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Les pêcheries de thonidés représentent 7.9% de la production mondiale de produits de la mer. La plupart des stocks de thons sont pleinement exploités, et certains surexploités, et tous font face à une pression de pêche croissante. En raison de l'extension des zones de pêche, les évaluations des stocks dépendent en grande partie des captures commerciales. Toutefois, les données commerciales peuvent varier au cours du temps étant donné que les pêcheurs peuvent investir dans des engins de pêche et de l'équipement, s'établir au large des côtes, ou commencer à pêcher dans de nouvelles zones. Peu d'attention a été portée à la réponse des pêcheurs aux mesures de gestion ou aux conséquences de l'investissement technologique. L'objectif de la présente thèse est d'étudier les effets de stratégies de pêche et les réponses adaptatives des flottes de senneurs sur les thons tropicaux et la faune associée dans l'Océan Atlantic Est et dans l'Océan Pacifique Est. Dans un premier temps, nous montrons comment l'introduction de nouvelles technologies a eu un effet direct en augmentant la puissance de pêche, et un effet indirect en entraînant une modification des zones pêche. Nous étudions les effets de deux fermetures spatio-temporelles sur la dynamique de la flotte de senneurs européens. La première mesure de gestion a diminué les jours où des captures sont réalisées, les carrés avec capture à l'intérieur de la zone partiellement fermée, tandis que la pêche sur DCP a été redistribuée à l'extérieur de la zone et aucun changement n'a pas été enregistré pour la pêche sur banc libre. La seconde fermeture de pêche a entraîné une augmentation de toutes les activités de pêche en dehors de la zone. Dans l'Océan Pacifique Est, la flotte de senneurs mexicains a réagit à la fermeture d'une saison de pêche en diminuant le nombre de jours passés à quai. Par conséquent, le nombre de calées sur bancs associés aux dauphins a augmenté, et les niveaux de capture observés avant la mesure de gestion ont été maintenues. Nous analysons les effets des stratégies de senneurs de l'Union Européenne sur les prises accessoires. Nous mettons en évidence que la composition des espèces de requins capturés sous DCP et les raies capturées sur bancs libres ont changé au cours du temps. Nous estimons également que plusieurs types d'espèces peuvent être capturés par mode de pêche. / Tuna and tuna-like fisheries represent 7.9% of the global production of marine capture fisheries. Most tuna stocks are fully exploited and some overexploited, facing growing fishing pressures. Due to the extent of fishing grounds, stock assessments depend largely in commercial data, which vary over time because fishermen may invest in fishing technology, expand offshore, or start fishing in different areas. However, little attention has received the responses of fishermen facing management regulations or the effects resulting from technological investment. For these reasons the aim of this study was to investigate the effects of fishing strategies developed by purse seine fleets on tropical tunas and on associated fauna in the eastern Atlantic and eastern Pacific oceans. The continuous introduction of new fishing technology in the French fleet in the 1980s and the 1990s evidenced a direct increase in fishing power when large yellowfin in free-swimming school is targeted and likely an indirect effect by modifying the fishing grounds characterizing FAD-fishing on small size categories. The consequences of the two time-area closures on the spatio-temporal dynamics of the European Union fleet were investigated. The regulation on FADs resulted in a decrease in the days with catch and successful squares inside the restricted area, reallocating FAD-fishing outside the area while no change in free-swimming school fishing was observed. The no-take time-area increased all fishing activities outside the restricted area with apparently no gain in terms of protection of juveniles. In the eastern Pacific as a response to a closed season the Mexican fleet reduced days in port and consequently the number of sets on dolphin-associated schools increased, maintaining the catch levels observed before the regulation. The study of the effects of the EU fleet fishing strategies on bycatch over two time periods showed that the species composition of sharks caught on FADs and may be for rays caught on free-swimming schools changed over time. We also estimated the total number of species that can be potentially be caught by fishing mode.

Once so abundant as to be called the ‘common’ angelshark, Squatina squatina has been extirpated from nearly the entirety of its historical range, from the eastern North Atlantic, to the Mediterranean Sea [International Union for the Conservation of Nature (IUCN) Red List: Critically Endangered]. The angelshark now only occurs in any abundance in the waters surrounding the Canary Islands. I present the first genetic assessment of the angelshark’s population dynamics and diversity from three locations within the Canary Islands archipelago: Gran Canaria, Tenerife, and Lanzarote. Using a suite of individual mitochondrial genome regions [Control region (CR), NADH dehydrogenase subunit 2 (ND2), NADH dehydrogenase subunit 4 (ND4), and Cytochrome c oxidase subunit 1 (COI)], the complete mitogenome, and nuclear markers [microsatellites and Internal Transcribed Spacer 2 (ITS2)] this work aimed to i) assess the genetic diversity of the angelshark in comparison to other endangered or historically overfished elasmobranchs, ii) examine the relative nucleotide variability across different marker sets, and iii) assess fine-scale multi-locus population structure within the Canary Islands, as well as broad-scale population genetic structure of angelsharks throughout its historic Eastern Atlantic and Mediterranean range. Results revealed exceptionally low genetic diversity across all individual mitochondrial regions sequenced (CR, π % = 0.0046 ± 0.016; ND2, π % = 0; ND4, π % = 0; COI, π % = 0), yielding some of the lowest values reported to date in any elasmobranch. Mitogenome analysis followed this low diversity trend with only 11 single nucleotide polymorphisms seen across all Canary Island individuals in a genome of 16,689 bp (π % = 0.0257 ± 0.0166). Furthermore, screening of 35 microsatellite markers across 34 individuals revealed all but two loci to be monomorphic and nuclear ITS2 showed negligible diversity. Lanzarote showed significant population differentiation from both Gran Canaria (ΦST = 0.073, p = 0.004, FST = 0.113, p = 0.00) and Tenerife (ΦST = 0.029, p = 0.001, FST = 0.065, p = 0.001) at the CR. Haplotype analysis of whole mitogenomes also demonstrated Lanzarote individuals forming a separate lineage from angelsharks at the other two islands. Broad- scale structure across the angelshark’s historical range was detected between the Canary Islands and Mediterranean (ΦST = 0.792, p = 0.000, FST = 0.785, p = 0.000), indicating a regional break between populations. The exceptionally low levels of genetic diversity in angelsharks in the Canary Islands, as well as indications of population isolation from the rest of the angelshark’s historical range, suggest an immediate need for strong conservation measures to ensure the protection and continued persistence of this highly vulnerable and ecologically unique species.

Vibrio cholerae é uma bactéria autóctone do ambiente aquático e pode causar sérios riscos à saúde quando cepas patogênicas são acidentalmente consumidas. V. cholerae se encontra associada aos copépodes em concentrações que podem alcançar mais de 1000 vezes a densidade das bactérias livres na água. Se ingerido, um único copépode pode conter a dose mínima de bactérias necessária para a manifestação da doença. Verificar a presença e a distribuição dos sorogrupos O1 e O139 no complexo estuarino de Santos-Bertioga e plataforma continental adjacente em associação com o zooplâncton e seus distintos grupos taxonômicos foi o objetivo desse trabalho. O zooplâncton (>330 µm) foi coletado e a detecção dos sorogrupos O1 e O139 realizada nas amostras totais e nos táxons mais abundantes através das técnicas DVC-DFA e DFA (Contagem direta de bactérias viáveis e ensaio de imunofluorescência direta). Amostras fixadas em formol foram maceradas e preservadas numa solução tampão estéril, previamente aos experimentos. Para o DVC-DFA, animais vivos foram selecionados, lavados, macerados e uma alíquota transferida para meio de cultura. A presença da bactéria no zooplâncton foi correlacionada a parâmetros abióticos e bióticos. O sorogrupo O1 foi detectado em 88% e O139 em 77% das amostras de plâncton no complexo estuarino de Santos-Bertioga, valores mais altos do que os publicados na literatura mundial para outros estuários. Para a plataforma, a presença dos sorogrupos foi menor devido à salinidade mais elevada. Foram testados isoladamente 43 táxons, pertencentes a 9 filos. Dados inéditos da associação entre Vibrio cholerae e quetognatos, estágios larvas de equinodermos, urocordados e ovos de peixes foram registrados. Este trabalho sugere a existência de um gradiente costa-oceano para V. cholerae aderido ao zooplâncton de águas costeiras e ampla capacidade de V. cholerae O1 e O139 em aderir a diversos táxons do zooplâncton marinho. / Vibrio cholerae is an autochthonous bacterium in the sea and may cause serious health problems when pathogenic strains are accidentally ingested. V. cholerae are found associated with copepods in concentrations up to a thousand times higher than the free bacteria in the water. If ingested, a single copepod may have enough bacteria necessary for human infection. The objective of this study was to verify the presence and distribution of Vibrio cholerae O1 and O139 serogroups over Santos-Bertioga estuarine complex and adjacent continental shelf in association with zooplankton and over its distinct taxa. Zooplankton (>330 µm) sampling was carried out and detection of V. cholerae O1 and O139 assessed in whole samples and on most abundant taxa by the DFA and DVC-DFA (Direct Viable Count and Direct Fluorescence Assay) methods. Briefly, formalin-fixed samples were grinded and preserved in a sterilized buffer solution previously to the experiments. Live animals were selected, washed and grinded and an aliquot transferred to culture media for the DVC-DFA assay. Presence of these bacteria on zooplankton was correlated with physical and biological parameters of the seawater. Serogroup O1 was found on 88% while O139 on 77% of the samples from Santos-Bertioga estuarine complex, values higher than the ones found in other estuaries in global literature. For the adjacent shelf, detection was smaller due to higher salinity. 43 taxa, belonging from 9 phyla were individually tested. Inedited data from the association of V. cholerae and chaetognaths, Urochordata, larval stages of Polychaeta, Echinodermata, and fish eggs were documented. This study suggests the existence of an inshore-offshore gradient in V. cholerae attached to zooplankton from coastal waters and the high ability of V. cholerae O1 and O139 to adhere on diverse marine zooplanktonic taxa.

Vibrio cholerae é uma bactéria autóctone do ambiente aquático e pode causar sérios riscos à saúde quando cepas patogênicas são acidentalmente consumidas. V. cholerae se encontra associada aos copépodes em concentrações que podem alcançar mais de 1000 vezes a densidade das bactérias livres na água. Se ingerido, um único copépode pode conter a dose mínima de bactérias necessária para a manifestação da doença. Verificar a presença e a distribuição dos sorogrupos O1 e O139 no complexo estuarino de Santos-Bertioga e plataforma continental adjacente em associação com o zooplâncton e seus distintos grupos taxonômicos foi o objetivo desse trabalho. O zooplâncton (>330 µm) foi coletado e a detecção dos sorogrupos O1 e O139 realizada nas amostras totais e nos táxons mais abundantes através das técnicas DVC-DFA e DFA (Contagem direta de bactérias viáveis e ensaio de imunofluorescência direta). Amostras fixadas em formol foram maceradas e preservadas numa solução tampão estéril, previamente aos experimentos. Para o DVC-DFA, animais vivos foram selecionados, lavados, macerados e uma alíquota transferida para meio de cultura. A presença da bactéria no zooplâncton foi correlacionada a parâmetros abióticos e bióticos. O sorogrupo O1 foi detectado em 88% e O139 em 77% das amostras de plâncton no complexo estuarino de Santos-Bertioga, valores mais altos do que os publicados na literatura mundial para outros estuários. Para a plataforma, a presença dos sorogrupos foi menor devido à salinidade mais elevada. Foram testados isoladamente 43 táxons, pertencentes a 9 filos. Dados inéditos da associação entre Vibrio cholerae e quetognatos, estágios larvas de equinodermos, urocordados e ovos de peixes foram registrados. Este trabalho sugere a existência de um gradiente costa-oceano para V. cholerae aderido ao zooplâncton de águas costeiras e ampla capacidade de V. cholerae O1 e O139 em aderir a diversos táxons do zooplâncton marinho. / Vibrio cholerae is an autochthonous bacterium in the sea and may cause serious health problems when pathogenic strains are accidentally ingested. V. cholerae are found associated with copepods in concentrations up to a thousand times higher than the free bacteria in the water. If ingested, a single copepod may have enough bacteria necessary for human infection. The objective of this study was to verify the presence and distribution of Vibrio cholerae O1 and O139 serogroups over Santos-Bertioga estuarine complex and adjacent continental shelf in association with zooplankton and over its distinct taxa. Zooplankton (>330 µm) sampling was carried out and detection of V. cholerae O1 and O139 assessed in whole samples and on most abundant taxa by the DFA and DVC-DFA (Direct Viable Count and Direct Fluorescence Assay) methods. Briefly, formalin-fixed samples were grinded and preserved in a sterilized buffer solution previously to the experiments. Live animals were selected, washed and grinded and an aliquot transferred to culture media for the DVC-DFA assay. Presence of these bacteria on zooplankton was correlated with physical and biological parameters of the seawater. Serogroup O1 was found on 88% while O139 on 77% of the samples from Santos-Bertioga estuarine complex, values higher than the ones found in other estuaries in global literature. For the adjacent shelf, detection was smaller due to higher salinity. 43 taxa, belonging from 9 phyla were individually tested. Inedited data from the association of V. cholerae and chaetognaths, Urochordata, larval stages of Polychaeta, Echinodermata, and fish eggs were documented. This study suggests the existence of an inshore-offshore gradient in V. cholerae attached to zooplankton from coastal waters and the high ability of V. cholerae O1 and O139 to adhere on diverse marine zooplanktonic taxa.

Contrairement au requin mako, l´évolution des débarquements de requins peau bleue en Atlantique nord-est a connu une augmentation durant les deux années 2012 et 2013. Les requins vendus à la criée sont majoritairement juvéniles, l´âge de maturité étant tardif chez les deux espèces. Les stratégies alimentaires du peau bleue et du mako ont été étudiées par des analyses des contenus stomacaux associés aux isotopes stables. Le large spectre de proies identifiées confirme le caractère généraliste et opportuniste de leur alimentation. Les résultats indiquent que les céphalopodes sont les proies principales du requin peau bleue et que les téléostéens, en particulier le balaou de l´Atlantique (Scomberesox saurus), sont les principales proies du requin mako. Leur place de prédateurs supérieurs dans l´écosystème marin pélagique a été confirmée par leur niveau trophique à partir, 1) des contenus stomacaux : 4,8 pour le requin bleue et à 5,0 pour le requin mako, et 2) des ratios isotopiques : 5,2 et 5,3 respectivement. Les signatures isotopiques ont montré certaines incohérences en terme de fractionnement entre les requins et leurs principales proies qui peuvent s´expliquer par le caractère opportuniste et migratoire des requins mais également par leur métabolisme. Les teneurs en mercure total (Hg) observées dans la chair consommée des requins peau bleue et requin mako sont, en moyenne, en dessous du seuil limite autorisé par l´Union Européenne (1 mg/kg de chair fraîche). Cependant, les grands individus accumulent des quantités élevées, les requins peau bleue de plus de 248 cm et les requins mako de plus de 178 cm s´avérant majoritairement impropres à la consommation. / Over the past two years, landings of mako have decreased and those of blue shark increased. The sharks landed in a fish market are mainly juvenile, the maturity age being late for both species. Feeding strategies were studied for blue shark and shortfin mako on the basis of stomach content and stable isotope analyses. The high number of identified prey species confirms these sharks’generalist and opportunistic diet. Results showed that cephalopods were the main prey for blue shark, while teleosts, especially Atlantic saury (Scomberesox saurus), were the main prey for shortfin mako. Their top-predator status in the marine pelagic ecosystem was confirmed by their estimated trophic levels from 1) stomach content analyses: 4.8 for blue shark and 5.0 for shortfin mako, and 2) stable isotope ratios: 5.2 and 5.3 respectively. The stable isotope ratios showed some incoherence in fractioning between sharks and their prey. This may be explained by their opportunistic diet and the migratory behaviour of shark, associated with their metabolism. The mercury mean level in the muscle of blue shark and shortfin mako was below the maximum limit allowed by the European Union (1mg/kg fresh meat). However, large sharks showed higher mercury levels. Shark meat was considered unfit for human consumption for blue shark bigger than 248 cm and for shortfin mako bigger than 178 cm. Some tests were undertaken under real longline fishing conditions to investigate ways to reduce shark catches. The results showed that electromagnetic waves were ineffective to reduce catches of blue shark.