The genus Perkinsus includes protistan parasites infecting marine molluscs throughout the world, some of which are associated with mass mortalities. Life cycle involves vegetative proliferation within the host, by which a cell named trophozoite undergoes successive bipartitioning. Other stages have been observed in vitro or in vivo, depending on the species: hypnospore, zoosporangium and zoospore. Molecular taxonomy supports a close affinity between dinoflagellates and Perkinsus spp. Six species of Perkinsus are currently considered valid: P. marinus, P. olseni, P. qugwadi, P. chesapeaki, P. andrewsi and P. mediterraneus. Histology and, above all, incubation of host tissues in Ray's fluid thioglycollate medium (RFTM) are classic diagnostic methods. In addition, more sensitive and quicker molecular diagnostic techniques based on either immunoassays or PCR have been developed for Perkinsus spp. Epizootiological studies have shown a marked influence of water temperature and salinity on P. marinus infection in oysters Crassostrea virginica, thus determining parasite geographical range and temporal disease dynamics (seasonality). In vitro cultures have been established for four Perkinsus spp. Immune response to infection varies depending on host and involves phagocytosis or encapsulation of the parasite cells by host haemocytes. A polypeptide is secreted by clam Tapes philippinarum haemocytes that could kill the parasite. In vitro cultured P. marinus cells secrete proteases that are likely involved in degradation of host tissues. P. marinus can suppress the toxic oxygen radicals produced by host haemocytes. In addition to host death, sublethal effects caused by Perkinsus spp. (reduction of fecundity, growth, and condition) may have significant ecological and economic implications. Various strategies have been assayed to mitigate the consequences of P. marinus epizootics on the oyster industry: modifications of management/culture procedures, selective breeding to obtain resistant oyster strains, and the use of triploid oysters and allochthonous oyster species. Some chemotherapeutants have been proved to inhibit or kill parasite cells in vitro.

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.

The amino acid compositions of whole body tissue of European seabass, gilthead seabream and turbot of two different size classes were determined. No significant differences were detected between species and the composition was not affected by body size. Based on whole body indispensable amino acids (IAA) to total IAA ratios (A/E ratios), the IAA requirement profiles for the three species were estimated and compared to data available to date for some amino acids, obtained using dose-response curves.

Feeding guides for salmonid fishes have been available from various sources for many years. These feeding guides have originated in one way or another from earlier feeding charts of the 1950-60s when meal-meat mixture diets were widely used. Few of the feeding guides available today are based on actual bioenergetics data at different water temperatures and are adapted to high energy diets. New feeding standards have been developed based on principles of nutritional energetics in which the digestible energy content of diet, digestible protein and energy ratio and the amount of digestible energy required per unit of live weight gain are taken into account. The gain expressed as retained energy in carcass and maintenance energy at different water temperatures is the main criteria for energy and feed allocations. Series of bioenergetic models were developed based on these principles and a stand-alone multimedia program was written to facilitate computation of the models. This program predicts growth and energy, nitrogen and phosphorus retention, requirements and excretions to determine feeding standards, waste outputs and effluent water quality based on a biological method. The models require initial and final body weights, water temperature, growth coefficient, carcass energy content and waste coefficients to estimate input and output. Accurate determinations of the thermal-unit growth coefficient, apparent digestibility coefficients and retention efficiencies are essential and these coefficients are determined by biological experiments in the laboratory and field. Oxygen requirement is included to aid environmental control in fish culture system. The Fish-PrFEQ program also contains modules for production records, performance calculations and data base management for input and output data which may be exported for further data and graphic manipulations.

A study was carried out to determine the effect of feeding level and water temperature on growth and feed efficiency, nutrient and energy utilization and waste outputs of rainbow trout. A practical diet was fed to near-satiation to groups of fish reared at 6, 9, 12 and 15 °C. At each temperature, the feed intake of other groups of fish was restricted to about 85 % or 70 % of the amount of feed consumed in the previous week by the fish fed to near-satiation. Total feed intakes over 12 weeks were, on average, 76 % and 65 % of total feed intake of the near-satiety group for R1 and R2, respectively. Reducing the feed allocation resulted in significantly (P < 0.05) lower weight gains compared to feeding to near-satiation regardless of the rearing temperature. Feeding level and water temperature had no significant (P < 0.05) effect on feed efficiency, carcass composition or efficiencies of digestible nitrogen and digestible energy retention. Increasing temperature resulted in an increase in the apparent digestibility of dietary dry matter, nitrogen and energy (P < 0.05). The increase in digestibility of dry matter and nitrogen with increasing temperature resulted in higher estimated total solid and solid nitrogen waste outputs per kg fish produced (P < 0.05) at lower water temperatures. Estimated dissolved nitrogen and phosphorus waste outputs (g/kg fish produced) were not affected by the feeding level or water temperature. A highly significant (P < 0.01) linear relationship was observed between metabolizable energy (ME) intake above basal metabolism and recovered energy. The efficiency of ME utilization for growth (Kpf) was 0.61 and this coefficient was not affected by feed intake or water temperature. Protein and lipid were deposited in a constant ratio (1 kJ protein gain: 1.4 kJ lipid gain) regardless of ME intake or water temperature.

An ecological risk assessment (ERA; also known as productivity and susceptibility analysis, PSA) was conducted on eleven species of pelagic elasmobranchs (10 sharks and 1 ray) to assess their vulnerability to pelagic longline fisheries in the Atlantic Ocean. This was a level-3 quantitative assessment consisting of a risk analysis to evaluate the biological productivity of these species and a susceptibility analysis to assess their propensity to capture and mortality in pelagic longline fisheries. The risk analysis estimated productivity (intrinsic rate of increase, r) using a stochastic Leslie matrix approach that incorporated uncertainty in age at maturity, lifespan, age-specific natural mortality and fecundity. Susceptibility to the fishery was calculated as the product of four components, which were also calculated quantitatively: availability of the species to the fleet, encounterability of the gear given the species vertical distribution, gear selectivity and post-capture mortality. Information from observer programs by several ICCAT nations was used to derive fleet-specific susceptibility values. Results indicated that most species of pelagic sharks have low productivities and varying levels of susceptibility to pelagic longline gear. A number of species were grouped near the high-risk area of the productivity-susceptibility plot, particularly the silky (Carcharhinus falciformis), shortfin mako (Isurus oxyrinchus), and bigeye thresher (Alopias superciliosus) sharks. Other species, such as the oceanic whitetip (Carcharhinus longimanus) and longfin mako (Isurus paucus) sharks, are also highly vulnerable. The blue shark (Prionace glauca) has intermediate vulnerability, whereas the smooth hammerhead (Sphyrna zygaena), scalloped hammerhead (Sphyrna lewini), and porbeagle (Lamna nasus) sharks are less vulnerable, and the pelagic stingray (Pteroplatytrygon violacea) and common thresher (Alopias vulpinus) sharks have the lowest vulnerabilities. As a group, pelagic sharks are particularly vulnerable to pelagic longline fisheries mostly as a result of their limited productivity.


The impact of metals (silver, cadmium, copper, mercury and zinc) on metallothionein (MT) and malondialdehyde (MDA) levels of the oyster (Crassostrea gigas) and the mussel (Mytilus edulis) was studied after 4 or 21 days of metal exposure. Moreover, total protein levels were determined. After 4 days of metal exposure, although C. gigas and M. edulis accumulated cadmium and mercury concentrations in the gills and digestive gland, no significant variation of total protein level was occurred. After 21 days of exposure, metals were bioaccumulated in the gills and the digestive gland of both mollusks. A decrease of total protein concentrations in the gills of oysters and the digestive gland of mussels and an increase on metallothionein concentrations in the gills of both mollusks were observed. An increase of MDA levels was noticed for the gills and the digestive gland of mussels exposed for 21 days to either cadmium, silver or mercury whereas a decrease of MDA levels was observed in the gills of the oysters exposed for the same time to the same metals. The levels of proteins, MDA and MT were metal, species or organ dependent.

An individual-based model named OSMOSE (Object-oriented Simulator of Marine Ecosystems Exploitation) is used to investigate the dynamics of exploited marine fish communities. It allows the representation of age- and size-structured populations comprised of groups of individuals that interact within a spatialized food web. Within each group, which constitutes the basic interaction entity (the ‘super-individual’ in individual-based modelling terminology), fish belong to the same species, have similar biological parameters and behaviour rules. Somatic growth, reproduction, predation and starvation processes are modelled. Two rules apply for the predation process: for a given fish group, prey selection depends both on the spatial and temporal co-occurrence of the predator and its prey, and on the respective lengths of the prey versus the predator. Thus, fish feed regardless of the taxonomy of their prey. The strength of both predation and competition relationships therefore vary according to changes in relative species abundance. Preliminary investigations are conducted on a theoretical community comprising seven interacting species. The simulation results show how community stability can emerge from variability in species biomass. It is thus suggested that size-based trophic interactions, along with the existence of multiple weak links and species redundancy, favour community persistence and stability.

This review summarizes the current state of knowledge regarding the two primary proliferative diseases of commercially important marine bivalves. Disseminated neoplasia is characterized by the presence of large (2−4 times the diameter of normal hemocytes), anaplastic, circulating cells that have a hyperchromatic and often pleomorphic nucleus containing one or more prominent nucleoli. Prevalence exceeding 90% has been reported; the disease is progressive and can result in significant mortality of affected populations. Softshell clams, Mya arenaria, and mussels, Mytilus trossulus, from the east and west coasts of North America, respectively, and cockles, Cerastoderma edule, from Ireland, appear to be especially susceptible. Disseminated neoplasia can be transmitted to uninfected individuals, indicating an infectious (perhaps viral) etiology, the expression of which may be aggravated by environmental degradation. Gonadal neoplasia consists of small, basophilic, undifferentiated cells that originate as small foci in gonadal follicles where they proliferate and eventually invade surrounding tissues. This disease primarily affects M. arenaria in Maine (USA) and Mercenaria spp. in Florida (USA) at prevalences up to 50%. Most affected individuals are female. Limited field studies to date indicate that the disease progresses slowly and mortality rates are low. The major impact is most likely a reduction in reproductive effort. The finding that prevalence of gonadal neoplasia is higher in hybrid Mercenaria spp. suggests a genetic etiology. Precise determination of the etiology and other aspects of both diseases will benefit greatly from future advances in cellular and molecular biological techniques.

Characteristics of Lactic Acid Bacteria (LAB) isolated from rotifers, Brachionus plicutilis, resembled those of Lactobacillus plantarum or Carnobacterium sp. It was investigated whether the artificial maintenance of a high concentration of LAB in rotifers might increase their dietary value for turbot larvae, particularly when the fish were infected with pathogenic Vibrio sp. One LAB strain was cultivated, then introduced daily into the enrichment medium of rotifers. In this way, LAB were retrieved in large amounts in turbot, and a significant limitation of larval mortality rate was observed when turbot were challenged with pathogenic vibrio at day 9. The inoculum concentration of LAB had a decisive effect on survival rate, and the optimum was between 107 and 2 × 107 Colony Forming Units (CFU) daily added per ml of the enrichment medium (53% survival rate after 72 h of challenge, versus 8% for the infected control group without LAB).

A model to estimate the waste production from sea cage culture was established. Using known feed inputs of nitrogen, phosphorus and organic matter, the model quantifies waste discharge from seabream culture. Daily feed intake and growth in Sparus aurata fed a commercial diet with known composition were measured and found to be dependent on fish weight and water temperature. Digestibility of the commercial feed was measured using chromic oxide as a marker and collection of feces by stripping. The proximate composition of Sparus aurata at different sizes was determined and nitrogen and phosphorus content were on average 28.5 and 7.2 g·kg−1 body mass, respectively. Excretion of ammonia-nitrogen and inorganic phosphorus after metabolic processes was calculated as the difference.

The general principles behind the bioenergetic approach for predicting growth, as well as for decreasing feed and nutrient losses, have been set forth for salmonids. Given the diversification of fish farming activities around the world and the ever increasing concern for water quality management, it becomes essential to verify whether an approach developed for salmonids is applicable to other species. Given this general background, an attempt is made here to check the theoretical assumptions and technical considerations behind the bioenergetic principles developed for rainbow trout with other freshwater or marine species. From a conceptual point of view, recent literature data do indicate that as far as nitrogen or energy balance is concerned, the general scheme is as valid for marine species as it is for salmonids, even in quantitative terms. Given the methodological tools available today, it should not be difficult to reduce feed and nutrient losses and to estimate the potential environmental loadings using the same principles for non-salmonids.

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.

The French oyster farming industry relies almost exclusively on juveniles collected from the natural environment; the supply of spat produced by hatcheries is low, about 10 % of the industry's requirements. Development through selective breeding of oyster stocks which are better suited for aquaculture purposes, is likely to reverse this tendency since only hatcheries will be able to supply such animals. Scallop farming, which at present is poorly developed in France, relies exclusively on hatchery produced spat. Although hatchery technology is constantly being improved, significant production problems remain which must be solved before hatcheries become a major supplier of juveniles for the industry. This paper describes the present state of hatchery technology in France based on experimental results obtained with the great scallop Pecten maximus and the Pacific oyster Crassostrea gigas, over the past ten years. Compared to the great scallop, the Pacific oyster has higher D larva yields (60 % for C. gigas vs. 30 % for P. maximus) and a faster larval growth rate (10 μm·d−1 for C. gigas vs. 5 μm·d−1 for P. maximus). However, Pacific oysters have a greater heterogeneity during larval development and higher mortality rates (40 % for C. gigas vs. 25 % for P. maximus) which produce lower overall yields of pediveliger larvae ready-to-set for Pacific oysters (15 %) compared to the great scallop (30 %). Development of continuous larval and post-larval culture methods along with development of continuous phytoplankton technology offers one of the most promising methods to improve molluscan hatchery techniques.

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.

Neural networks provide a "black box" model for explaining and predicting trout abundance with 8 environmental variables. This work investigates the specific effect of each variable, by inputting fictitious configurations of explanatory variables and by checking the responses of the model. The comparison between this response of the model to environmental variables on one hand, and results from field observations on the other hand, shows similarities and indicates neural network modelling can be trusted. The elevation appears to be the major explanatory factor. The influence of shelters, bottom velocity and Froude number also play an important role. When considered separately, depth does not have a notable influence on the density of trout. Such confirmations of field observations suggest that these models can be used to obtain a clear identification and hierarchization of the factors influencing the abundance of trout and the mode of action of the factors. This approach can be extended to other applications in quantitative ecology in which non-linear relationships are usually observed.

Determining the timing or frequency of movement of fish and the relative importance of different habitats is difficult. Advances in otolith chemical techniques and interpretations (including elemental ratios and stable isotopes) suggest that this is a powerful method for determining movement of fish. To date, the majority of applications have involved marine fish, however, otolith chemistry has the potential to determine movements of diadromous and freshwater fish; I therefore review freshwater applications of otolith chemistry in this paper. Despite some limitations regarding strontium:calcium (Sr:Ca) ratios (e.g. Sr concentration of the water is not always measured, Sr:Ca ratios in freshwater can exceed marine waters, and mixed results for the relationship between otolith Sr and salinity), they have been widely used for a variety of applications involving diadromous species and more recently freshwater fish. In addition, barium:calcium (Ba:Ca) ratios have recently been used to determine movements of diadromous and estuarine species, as ambient ratios are possibly linked to environmental flows. Several studies have also investigated the use of multielemental otolith composition to discriminate between groups of fish collected from different lake or river systems, but a wider range of applications are possible. Several applications of Sr isotopes have also been investigated, most of which is focused on salmonids (e.g. distinguishing fish from different river systems, determining movement history of individual fish). Relatively few studies have investigated the use of other isotopes (e.g. oxygen, sulphur) for determining movements. Otolith elemental ratios and stable isotopes have great potential to determine movements of freshwater species, with possible applications likely to increase as analytical technology improves.

This study provides a historical overview of the use of drifting fish aggregating devices (DFADs) in purse seine fisheries since the early 1990s, using global tuna fisheries datasets from the four tuna Regional Fisheries Management Organizations (RFMOs). Tropical tuna purse seine fisheries typically target large yellowfin (Thunnus albacares) and bigeye (Thunnus obesus) tunas on free-swimming schools and skipjack (Katsuwonus pelamis) and juveniles of yellowfin and bigeye associated with drifting objects. DFADs have enabled global skipjack catches to markedly increase, and have also introduced major scientific issues for all tuna-RFMOs. In particular, they have strongly modified the fishing strategies of purse seiners that fish on a combination of free-swimming and DFAD-associated schools. Consequently, the cumulated search time traditionally used to quantify nominal fishing effort to assess the status of tuna stocks is inconsistent and cannot be used to derive time series of abundance indices from catch-per-unit of-effort (CPUE). In addition, the lack of information available on the construction, deployment, and use of DFADs has prevented effective monitoring of the fishing pressure over the last two decades exerted by purse seine fleets using this fishing mode. Juveniles of tropical tunas represent a substantial proportion of purse seine catch on DFADs in the three oceans, which has raised particular concern for some bigeye stocks that have been subject to overfishing in the past. Catches of juvenile tunas by DFAD fishing may also result in a decrease in recruitment for fisheries that target adult tunas such as longliners. In addition, some demographic parameters of tunas and other species associated with DFADs may be affected by the resultant habitat modification arising from the widespread deployment of DFADs. Evidence in the literature and provided by the ratio-estimator method suggest that fishing DFAD-associated schools may result in about 100 000 t of bycatch and discards annually. In addition, there is further potential for ghost fishing related mortality of sensitive species such as marine turtles and pelagic sharks. In this context and following a precautionary approach, we finally discuss the increasing need for all tuna-RFMOs to reduce, or at least monitor and control, the use of DFADs to mitigate their adverse effects not only on yellowfin and bigeye stocks but also on open-ocean ecosystems.

Bivalve molluscs are filter feeders and as a consequence they may bioaccumulate in their tissues viruses that infect humans and higher vertebrates. However, there have also been described mortalities of bivalve molluscs associated with viruses belonging to different families. Mass mortalities of adult Portuguese oysters, Crassostrea angulata, among French livestocks (between 1967 and 1973) were associated with irido-like virus infections. Herpesviruses were reported in the eastern oyster, Pacific oyster and European flat oyster and lately in scallops and clams. Disseminated neoplasia, a proliferative cell disorder of the circulatory system of bivalves, although of uncertain aetiology, has been suggested to be caused by retroviral infections. Other viruses described in bivalves are interpreted as members of the Papovaviridae, Togaviridae, Reoviridae, Birnaviridae and Picornaviridae. However, the lack of bivalve cell lines renders difficult virus isolation from molluscs although some viruses can be isolated in fish cell lines.

The use of a shoal analysis and patch estimation system (SHAPES) to analyse hydro-acoustic data is discussed. SHAPES was used to detect and characterise sardine schools from four echo integration surveys off the coast of South Africa. Methods of school detection and characterisation, assumptions made and corrections applied to school variables are presented. Measurements of school morphology and internal school features are discussed and compared to other relevant works. Significant relationships were established, both between measures of school morphology and internal density structure. Several variables showed significant differences between surveys. Composite factors derived from principle component analyses showed that morphological variables are the most important school descriptors. No differences in the loading of composite factors between surveys are evident. This suggests an inherent spatial and temporal stability in sardine school characteristics. This fact may prove beneficial for comparisons of school structure between co-occurring fish species and possibly aid fish school identification in the future.