To better understand the molecular mechanisms involved in the biodegradation of hydrocarbon compounds from the “Erika” oil-spill, we have studied the ability of Marinobacter hydrocarbonoclasticus strain sp 17 to cope with hexadecane as sole carbon and energy source. Growth kinetics of cultures shifted from acetate to hexadecane revealed the presence of a 20 hours adaptation phase. Changes in global protein expression in response to hexadecane was analyzed by two-dimensional gel electrophoresis. Of the 370 proteins detected 42 had their expression level altered in presence of hexadecane indicating that alkane adaptation may involve many cellular functions.

Inshore marine areas host key habitats for the biological cycle of many marine populations, but are subject to strong anthropogenic pressure. Uses of inshore areas are multiple and often give rise to conflicting interests. In this context, marine protected areas (MPAs) and artificial reefs (ARs) are increasingly regarded as interesting management measures, in that they contribute to ecosystem conservation, fisheries sustainability, and because they can be helpful in zoning coastal areas in order to reduce conflicts between users. Beyond these expected benefits, it is important to appraise whether MPAs and ARs meet managers' objectives. This review focuses on the interaction between ecological sciences and management in the purpose of establishing or monitoring MPAs and ARs. We first study how objectives have to be formalized through management plans, and which kinds of information need to be collected in this respect. We then report management objectives related to MPAs and ARs, and list corresponding observed effects. Finally, we discuss the present role of monitoring and scientific research in the management process and propose a few perspectives for scientific research.

Brown ring disease (BRD) in Ruditapes philippinarum and Ruditapes decussatus is a shell disease caused by Vibrio tapetis. This disease has begun in 1987 in clams beds in Brittany (France) and then has spread along the European Atlantic coast. Since about fifteen years, research on BRD has progress a lot and the purpose of this review is to give a short description of BRD in clams in retrospect and in addition of recent and pertinent results. Diagnosis including isolation, biochemical, serological and molecular characterization has been developed to identify and detect the pathogen. Therefore, Vibrio tapetis-like strains has been detected in other host specie, in cultured fishes during mortalities, such as the wrasse, Symphodus melops in Norway and the halibut, Hippoglossus hippoglossus in Scotland. Mechanisms of host-pathogen interactions modulated by environmental factors were studied using in vivo bacterial challenge and in vitro bio-assays. According to these studies, adherence and cytotoxic factors have been yet identified as virulence factors; identification and characterization of virulence genes are in progress. Field and experimental studies confirmed the significant effect of temperature on the development of BRD and on clam defense related activities. A significant increase in temperature over 21 °C may have a preventive effect on the development of the disease.

The Gambia Estuary, a “normal” estuary with a decreasing salinity gradient from the mouth towards the head, is moderately exploited by small-scale fisheries and does not receive any severe pollution from either agriculture or industrial activities. Neither the Gambia River nor its estuary are artificially impounded. As the last large West African estuary free of major human disturbance, it is of considerable interest for comparative studies on the effect of major environmental perturbations in West African estuarine ecosystems. The aquatic environment and fish communities of the Gambia Estuary (about 250 km long) were studied by purse seine sampling at different periods in the river cycle, covering all hydro-climatic seasons that are characteristic of West African estuaries. Emphasis was placed on the diversity, composition, structure and distribution of fish assemblages in relation to fluctuations in physico-chemical factors such as water temperature, salinity and turbidity. Results on the aquatic environment, mainly the salinity range (from freshwater to 39) and dissolved oxygen (never a limiting factor for fish in the estuary) and on the main characteristics of the fish fauna (high diversity of life cycles, all the ecological categories represented) indicated that the Gambia Estuary was free of major climatic perturbation and reinforced the choice of this system as a reference for the study of the effects of major perturbations on estuarine tropical fish communities.

Levels of nickel and vanadium, trace metals found in high concentration in the oil spilled from the “Erika” tanker off Brittany (France) in December 1999 (41 ± 1 and 87 ± 3 mg kg−1 respectively), have been monitored over a one-year period following this accidental event in several benthic invertebrates. Ni and V in mussels (Mytilus edulis) and oysters (Crassostrea gigas) soft tissues were analysed twice a month by graphite furnace atomic absorption spectrometry and a scallop (Pecten maximus) shell daily growth bands were sampled every three bands by laser ablation and analysed by ICP-MS for these two contaminants. Survey data for mollusc tissues were compared with reference data arising from the national monitoring database. Ni concentrations in dried tissues, comparable with reference data (1.8 ± 0.9 µg g−1 in mussels and 1.2 ± 0.5 µg g−1 in oysters) do not show any additional input during the whole period. Conversely, a sharp increase in vanadium concentrations (up to 4.6 and 3.2 µg g−1 for mussels and oysters respectively) is observed around May 2000, i.e. 5 months after the wreck, compared with the monitoring data (1.4 ± 0.6 µg g−1 in mussels and 1.3 ± 0.6 µg g−1 in oysters). Furthermore, no Ni peak is detectable in the time profiles of scallop shell growth bands where a V peak is observed also in May 2000. This study shows that although a “mussel-watch-type” network, based on the monitoring of vanadium concentration in mollusc tissues, is able to identify contamination due to oil spills, similar information might be obtained a posteriori by analysing daily growth bands of scallop shells.

The main microbial diseases affecting marine cultured bivalves have been revised on the basis of the etiologic agents, pathogenesis and pathogenicity. Several recent bivalve-interaction models have been studied, including Pecten larvae-Vibrio pectinicida, brown ring disease, juvenile oyster disease, Pacific oyster nocardiosis and summer mortalities of oysters. In addition, the taxonomy and phylogeny of new potential bivalve pathogens and their virulence factors have been established. Facing the difficulty of identifying bacterial strains associated with molluscan diseases (mainly vibriosis), polyphasic approaches have been developed to correlate the phenotype and genotype of potential pathogens. By evaluating likely virulence mechanisms, developing biotests to screen virulent strains and characterising the genes implicated in pathogenesis, a new generation of diagnostic tools, based on potential virulence, will be developed. Acquisition of pertinent diagnostic tools will be of major benefit in disease management, health surveillance and monitoring will contribute to maintaining sustainable aquaculture industries.

Marine Protected Areas (MPA) are often contemplated as a tool for the sustainable management of exploited resources and ecosystem conservation. This paper proposes an approach to establish a statistical diagnostic of the effects of MPAs on fish assemblages, and define corresponding ecological indicators. This requires choosing relevant variables (abundance, diversity, demographic parameters ...) and appropriate statistical methods. The study was based on data from the Abore reef Reserve in New Caledonia. Two sets of methods: 1-inferential linear models (ANOVA, GLM); 2- Partial Least Squares (PLS) methods of regression, were used to test the effects of this MPA. PLS enabled us to test simultaneously within a model, density, species richness, biomass and mean size variables of fish community to retain the most sensitive and relevant ones. Habitat variability was also taken into account in these models. Species were grouped according to several criteria: 1- feeding habit; 2- taxonomy; 3- mobility; 4- adult size; 5- demographic strategy. No significant effect of the opening of the Abore reef to fishing was found for mobility. Feeding habit was the only criterion for which the results from the inferential models and PLS showed a significant effect of reserve status for all variables. Species richness, density, and to a lesser extent mean size, were sensitive to the removal of reserve status, but not biomass. Results from ANOVA and PLS regression were consistent but the latter allows a more holistic approach as it integrates all variables within a single model.

The Gambia Estuary is one of the last estuaries in West Africa not to have been affected by strong environmental changes and adverse human disturbances. In order to describe the spatio-temporal change in fish biomass in this estuary, and the seasonal changes in fish size classes, five research surveys have been conducted at characteristic periods in the river's water regime and meteorological seasons. The fish assemblages were sampled by two vertical echosounding protocols: mobile surveys (zigzag transects) in the estuary and moored stations. The two sampling methods produced a similar image of the fish assemblages in terms of the distribution of total biomass and target strength distributions. Large fish aggregations were detected in the most marine area at the end of the wet season, and fish biomass increased through the dry season in the upstream zone. Fish were smaller at the beginning of the wet season and they were always larger in downstream areas.

The petroleum spilt by the tanker “Erika” contained environmentally high concentrations of nickel (45 mg kg−1) and vanadium (83 mg kg−1). Our aim was to show that nickel and vanadium concentrations in marine organisms could be used as tracers of their exposure to oil deposits along the coast. Two biomarkers were determined, condition index (CI) and metallothionein levels. Samples were collected monthly from January to May 2000 from five sites along the coast of Vendée and Loire Atlantique: (1) Lérat, (2) La Govelle, (3) Saint Gildas, (4) La Bernerie and (5) La Fosse. Among benthic invertebrates, mussels Mytilus edulis (filter-feeders), periwinkles Littorina littorea (grazing-feeders) and dogwhelks Nucella lapillus (carnivora, bivalve predators) were selected. In addition, mussels were collected from a control site, Fier d'Ars (Ré Island). The species chosen as bioindicators have responded to the presence of oil in their environment by accumulating nickel and vanadium. The bioaccumulation of vanadium occurred early one month after oil spill whereas nickel bioaccumulation was deferred, probably as a consequence of a lower stability of vanadylporphyrins compared to nickelporphyrins which are known in particular for their role in stabilizing emulsions (film at the water/oil interface). Interspecific differences may be explained by different food habits: periwinkles grazed contaminated algae; mussels as filter-feeders retained particles and colloids from the water column; dogwhelks fed on mussels. Spatio-temporal changes of nickel and vanadium concentrations may result from (i) the arrival of new oil slicks, (ii) the action of cleaning of the coasts contributing to the re-suspension of petroleum. In all of the three species, few changes of the CI were observed from site to site. CI variations were linked to sexual ripening in mussels. Mussels originating from the control site showed MT concentrations significantly lower than those in specimens from impacted sites. The highest MT concentrations were observed in January and February, and then a consistent decrease was registered in March and May. MT concentrations in periwinkles increased very significantly in March and May. An increase in MT concentrations was also shown at this period in dogwhelks. Depending on the species, positive correlations were shown between MT and nickel and/or vanadium concentrations.

The current status of the Haplosporidia is reviewed as well as recent information on Haplosporidium nelsoni, the causative agent of MSX disease in oysters. Recent molecular phylogenetic analyses with greatly increased taxon sampling support monophyly of the Haplosporidia and hypothesize placement of the group as sister taxon to the phylum Cercozoa. Oyster pathogens in the genus Bonamia should be considered haplosporidians based on molecular sequence data. Thus, the group contains 4 genera: Uropsoridium, Haplosporidium, Bonamia and Minchinia. Molecular phylogenetic analyses support monophyly of Urosporidium, Bonamia and Minchinia, but Haplosporidium forms a paraphyletic clade. Reports of haplosporidia worldwide are reviewed. Molecular detection assays have greatly increased our ability to rapidly and specifically diagnose important pathogens in the phylum and have also improved our understanding of the distribution and biology of H. nelsoni and H. costale. Much of the data available for H. nelsoni has been integrated into a mathematical model of host/parasite/environment interactions. Model simulations support hypotheses that recent H. nelsoni outbreaks in the NE United States are related to increased winter temperatures, and that a host other than oysters is involved in the life cycle. Evidence is presented that natural resistance to H. nelsoni has developed in oysters in Delaware Bay, USA. However, in Chesapeake Bay, USA H. nelsoni has intensified in historically low salinity areas where salinities have increased because of recent drought conditions. Efforts to mitigate the impact of H. nelsoni involve selective breeding programs for disease resistance and the evaluation of disease resistant non-native oysters.

A fyke net survey of the juvenile and small fish assemblage of the Gambia estuary was conducted on three sampling occasions during the maximum recruitment season, from May to November 2002. This is the first detailed description of that particular component of the fish community in the Gambia estuary. The overall fyke net fish assemblage comprised 51 species, with a majority of young individuals of large and medium size species and the adults of small species. This assemblage is defined as the “small fish component of the mangrove channels”. The assemblage is dominated by true estuarine and certain marine species, all able to complete their life cycle within the estuary. The sea spawning species whose juveniles use the estuary mainly as a nursery ground, are not very diverse or abundant during the recruitment season. They are limited to the lowest part of the estuary due to the low salinity prevailing in the middle and upper reaches during the rainy season. This suggests that extreme seasonal variability (river flooding) in certain West African tropical estuaries at the time of maximum recruitment by certain marine species may reduce the nursery ground value for these taxa.

A mass-balanced trophic model was developed for the coral reef lagoon of Uvea atoll (New Caledonia) using the Ecopath software. The model accounts for both pelagic and soft-bottom communities to describe the whole trophic structure and biomass flows in the shallowest part of the atoll lagoon. Phytoplankton production approximately equals the benthic primary production. Benthic biomass accounts for more than 80% of the total living biomass in the shallow lagoon. The benthic domain requires input of food from the pelagic system (mainly zooplankton) and from adjacent areas to sustain the biomass of predatory fishes. Predation pressure was found to be a major force structuring the food web, but it is also suggested that water circulation within the lagoon influences the amount of primary resources, such as plankton, benthic microphytes and detritus.

Oil spills are an important source of PAHs in marine and coastal areas and comprise a short- and long-term threat for aquatic organisms. Some PAHs are known to be toxic, in particular mutagenic and/or carcinogenic, and their toxicological effects must be evaluated. Here, the impact of the “Erika” oil spill, which occurred at the end of 1999, was studied by combining chemical (PAH analyses) and toxicological approaches (biological effect assessment). “Erika” elutriates have been found to be more toxic than the elutriate obtained with a crude oil, Bal 250, inducing deleterious effects in Mytilus galloprovincialis and Crassostrea gigas embryos and in Isochrysis galbana algae. The embryotoxicity test in mussel is more sensitive than growth test in I. galbana. Naphthalenic compounds make up more than 95% of total PAHs quantified in elutriates. “Erika” elutriates are enriched with naphthalene, methyl-naphthalene, anthracene and higher-molecular-weight compounds. On the contrary, Bal 250 elutriate is characterized by the highest dibenzothiophene, methyl-dibenzothiophene and dimethyl-dibenzothiophene levels. Weathering does not highly affect the toxicity of the “Erika” oil. This study also confirms the potential impact of the “Erika” fuel on the biological quality of sea water and sediments from Traict du Croisic on the Atlantic coast of France.

Our understanding of the microcell oyster parasites of the genera Bonamia and Mikrocytos has expanded in recent years with the application of ultrastructural and especially molecular biological research approaches. Molecular phylogenetic analyses of SSU rRNA genes have united three species, Bonamiaostreae, Bonamiaexitiosa, and Mikrocytos (now Bonamia) roughleyi, in a microcell clade within the Haplosporidia, supporting both early and recent ultrastructural observations. Ultrastructural and molecular phylogenetic evidence has emerged that Mikrocytos mackini, on the other hand, is a unique protist with unusual adaptations for a parasitic existence. DNA probes and polymerase chain reaction (PCR) assays promise new insights into the life cycles, transmission, and diversity of these organisms. The development of Ostrea edulis lines selected for B. ostreae resistance will increase the viability of aquaculture industries for this species and, combined with rapidly developing biotechnological approaches for studying host defenses and host-parasite interactions, will allow greater insight into the nature of phenomena such as resistance and tolerance to disease in oysters.

West African marine ecosystems are very productive and sustain important fisheries that have developed rapidly in the last decades. The analysis of the fishing impact on exploited resources is usually conducted through single-species assessments. In this study, we propose a complementary approach that enables to account for some ecosystem effects of fishing. In Guinea and Senegal, fisheries have developed relatively recently and at the same time, the collection of landings and surveys data has been carried out. In consequence, the data collection extends from a period where stocks could be considered as non exploited to a situation of overexploitation. This case study is analysed in order to detect shifts in the ecosystem structure in response to increasing fishing pressure. To this aim, trophic spectra and long time series of mean trophic level are examined for demersal fish communities. Trophic spectra display either the distribution of the demersal community biomass or the commercial catches according to trophic level classes. Some substantial and statistically significant changes in the trophic structure of the Senegal and Guinea ecosystems were observed. In particular, the biomass of the high trophic levels decreased whereas the lower trophic levels displayed a relative stability or an increase. This could be linked to a “top-down” fishing effect due to a release of predation on the lower trophic levels of the demersal fish community. In Senegal, the mean trophic level decreased significantly for both the catches and the demersal community biomass. Such a decrease was also observed for the coastal demersal biomass in Guinea. This showed that fishing activities had an impact on the trophic structure of the ecosystem, and a “fishing down marine food web” effect was shown in West Africa for the first time.

The West-African neighbouring Gambia and Saloum estuaries function in different ways, the first being normal (saltier waters in the lower river, salinity range 0-38) and the second being inverse (saltier waters in the upper river, salinity range 36-90). The common cichlid species Sarotherodon melanotheron was collected in both systems over 16 months (June 2001 to September 2002) at five locations. We quantified reproductive traits from macroscopic examination of the gonads, oocyte counts and measurements, and growth from interpretation and measurements of an otolith sub-sample. There was a clear seasonal cycle of reproduction in the estuaries with a peak at the beginning of the wet season (May-July). Size at maturation was smaller in the more saline environment, the Saloum, for both females (170 mm in Gambia and 131 mm in Saloum) and males (162 and 113 mm respectively). The relative fecundity was lower and the oocyte size was bigger in the freshwater location of the Gambia river. Growth, estimated by counting the annual opaque zones on whole otoliths, was reduced in the hypersaline environment of the Saloum (L∞ = 198 mm, K = 0.26). Differences are less obvious between the growth in the Gambia (L∞ = 238 mm, K = 0.21) and that in the Saloum with a salinity of less than 60 (L∞ = 244 mm, K = 0.22). All these observations suggest that S. melanotheron is able to withstand saltier environments by limiting its growth, reducing the size-at-maturity, and changing its fecundity, but the most profound changes are only visible in hypersaline conditions.

Results of an annual survey of fishing activities and catches in the Gambia estuary (200 km long), carried out from June 2001 to May 2002, indicated that fishing effort targets mainly (66% of fishing trips) shrimps. As a result of the globalisation of fish markets, the fishery has become a quasi mono-exploitation of shrimp for exporting. At the opposite, fishing activities focusing on fish were low and carried out with large and medium mesh drift nets, gill nets and surrounding nets (17% of fishing trips), handlines and longlines (15%). The annual catch, estimated at 2350 tonnes for the estuarine part of the River Gambia, consisted of 1800 t of fish and 550 t of shrimp. Stownets were the most efficient gear accounting for 50% of the total production (550 t of shrimp and 600 t of fish) while other significant techniques were mainly drift nets (21%), longlines (11%) and gillnets (5%). Fish catches were composed with 55 fish species among which 16 species accounted for 90% of the annual catch. The average catch length of these first sixteen species was 295 mm, clearly demonstrating that fishing for fish was targeting large fish. The effects of the targeted shrimp exploitation resulted in a low fishing effort for fish leading to low fish landings and consequently to an under exploitation of fish resource in the Gambia estuary.

Immunological alterations may be used as ecotoxicological biomarkers to detect and monitor biological effects of chemical contaminants in polluted environments. This study reports on a survey of Pacific oysters from the Atlantic coast of Britanny (France) after the “Erika” oil spill. Reared stocks were sampled twice a year from November 2001 to March 2003 at three impacted sites and at an additional site outside the spill area. A multiparametric diagnosis of the immune system was performed on individual hemolymph samples to identify structural, immunopathological alterations and functional impairment of immunocompetent cells. One year after the spill, severe immunological alterations were observed in a site heavily impacted by oil. Since the oysters there had higher contents of PAH compared to the other sites, it was suggested that chronic contamination, possibly generated by oil trapped in the sediments, had induced immunotoxicity. Moreover, moderate variations in some hemolymph parameters observed at the non-impacted area strongly suggested that natural environmental factors may have generated physiological stress. An immunotoxicological index applied here in order to integrate all measurements of defense-related functions appeared to be an efficient tool to identify samples suffering immunological stress.

Conventional “spaghetti” tags and tags originally designed for “sport fishing” and called Betyp tags, were used during a tuna tagging program conducted on board Dakar baitboats in 1999. With the aim of comparing the recapture rate of both types of tags, additional information obtained from previous tagging trips are used in a Bayesian context to set up an informative prior for conventional tags. We show in this study (1) how to account for the sampling uncertainty in the construction of the Beta prior with a likelihood method, and (2) how a simulation-based alternative can be useful for performing the probability density function of the difference between two posterior recapture rates. On the light of the resulting simulated difference we found that Betyp tags have a very strong negative effect on the return rate of bigeye tuna (−19.6% on average). For skipjack the strength of evidence concerning the decrease in recapture rate due to the implementation of Betyp tags (−3.2%) was supported only at a 10% level. The Bayesian approach is compared with the conventional “frequentist” approach and with a likelihood method allowing for the integration of previous information. The results obtained from different approaches indicate that the choice of the method, as well as the choice of the prior, does not modify the conclusion of the study. Potential causes for explaining the lowest efficiency of Betyp tags are discussed.

The transfer of polycyclic aromatic hydrocarbons (PAHs) from bivalves, through the food chain to vertebrates was of concern. Our research aimed at estimating potential effects for consumers resulting from the ingestion of seafood contaminated by oil spill pollutants. After the “Erika” wreck, mussels (Mytilus sp.) were collected from sites of the Atlantic coast impacted to various degrees by the oil slick and constituted contaminated food for rats during 2 and 4 weeks. Genotoxic damage were studied in rats by means of COMET assay carried out in liver, bone marrow and peripheral blood. Biochemical and genomic effects such as the induction of CYP 1A1 and the expression of cytochrome genes were measured in rat livers. The most sensitive biological parameter reflecting the transfer of contaminants via the food appeared to be DNA breaks studied by means of the COMET assay. Genotoxic damage, observed mainly in the liver, were rather moderate and remained not persistent. This study underlined the bioavailability of pollutants in fuel oil contaminated mussels for consumers, and the complexity of the contamination consecutive to the oil spill. The occurrence of related PAH compounds in addition to non-substituted PAHs in fuel oils and mussels raised the question of their implication in the registered effects.