Ammonium and nitrite oxidizing bacteria were enriched in separate cultures using a primary inoculum of water from an enclosed shrimp rearing facility. Each enrichment was continued by transfer to increasing volumes of medium up to 151. Seventy four strains of heterotrophic bacteria were isolated; seventeen from each primary inoculum, and twenty from each of the 151 enrichments at the time when all the ammonium or nitrite had been utilized. All the isolates, described by 101 characters, were subjected to numerical taxonomy. During the enrichment for ammonium oxidizers, astrong selective pressure led to the disappearance of some strains, mostly enterobacteria. Two taxonomic groups composed of pseudomonads and asporogenous Gram positive rods were associated with the ammonium oxidizers. The population was characterized by an inability to use amino acids as carbon and energy sources. In contrast, the strains associated with nitrite oxidizers were able to use all the carbon and energy sources tested. Many of these strains were Gram positive, asporogenous aerobic rods, others were Gram negative pseudomonads.

A protocol for the extraction of genomic DNA from teleost fish was developed and produced high molecular weight DNA from English sole, white sucker and rainbow trout. A protocol for polymerase chain reaction (PCR) of tumour suppressor gene p53 from rainbow trout genomic DNA was developed. Several primers were chosen inside exon 5 and 9 and exon 6 and 7. A successful PCR method yielded the conserved exon 5 to 9 region of genomic rainbow trout p53 in two fragments: fragment 1 comprising exons 5 and 6 and fragment 2 spanning the region of exons 7 to 9. The apparent molecular weight of fragments 1 and 2 were 510 and 760 base pairs respectively. The sequences of both fragments including the introns were determined and gave 515 and 793 bp for the two PCR fragments. These sequences will facilitate examination of tumour suppressor gene p53 conserved exons from genomic DNA e.g. for study of p53 mutations in fish.

In order to manage the fish stock of the Senegal coastal zone it is necessary to carry out direct assessment surveys by acoustic methods. Acoustic surveys were carried out in this region from a sports-fishing boat, using a split-beam echo sounder in vertical mode, in areas with depth less than 15 m. On a short time scale, spatial structure of the fish population remained stable. The average acoustic biomass detected was variable, but we observed a relative stability of target strength distribution of single fish. The use of acoustic methods in these areas of shallow depths, the consequences of escape behaviour of the fish, and sampling strategies are discussed.

The broad-scale effects of salmon farming on benthic and epibenthic macrofaunalcommunities of four Scottish sea lochs (Kishorn, Duich, Hourn and Nevis) with differentaquaculture loadings were investigated based on the first benthic surveys to be undertakenin these lochs. Significant variation in the benthic communities was identified betweenlochs, mainly related to differences in the abundance of echinoderms and polychaetes (thedominant components of the benthic communities). Variance partitioning using partialredundancy analysis suggested that approximately 9.6% of this variation could be relatedto aquaculture activity in the lochs (as expressed through “production” and previouslymodelled “impact” levels), as compared to 20.6% attributable to measured environmentalfactors. Epibenthic communities were dominated by echinoderms and arthropods and there wasno significant between-loch variation in epibenthic community composition. No significantdifferences were apparent in the benthic or epibenthic community assemblages betweensamples taken within 2000 m of a fish farm and those taken beyond this distance. Ingeneral, our results support previous studies suggesting a spatially limited impact ofsalmon culture installations on the benthos, although impacts on the aquatic food web on awide spatial scale cannot be ruled out and the link between benthic community variationand aquaculture variables identified through variance partitioning requires furtherinvestigation.

Cette étude s'appuie sur l'utilisation successive de plusieurs méthodes d'analyses multivariées pour réaliser une typologie de la flottille chalutière du port de Sète, principal port de pêche français de la Méditerranée. Les unités de pêche étudiées sont représentées à l'aide d'un profil annuel de la composition spécifique de leurs débarquements. Cinq stratégies de pêche ont ainsi pu être identifiées. La mise en œuvre d'une méthode de segmentation permet une caractérisation formelle de ces différentes stratégies à l'aide d'objets symboliques. Les stratégies sont étudiées en référence à plusieurs caractéristiques générales couramment utilisées en gestion des flottilles de pêche (puissance, longueur, âge du bateau, etc.). L'analyse typologique mise en œuvre au cours de l'étude permet de caractériser nettement deux grandes logiques d'exploitation, l'une orientée vers la recherche d'un très petit nombre d'espèces (Engraulis encrasicolus, Sardina pilchardus), l'autre déterminée par une grande diversité des captures. Elle permet également d'apprécier comment les captures d'espèces peu représentées dans certaines stratégies peuvent contribuer significativement à l'exploitation d'une ressource.

Determining age is an important step when assessing growth, mortality, and yield ofcultivated and wild populations, but studies linking shell growth marks in the pearloyster Pteria sterna with the age of individuals are lacking. Thirtyjuveniles (20.0 ± 1.2 mm shell height), collected from a winter spatfall, were marked withthe fluorochrome calcein and kept in the field in culture containers. After day 16, thejuveniles were cleaned and their shells cut along the sagittal axis to determineperiodicity of micro growth bands formed in the inner shell layers and to estimate age.During this trial, fluorescent calcein marking succeeded in individuals larger than 20 mmshell height; these formed an average of 15 micro growth bands over the 16 days,representing 1 band per day. The marker created a wide fluorescent band containing threemicro growth marks, suggesting that calcein was incorporated into the shell over the firstthree days. The use of calcein was found to be an accurate method for validating the microgrowth band frequency of formation in P. sterna juveniles, which in turncan help to estimate age.

A parameter of a model becomes a decision support indicator if it is used as an argument of a decision function. This implies consideration of a wider model than the initial one and to acknowledge its complexity. It is also necessary to include the estimation of parameters in indication theory and to consider a data driven approach. Data analysis leads us to provide sets of indicators. With reference to the statistical concept of sufficiency (Fisher 1925), such a set may also be considered as a set for indication, equivalent to the original data for any subsequent purpose of indication. From the same data set, several models may be built providing different sets for indication. None of them can be considered as the best; this depends both on the context (e.g. fishing practices) and on the addressed questions. No model must be chosen to the exclusion of alternatives: an illustration is given with models in relation to a catch-effort data set, with a case study on Senegalese small scale fisheries.

Tropical shrimp fisheries are characterized by various interactions with their natural environment and with other fisheries. These latter interactions can be explained by the high quantity of bycatch taken by industrial trawler fleets, which has a significant impact on fish populations associated with shrimps and thus also on finfish fisheries. Bycatch also includes emblematic species, which are subject to strict conservation measures decided by the international community. It seems important to identify and assess the biological and economic consequences of different mitigation measures (increase of mesh size, turtle excluder devices and bycatch reducing devices). This communication is based on case studies undertaken on the Indian white prawn (Fenneropenaeus indicus) and speckled shrimp (Metapenaeus monoceros) fisheries in Madagascar and on the brown shrimp (Farfantepenaeus subtilis) and pink spotted shrimp (Farfantepenaeus brasiliensis) fishery in French Guiana. A review of the impacts of these fisheries on resources and ecosystems is made and some results of experiments on mitigation devices given. Finally, the results of simulations obtained using a multi-species, multi-fleet, age-structured bioeconomic model, including modifications of catchability and costs related to the adoption of these devices, is presented and discussed.

Dans les régions tropicales coralliennes, on a parfois recours au potentiel de production halieutique par unité de surface là où les méthodes classiques d'évaluation s'appliquent difficilement. Dans la région caraïbe, de nombreuses estimations de production halieutique relative, tant potentielle que réelle, sont disponibles sans qu'il soit toujours possible de les comparer de façon rigoureuse. En Martinique, les pêcheries côtières ont produit en 1987 en moyenne 1,14 t.km−2.an−1 d'espèces démersales, avec des productions par strate comprises entre 0,24 et 8,45 t.km−2.an−1. La production relative moyenne pour les espèces néritiques est de 1,68 t.km−2.an−1. La comparaison des productions relatives observées d'un secteur ou d'une ile à l'autre est susceptible de contribuer de façon importante à l'évaluation de l'état d'exploitation des ressources, à condition que les méthodologies d'estimation soient explicitées et qu'une connaissance suffisante de l'effort de pêche et du contexte écologique soit disponible.

Des paramètres de la reproduction d'une population isolée du tilapia Sarotherodon melanotheron ont été étudiés durant 2 années consécutives et comparés avec les données de la littérature obtenues sur des populations vivant dans son milieu naturel. Le sexe-ratio (année 1 : 1:2,69; année 2 : 1:1,96) en faveur des femelles varie de façon saisonnière. Les mâles atteignent la maturitésexuelle plus rapidement (année 1 : 129 mm LS ; année 2 : 126 mm LS) queles femelles (année 1 : 135 mm ; année 2 : 136 mm LS). Le cycle dematuration des gonades est continu. Ces résultats sont dans l'ensemblesemblables à ceux obtenus dans le milieu naturel de l'espèce. Cependant,une fécondité inférieure et un diamètre ovocytaire plus grandsont notés dans le lac d'Ayamé. Le facteur de condition moyen despopulations du lac, intermédiaire entre des valeurs observées dans lesmilieux lagunaires, indique une bonne adaptation de l'espèce aux conditionsd'eau douce du lac.

Hatchlings of clown loach (3.8 mm in total length, TL) are pelagic. When reared at 26−28 °C, they become benthic 3 days after hatching (dah), when their swim bladder is inflated. The fin development sequence (pectorals  <  caudal  <  dorsal  =  anal  <  pelvic) is typical of the clade Ostariophysi. All fins and finrays are fully elongated at 20 mm TL, but the finfold persists until 25 − 26 mm TL (start of juvenile stage). Melanophores appear at 3 dah, they form a 5-bar pattern at 5 dah, then two bars (III and V) vanish progressively, producing at 26 mm TL the 3-bar pattern that is typical of adults. Throughout the ontogeny, the pigment pattern exhibits a structural regularity (bars spaced at regular intervals), which is interpreted in a functional perspective by reference to the maintaining of crypsis and signalling throughout. Exogenous feeding commences at 4 dah (5.5 mm TL). Food intake (FI) increases rapidly, from 6% wet body mass (WM) at 5.5 mm TL to  >20% WM in fish  > 7 mm TL. Gut evacuation rate (Rg) increases with increasing meal size and fish size, as a result of gut coiling (from 8 to 15 mm TL), and is highest at 11 mm TL (about 10% WM h-1 in fish feeding maximally). The allometric increase of FI and Rg during the early larval stages is accompanied by increasing capacities for growth, so early sizes differences amplify rapidly during the ontogeny. Nevertheless, growth remains slow (mean of 0.4 mm TL day-1 from 4 to 29 dah; 0.9 mm TL day-1 for top growers). By contrast, unfed fish display long resistance to starvation (until 14−15 dah). The combination of slow growth and long resistance to starvation is discussed in respect to the reproductive phenology of the species, as the capacity of making metabolic economies prevails over fast growth for seasonal strategists spawning mainly at the start of the rainy season.

Split-beam hydroacoustic techniques have been used to enumerate adult Atlantic salmon (Salmo salar) passage on the River Wye since 1994. Aggregations of aquatic macrophytes, principally Ranunculus fluitans, are seasonally present at the monitoring site. At high densities, these macrophytes return target strength (TS) values similar to those of adult salmon. Target direction-of-movement information readily resolves upstream-migrant salmon from static- or downstream-traveling macrophytes. However, Atlantic salmon are iteroparous, and downstream-migrant kelts must be factored into the acoustic estimates. Net upstream target movement and/or TS were not reliable indicators of salmon passage at the River Wye site when aquatic macrophyte aggregations were present. In 1995, a subset of data (n = 71) was selected from the ongoing monitoring program to determine the feasibility of resolving salmon from macrophytes using acoustic parameters other than target direction-of-movement or mean TS. Individual targets were visually identified as either salmon or macrophytes based on concurrent video records. Distributions of available acoustic parameters were statistically compared between the two target-types using a two-tailed t-test assuming equal variance (P = 0.05). Available acoustic parameters included echo position, pulse width (at –6, –12, and –18 dB power points), amplitude, beam pattern factor and target strength. Pulse width standard deviation (PWSD) measurements were determined to be the most effective individual parameters for discriminating macrophytes from salmon. Based on PWSD at the –6 dB echo power points, 77% of all macrophyte targets were removed from the mixed data set. Multiple selection criteria increased total target discrimination. Applying a combination of –6 and –12 dB PWSD, and Y–axis target slope criteria rejected 94% of all macrophytes, retaining all salmon targets.

Crassostrea gigas larvae were collected in the bay of Arcachon in July 1985, 1986 and 1987. Larval samples were collected daily at high tide, during at least the first 12 days of pelagic life and every hour during 1 day and night cycle, 6 days after spawning. Epifluorescence microscopy was used for detecting ingestion and digestion of nanoplankton and thin sections were made to try to determine the algal species ingested. The first algal uptake occurred 48 hours after fertilization. and different stages or digestion were noted from the 3rd day. No relationship between ingestion or digestion and the age of the veligers was observed. There was no difference in the feeding activity during day and night. Because the nutrition index was high (70%) the feeding behaviour of the larvae was apparently normal. Nevertheless the intensity of algal uptake was weak. The presence of diatoms in the digestivetract suggests that the Bacillariophyceae play a significant role in the nutrition of veligers in nature.

Jusqu'aux années 1970, qui marque l'abandon de cette activité, la pêche estivale de la sardine (Sardina pilchardus, Walbaum) dans le golfe de Gascogne connaissait de fortes variations de rendement à l'échelle de quelques jours. Ces fluctuations affectent différemment chacun des secteurs de pêche soit les baies de Douarnenez, Audierne et Concarneau à la pointe sud-ouest de la Bretagne, ou les zones de Belle-Ile, Quiberon, Le Croisic et les ports des Sables d'Olonne et de Saint Gilles-Croix-de-Vie dans la partie centrale du golfe de Gascogne. A l'échelle de 2 à 4 jours, le vent induit des variations hydrologique et courantologique différentes suivant ces lieux géographiques. En chacune de ces zones de pêche, exceptée celle d'Audierne, des relations significatives ont été obtenues à partir du calcul de régression entre les prises par unité d'effort ou PUE et des composantes de vent spécifiques ou un index conjuguant l'amplitude de la marée et la vitesse du vent. Toutes ces relations présentent le même profil; les PUE augmentent avec la vitesse du vent jusqu'à un optimum pour 5 à 6 m.s−1; au-dessus de ce seuil, les rendements décroissent en fonction du renforcement du vent jusqu'à ce qu'il y ait arrêt de la pêche. Cette valeur de 5 à 6 m.s−1 correspond également à un optimum pour la stabilité verticale de la couche d'eau superficielle et pour le développement phytoplanctonique. Le mélange turbulent induit dans la colonne d'eau par le vent fort détruit les structures physiques et limite le développement de la biomasse phytoplanctonique; au contraire, l'absence de brassage, par vent faible, dans des conditions estivales d'ensoleillement renforce les gradients thermiques de la mer et restreint le renouvellement de la couche euphotique en sels nutritifs. Ces facteurs limitants peuvent expliquer la non-linéarité des relations pêche/vent. La spécificité locale de ces relations pour une composante particulière du vent est en accord avec les variations des structures thermiques horizontales et verticales induites par la circulation résiduelle. Les fluctuations du vent en vitesse et en direction expliquent 44 à 76 % de la variabilité des captures de sardines à l'échelle de quelques jours. L'indice composé de l'amplitude de la marée et de la vitesse du vent intervient pour 25 à 38 % de cette variabilité pour les zones de Douarnenez et de Quiberon. L'importance de ces facteurs pourrait résulter de la forte sensibilité de la sardine aux variations environnementales et met en évidence l'amplitude de la variabilité d'abondance des captures due à des facteurs non prévisibles.

Information about the spatial distribution of bycatch species and their spatial overlap with the target species is essential for fisheries management. The present study used fishery-dependent data (vessel monitoring systems, logbooks and official daily landings) to study the spatial distribution and overlap between black scabbardfish Aphanopus carbo and leafscale gulper shark Centrophorus squamosus taken by the longline fishery operating off mainland Portugal. The geostatistical method kriging was applied to estimate the distribution of the leafscale gulper shark in relation to black scabbardfish and thus assess the impact of the fishery on the leafscale gulper shark. Results indicate that in fishing grounds where the black scabbardfish is more abundant, the relative occurrence of deepwater sharks is reduced. These findings have implications for alternative management measures to be adopted in this particular fishery, particularly where it concerns the minimization of deepwater shark bycatch.

Myxozoans are metazoan parasites which are highly pathogenic in commercially importantfish, particularly in aquaculture. Enteromyxosis is an economically significant diseasecaused by the myxosporean parasite Enteromyxum leei.Presently, early diagnosis of enteromyxosis in sharpsnout seabream was achieved bymonitoring fish on a time-scale scheduled basis in combination with a validated moleculardiagnostic technique. Two different successive fish batches of a commercial fish farm weremonitored starting from the first month of on-growing in sea cages until fish reachedcommercial size. Fish weight and water temperature differentially ranged between them.E. leei detection was performed both by classical microscopicobservation of fresh smears and by quantitative polymerase chain reaction (qPCR) whileprevalence, mean intensity and mortality rate were calculated. In total, 520 fish werescreened; 320 from the first batch and 200 from the second one. Parasitosis illustrated aseasonal occurrence pattern (spring and summer). When qPCR was used as a diagnosticmethod, enteromyxosis was diagnosed earlier with more increased prevalence compared to themicroscopic observation. In this case, the parasite was detected at the lowest watertemperature that has ever been recorded (14.7 °C), during the first month of on-growing in sea cages. The two-factorcombination of water temperature and fish weight proved to be the most significant factorthat could determine the emergence and development of parasitosis and smaller fish provedto be more susceptible. Mortality was influenced by both prevalence and intensity ofparasitosis. An earlier diagnosis and identification of all developmental stages of theparasite throughout its life cycle was verified with qPCR, significantly before anyoutbreak occurred. The latter could become a key diagnostic tool for the control ofenteromyxosis, allowing stakeholders and fish farmers to adopt all necessary precautionarymeasures minimizing economic loss in sharpsnout seabream intensive farming.

Simulation of fisheries systems is a widely used approach that integrates monitoring and assessment tools. We applied the ALADYM (age-length based dynamic model) simulation model to three different studies aimed at investigating correlations between pressure and population metrics, exploring the viability of different mortality levels in long-term scenarios and predicting the effects of combined management measures. Uncertainty was incorporated into the simulations following the Monte Carlo paradigm. Three stocks were used for these exercises: red mullet in the central-southern Tyrrhenian Sea and European hake in both the Bay of Biscay and the Aegean Sea. The analysis of the relationships between total mortality and indicators highlighted significant pairwise negative correlations for red mullet. These signals of decline were supported by the spawning potential ratio indicator (mean exploited to mean unexploited spawning-stock biomass ESSB/USSB), which was low compared to target levels. It only remained within safe bounds (>0.2; probability: 0.90–0.95) at total mortality levels lower than 1.6. The simulation results for European hake in the Bay of Biscay showed that a sustainable exploitation rate might range from 0.87 to 1.04. The benefits of combined management measures were demonstrated for European hake in the Aegean Sea, and with a further dataset on the Eastern cod stock in the Baltic Sea.

Une analyse des correspondances multiples et une classification ascendante hiérarchique ont été utilisées pour étudier les variations de rendements par espèce entre 1972 et 1989 de navires de la pêche chalutière hauturière française. L'application de ces méthodes permet de mettre en évidence les relations parfois complexes qui lient les rendements des principales espèces débarquées au sein des rendements totaux et de dégager une partition des profils de rendements caractéristique de cette période. Les facteurs comme l'année et les secteurs de pêche sont ceux qui expliquent le mieux les variations observées; les variations saisonnières jouent un rôle secondaire. Les rendements augmentent et se diversifient entre 1972 et 1989. L'étude montre que ces évolutions peuvent être reliées pour une part à des changements dans les stratégies d'allocation d'effort de pêche et dans la composition des flottilles. Les chalutiers qui exploitaient traditionnellement le golfe de Gascogne au début des annéessoixante-dix ont reporté leur effort sur des secteurs situés plus au nord (nord de l'Irlande et ouest de l'Ecosse) et ont été remplacés par des chalutiers de taille et de puissance plus importantes. Dans les années quatre-vingt, une autre composante fait son apparition. Elle est constituée par des chalutiers de taille plus réduite qui exploitent des secteurs plus côtiers que les précédents.

Melicertus kerathurus represents an economically important resource for fisheries and aquaculture. Seven microsatellite loci from 373 specimens of M. kerathurus collected in different parts of the Mediterranean and NE Atlantic were identified. Four of these microsatellites showed a moderate level of polymorphism, with 2 to 14 alleles per locus, whereas three had a monomorphic profile. Observed and expected heterozygosity ranged between 0.28 to0.64 and 0.28 to 0.65, respectively. Three microsatellite loci deviated from Hardy-Weinberg equilibrium in some populations, with a deficit of heterozygosity. Mean Fst values showed significant differentiation among sample sites analysed and indicate that these loci are useful for the study of genetic variation in this species. These results may supply functional information on the population genetic structure of Melicertus kerathurus, valuable for future sustainable management strategies.

The commercial culture of several important species of fish has long been associated with productivity problems generally attributable to fertilisation rates, hatching rates, and embryonic development. Our present knowledge of the molecular processes accompanying fertilisation in fish is scant at best. Here, we examine how new findings about the molecular mechanisms underlying reproduction in other animal groups may help advance our understanding of how egg activation takes place in fish. A better understanding of egg activation in fish is likely to make a highly valuable contribution to future growth of the aquaculture industry.