastewater treatment plant outfalls or oyster aquaculture control sites to assess small scale spatial variation in contaminant uptake and oyster condition. Oysters were transplanted to sites in Coos and Netarts Bays, Oregon and Grays Harbor, Washington, then collected after 9 and 12 months. Two pharmaceuticals (miconazole and virginiamycin M1) were detected in spring samples and four alkylphenols (NP1EO, NP2EO, NP and OP) were detected in summer samples, with more frequent detections at wastewater sites. Contaminant concentrations were similar across site types, indicating that even in sparsely populated coastal areas (<25,000 in the watershed), shellfish are exposed to and uptake wastewater contaminants. Additionally, oyster condition was lower at wastewater sites compared to aquaculture sites, indicating a need to better understand whether contaminant exposure affects oyster condition.

Mariculture is known to contribute to oxygen depletion, pH decline and accumulation of nutrients and organic matter in sediments. However, studies on the bacterial vertical distribution of mariculture area are very limited. The bacterial abundance in the non-culture site (3.8 ± 0.8 × 10⁹ copies g⁻¹) was significantly higher than that in the three mariculture sites (1.2 ± 0.2 × 10⁹ copies g⁻¹), and bacterial diversity in the non-culture site was significantly higher than that in fish cage-TF (p < 0.05). The vertical distribution profiles of bacteria in non-culture and oyster culture sites were similar but very different from that of fish cage-TF. In addition, significant downward trends in bacterial abundance and diversity were observed as sediment depth increased (p < 0.05), and the most relevant environmental factors were moisture content, total nitrogen, total organic carbon and carbon/nitrogen. The dominant bacterial phyla in sediment were Proteobacteria, Chloroflexi and Bacteroidetes.

Biochemical and molecular responses were evaluated in oysters Crassostrea brasiliana collected from three oyster farms, at Guaratuba Bay, southern Brazil, forming a pollutant gradient: Farm 1 (reference site - farther from the urban area), Farm 2 (intermediate site) and Farm 3 (nearest to the urban area). Oxidative stress markers, DNA damage and transcript levels of CYP2AU1, CYP2-like1, CYP2-like2, SULT-like, GPx-like, SOD-like, CAT-like, GSTmicrosomal-like, GSTomega-like, FABP-like and ALAd-like genes were analyzed in the gills. The levels of polycyclic aromatic hydrocarbons, linear alkylbenzenes and polychlorinated biphenyls were also evaluated in the soft tissues of the oysters and in the sediment of the Farms. Higher GSTomega-like, CYP2AU1 and FABP-like transcript levels, GR and G6PDH activities and lipid peroxidation levels were observed in oysters from Farms 2 and 3, suggesting pollutant effects on oysters. Alterations in oxidative stress markers also suggest a response against a prooxidant condition in C. brasiliana due to pollutant effects.

Many cultured pearl farms are located in areas of the Pacific that have thriving, highly diverse fish communities but the impacts of farming on these communities are poorly understood. We studied the effects of pearl oyster farming on shore fish abundance and diversity in the lagoon of Ahe, French Polynesia by adapting roving diver census methods to the coral reef bommies of the lagoon and compared 16 sites with high pearl farming impact to others with no direct impact. Pearl farming has a slightly positive effect on reef fish abundance (N) and no significant impact on fish diversity (H) or community composition. This is important when considering the ecological sustainability of pearl farming in French Polynesia and suggests that a potential synergy between pearl farms and marine conservation should be further explored.

Pearl oyster aquaculture is a major activity in French Polynesia atoll lagoons. After the economic decline that characterized the last decade, concerns recently rose about discarded installations and materials that supported aquaculture practices and by facilities abandoned after they had to close their activities. In May 2013, a first inventory of the type and amount of pearl farms derelict gear (PFDG) was achieved on 47 sites in Ahe lagoon. Surveys were conducted within and outside the boundaries of aquaculture concessions. Twenty types of PFDG littered the lagoon floor and the water column. The most impacted areas were near abandoned grafting houses with up to nine types of PFDG. Forty-five percent of the sites were impacted, including outside concessions. While management authorities are fully aware of the problem, this first assessment is a wake-up call to stimulate the cleaning of lagoons, enhance awareness among farmers, and identify potential ecological consequences on lagoon ecosystems.

The most important oyster farming area in Europe is in a close proximity of two medium size merchant ports. Cargo ships deballast in this area before loading, releasing unwanted or noxious marine species. During a sampling campaign aboard these arriving ships, we found in some ballast water samples a huge number of potentially toxic dinoflagellates and some potentially pathogenic bacteria. A model was applied to find the potential geographical spread of the discharged ballast water. This model predicts the water to reach highly vulnerable shellfish farmed areas in six to eight days.

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.

Microplastic (MP) was investigated in Zhanjiang Bay, a semi-enclosed bay in south China and famous for considerable mariculture industry, to evaluate whether mariculture activities accelerated MP pollution. The MP abundances ranged from 0 to 2.65 n/m³ (number/m³), showing seasonal variances with higher levels in May and September and lower levels in January. In the inner part of the bay, a significantly high MP abundance and predominance of foam were found during the oyster breeding period, and pollution sources were prone to be single and extensive. This suggested that MPs were strongly influenced by the intensive plastic products for oyster culturing, especially during breeding. Moreover, plastic cages used for culturing were the main source of MPs in the central part of the bay. By conducting statistical analysis for eight representative bays, the economic growth, social development, agriculture structure, and aquaculture development were supposed to influence the local MP pollution level.

This editorial presents results of the MANA (MANagement of Atolls) project compiled in the form of a Marine Pollution Bulletin collection of 14 articles. MANA is a project funded by the French Agence National pour la Recherche that specifically addresses the development of knowledge and management tools for pearl farming atolls, with a focus on the spat collecting activity in French Polynesia. The 14 papers cover the range of thematic tasks described in the initial project, including atoll geomorphology and bathymetry, climate forcing, atoll lagoon and rim hydrodynamics, typology of atolls, evaluation of remote sensing data for monitoring atoll lagoons, and development of numerical models and spatially-explicit tools that altogether have contributed to the applied objectives. In addition, this editorial draws an update on the pearl farming industry in French Polynesia with the latest statistics, and discusses the next targeted priorities for research programs focusing on pearl farming atolls.