Chronic anthropogenic disturbance has left many marine systems at risk of degrading into undesirable states. In many cases, ecosystem shifts are triggered by catastrophic disturbance events that are beyond the control of local management, such as coral bleaching or cyclones. Recognition of this risk has instigated what has been referred to as a new paradigm for marine stewardship; managing areas with the explicit goal of maintaining ecosystem resilience. Despite this, there has been little synthetic influence of resilience theory on marine conservation planning. This thesis focuses on how to make good decisions regarding the selection of marine protected areas (MPAs), in the face of catastrophic disturbance events and for the conservation of highly dynamic marine systems. Large-scale catastrophic events, although rare, lie generally beyond the control of local management and can prevent marine reserves from achieving biodiversity outcomes. In Chapter 2, I formulate a new conservation planning problem that aims to minimize the probability of missing marine conservation targets as result of catastrophic events. To illustrate this approach, I address the problem of minimizing the impact of large scale coral bleaching events on a reserve system for the Great Barrier Reef, Australia. By explicitly considering the threat of catastrophic bleaching as part of the reserve design problem, it was possible to substantially improve the likely persistence of coral reefs within reserve networks, for a negligible increase in reserve cost. The results also demonstrate that simply aiming to protect the reefs at lowest risk of catastrophic bleaching does not necessarily lead to the best conservation outcomes. It is thought that recovery of marine habitats from uncontrollable disturbance may be faster in marine reserves than in unprotected habitats. But which marine habitats should be protected, those areas at greatest risk or those at least risk? In Chapter 3, I define this problem mathematically for two alternate conservation objectives and determine under which conditions each of the different protection strategies are optimal. With regard to the risk of uncontrollable disturbance, the optimal protection strategy depends on both the conservation objective and the expected rate of habitat recovery inside and outside protected areas. I illustrate this decision making with an example of cyclone disturbance of coral reefs on Australia’s Great Barrier Reef. An adequate consideration of risk can indicate surprising routes to conservation success. The resilience of coral reef systems is closely linked to the presence of grazing herbivores. Although herbivore populations are generally protected through permanent static reserves, the benefits of protection are dynamic in both time and space. Periodically moving protection between reefs allows access to the greatest potential benefits of reservation and can help address social reluctance to permanently close areas. Using analytic methods to solve a theoretical case study, I demonstrate that periodically rotating protection around a reef system can lead to greater average reef resilience than under static protection, but only if the overall level of reservation is high enough or the rotation does not include all reefs in the system. The past ten years have seen increasing enthusiasm for MPAs as a tool for pelagic conservation. However, numerous criticisms have been levelled against the use of place-based management in such a dynamic environment. Evidence, tools and information to address these criticisms and establish the feasibility and relevance of pelagic MPAs are dispersed across the conservation, oceanography and fisheries management literature. In Chapter 5, I review this information and present a synthetic framework for systematic planning of pelagic MPAs. Although many of the lessons learned so far about MPA design in coastal systems can be transferred to pelagic systems, there are some fundamental differences and new challenges involved in the conservation of patchy and highly dynamic resources. These challenges are very much at the leading edge of new conservation science and are likely to stimulate solutions with impact far beyond the design of pelagic MPAs.

The combined methods of stomach content analysis and stable 15N and 13C isotope biochemistry analysis were used to investigate the trophic dynamics and feeding ecology of coastal pelagic fishes in the waters off southeastern Florida, USA. The coastal pelagic fish complex includes blackfin tuna Thunnus atlanticus, dolphinfish Coryphaena hippurus, king mackerel Scomberomorus cavalla, little tunny Euthynnus alletteratus, skipjack tuna Katsuwonus pelamis, and wahoo Acanthocybium solandri. These coastal teleosts, particularly the tunas and wahoo, are primarily targeted by recreational anglers. However, there is a shortage of available trophic and diet composition data concerning these fishes of the coastal pelagic ecosystem. Stomach and muscle tissue samples were collected from the species of various lengths over a three-year period from March 2010 and March 2013. Across all six species, teleost fishes dominated the prey with an average 64.5% by occurrence, 63.7% by number, and 89.9% by weight. There were two dominant prey families: Clupeidae and Carangidae. Dolphinfish showed the lowest diet overlap among the six species, due to the highly diverse diet. The highest diet overlap occurred between king mackerel and little tunny. The mean δ15N ranged from 8.21 ‰ (wahoo) to 13.18 ‰ (king mackerel), and the mean δ13C ranged from -18.41 ‰ (king mackerel) to -16.70 ‰ (dolphinfish). Blackfin tuna exhibited the largest δ15N range (7.22 to 13.21 ‰), as well as the largest δ13C range (-19.13 to -12.99 ‰). The δ15N and δ13C signatures in the muscle tissue showed evidence of shifts to higher trophic levels with an increase in fish size and the formation of distinct trophic groups among the coastal pelagic predators. The δ13C also suggested an inshore-offshore spatial relationship among the coastal pelagic fish. The trophic dynamics and feeding ecology data generated by this study will provide valuable baseline data for the coastal pelagic complex and future ecosystem studies.

Animals living in marine sediments (the second largest habitat on earth) play a major role in global biogeochemical cycling. By feeding on organic matter from settled phytoplankton blooms they produce food for higher trophic levels and nutrients that can fuel primary production. In the Baltic Sea, anthropogenic stresses, such as eutrophication and introductions of invasive species, have altered phytoplankton dynamics and benthic communities. This thesis discusses the effects of different types of phytoplankton on the deposit-feeding community and the importance of benthic biodiversity for fate of the phytoplankton bloom-derived organic matter. Deposit-feeders survived and fed on settled cyanobacterial bloom material and in doing so accumulated the cyanobacterial toxin nodularin. Their growth after feeding on cyanobacteria was much slower than on a diet of spring bloom diatoms. The results show that settling blooms of cyanobacteria are used as food without obvious toxic effects, although they do not sustain rapid growth of the fauna. Since all tested species accumulated the cyanotoxin, negative effects higher up in the food web can not be ruled out. Both species composition and richness of deposit-feeding macrofauna influenced how much of the phytoplankton bloom material that was incorporated in fauna or retained in the sediment. The mechanism behind the positive effect of species richness was mainly niche differentiation among functionally different species, resulting in a more efficient utilization of resources at greater biodiversity. This was observed even after addition of an invasive polychaete species. Hence, species loss can be expected to affect benthic productivity negatively. In conclusion, efficiency in organic matter processing depends both on pelagic phytoplankton quality and benthic community composition and species richness. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: In press. Paper 5: Manuscript.</p>

La répétitivité de l’Eastern Mediterranean Transient et le changement climatique affecte les écosystèmes marins du Levantin. La compréhension des réponses du zooplancton à ces variations est donc d’une importance majeure pour les services écosystèmiques. Ce travail est le premier à étudier la variabilité saisonnière et interannuelle et les spectres de taille du zooplancton en relation avec l’environnement au point B2 (N34º14.856 ; E35º36.067, Liban Nord). Dans ce contexte, une série temporelle unique de 14 ans a été effectuée avec un filet de 52 µm et analysée à l’aide d’un système d’imagerie semi-automatique, le Zooscan, pour détecter un changement dans le système pélagique. Les résultats ont montré que la biomasse maximale du zooplancton a été couplée au bloom phytoplanctonique printanier. Alors qu’une abondance maximale de petits organismes a été observée en été suggérant une période de recrutement des organismes. Suite à l’EMT-like en 2005, la salinité a augmenté dans la zone d’étude et tout le bassin. L’abondance et la biomasse du zooplancton ont augmenté subitement, lié à une augmentation probable de la production du phytoplancton cependant masquée par un possible contrôle de type "top down". L’enrichissement de la couche de surface en nutriments anthropiques a mené à des périodes ponctuels plus ou moins productives. La structure en taille du zooplancton a varié en fonction des facteurs hydrologiques. L’analyse des pentes a présenté une variabilité interannuelle liée aux abondances du zooplancton. Tandis que les formes ont montré une domination des individus de grandes tailles en hiver et au printemps. Cette mesure automatique peut être utilisée comme proxy de changement dans l’écosystème pélagique. / The occurring of the cyclic Eastern Mediterranean Transient and the climatic change have effects on the Levantine marine ecosystem. Understanding the response of zooplankton to such variations is of importance for ecosystem services. This thesis represents a pioneer study in enlightening the seasonality and the interannuality, as well as the spectra size of the zooplankton at a fix point B2 (N34º14.856; E35º36.067, North Lebanon). In this context, a 14 years unique time-series was conducted by a 52 µm mesh size net and analyzed with a powerful synthetic index, the Zooscan to monitor changes in the pelagic system. The results found that the maximum zooplankton biomass was coupled to the phytoplankton spring bloom, whereas abundances increased in the summer possibly due to the recruitment. Following the EMT-like in 2005, the salinity increased in the study area and the whole basin. Zooplankton abundance and biomass increased abruptly possibly related to the enhanced primary production which is hidden by the "top down" control by zooplankton. Moreover, the nutrients enrichment of anthropogenic origin at the sea surface characterized the site by more or less productive occasional periods. The zooplankton size structure has also changed along the period depending on the hydrological factors. The spectral slope analysis showed an interannual variability according to the abundances. While the spectra shape analysis displayed a domination of big size individuals during winter and spring seasons. This automatic measurement highlighted the efficiency of detecting changes in zooplankton that can be related to broader ecosystem perturbation.

In 2010, the largest oil spill in U.S history occurred off the coast of Louisiana from April 20th to September 19th, when the well was declared officially sealed by the U.S Coast Guard, after releasing more than 4.4 million barrels of crude oil into the Gulf of Mexico (GOM) (McNutt et al., 2012). This spill was unique because it occurred in deep water approximately 1500 m below the ocean surface. Virtually nothing is known about the effects of oil spills on marine life in the deep sea, and there are limited data on mesopelagic and bathypelagic animals in the GOM before the Deepwater Horizon oil spill (DWHOS). The study presented here focuses on one of the most abundant and diverse groups of pelagic decapod crustaceans in the GOM – the family Oplophoridae and also includes one species from the family Pandalidae. Past studies on pelagic decapod crustaceans have been limited on both spatial and temporal scales. This study is unique because 1) it covers a large temporal range with data collected in 2011 and from 2015-2017, allowing for a more in-depth look at crustacean assemblage patterns, 2) it allows analysis of seasonality in reproduction, about which little is known for any deep-sea species, and 3) it assesses the potential effects of the Loop Current on species distribution and abundances, about which little is known. This information is important in understanding how the DWHOS may have affected the GOM ecosystem because pelagic decapod crustacean are intermediate components of the food web, and are in turn preyed upon by higher trophic levels. Unfortunately, there were little data on the mesopelagic ecosystem from this region before the spill, with the exception of a site in the eastern GOM (Standard Station, Hopkins et al., 1989; Hopkins et al., 1994). Therefore, these data, which incorporate samples taken one, five, six and seven years after the DWHOS, were analyzed with respect to year and season to determine if any trends were present. Results indicate that both biomass and abundance were significantly higher in 2011, than in subsequent years, indicating that the ecosystem has been declining since 2011. These two parameters were also lower in Loop Current water when compared to Common Water at all depths up to 1200 m, indicating that the Loop Current does have effects on deeper waters. The information obtained from this thesis will also act as a reference state for future studies in the GOM to monitor changes, or lack thereof, in the assemblage of deep-sea oplophorid and pandalid crustaceans.

La partie nord du Système du courant de Humboldt (NSCH) couvre moins de 0.1% de la surface océanique mondiale mais produit plus de poisons, en particulier d'anchois du Pérou (Engraulis ringens), par unité de surface que n'importe quelle autre région du monde. Bien que ce système produise suffisamment de macrozooplancton pour alimenter les populations de poisson fourrage, le manque d'informations sur ce compartiment limite nos capacités d'étude. L'objectif de cette thèse est d'étudier la dynamique de la distribution spatiotemporelle de la biomasse en macrozooplancton du NSCH en relation avec l'environnement physique et les poissons fourrage, à différentes échelles. Pour ce faire une méthode acoustique bi-fréquences a été développée et appliqué à des séries de données acoustiques historiques. Des informations à haute résolution ont ainsi pu être extraite sur la biomasse et les patrons de distribution du macrozooplancton, de la galathée pélagique 'munida', des poissons et des autres compartiments. Cette méthode nous a également permis d'estimer l'extension verticale de la communauté épipélagique (ZVEEC). Nous avons démontré que ZVEEC coïncide avec la limite supérieure de la zone de minimum d'oxygène (ZMO), ce qui permet de produire des donnés spatialisées à haute résolution de la limite supérieure de la ZMO et d'estimer le volume d'habitat de l'anchois. Notre estimation de biomasse en macrozooplancton, environ quatre fois supérieures aux estimations antérieures, est en accord avec les découvertes récentes sur l'écologie trophique des poissons fourrage du NSCH et fournit des éléments étayant les théories actuelles sur l'origine de la haute productivité en poissons du NSCH. L'étude des impacts des structures physiques de submeso- et mesoéchelle sur la distribution du macrozooplancton supporte l'hypothèse d'une structuration de type 'bottom-up'. Nous avons également mis en évidence l'impact de la structuration spatiale du macrozooplancton sur la distribution des poissons fourrage. Les données physiques et biologiques à haute résolution obtenues grâce à cette étude ouvrent de nouvelles perspectives pour réaliser des études écologiques intégrées à échelles multiples et pour calibrer les modèles biogéochimiques, trophiques ou End-to-End. / The Northern Humboldt Current system (NHCS) represents less than 0.1% of the world ocean surface but produces more fish, mainly Peruvian anchovy (Engraulis ringens), per unit area than any other region in the world. Although this system produces enough macrozooplankton to feed its high production of forage fish, the paucity of information on zooplankton hampers research in the system. The objective of this study was to investigate the multiscale dynamics of the spatiotemporal distribution of the macrozooplankton biomass off Peru in relation to the physical environment and their fish predators. For that a bi-frequency acoustic method was developed and applied to extract, from historical acoustic data, high-resolution information on the biomass and the patterns of distribution of macrozooplankton, the pelagic red squad 'munida', fish and other marine compartments. This method also allows estimating the vertical extension of this epipelagic community (ZVEEC). We demonstrated that ZVEEC coincide with the upper limit of the oxygen minimum zone (OMZ), which allowed both producing high-resolution spatial data of the upper limit of the OMZ and estimating the volume habitat of anchovy. The estimated macrozooplankton biomass was about four times higher than previously reported. This estimate is in agreement with the recent findings on forage fish trophic ecology and supports the current hypotheses explaining the NHCS high fish production. The study of the impacts of the submeso- and mesoscale physical structures on macrozooplankton provided evidence of the bottom-up physical effect on the distribution of macrozooplankton biomass. We also found further evidence of the structuring bottom-up effect that macrozooplankton exert on forage fish. The high-resolution biological and physical data obtained in this study opens new perspective to perform integrated multiscale ecological studies and to calibrate biogeochemical, trophic and End-to-End models.

Submitted by Silvana Teresinha Dornelles Studzinski (sstudzinski) on 2015-10-09T13:32:14Z No. of bitstreams: 1 LACINA MARIA FREITAS TEIXEIRA_.pdf: 1605999 bytes, checksum: 3291f09168d3ebd23eab03339dd4bd64 (MD5) / Made available in DSpace on 2015-10-09T13:32:14Z (GMT). No. of bitstreams: 1 LACINA MARIA FREITAS TEIXEIRA_.pdf: 1605999 bytes, checksum: 3291f09168d3ebd23eab03339dd4bd64 (MD5) Previous issue date: 2015-03-30 / Nenhuma / O fitoplâncton é formado por organismos bastante diversos, de origem polifilética, composto principalmente por seres unicelulares autótrofos, que não são capazes de vencer as correntes (FALKOVISK; RAVEN, 1997). A dinâmica, distribuição e estrutura das comunidades fitoplanctônicas podem ser explicadas por uma variedade de fatores bióticos e abióticos relacionados à heterogeneidade ambiental. O presente estudo teve por principal objetivo avaliar a influência da heterogeneidade espacial e da escala temporal na estrutura e dinâmica da comunidade fitoplanctônica em um lago raso subtropical (Lagoa Mangueira, RS). O estudo ocorreu na Lagoa Mangueira, (sul do Brasil), que é um ecossistema aquático raso (Zmax = 7 m), extenso (90 km de extensão, 3 – 10 km de largura), polimíctico quente, considerado oligo-mestrófico, sob influência direta de um banhado adjacente ao norte e tem suas margens amplamente habitadas por macrófitas aquáticas, especialmente ao sul. Amostragens foram realizadas na subsuperfície da água, trimestralmente, por dois anos, em 19 pontos, compreendendo as zonas pelágica e litoral e as regiões sul, centro e norte da lagoa, para análises abióticas e biológicas. Foram ainda efetuadas amostragens em curtos intervalos de tempo durante 60 dias nas zonas pelágica e litoral na região sul. A estrutura da comunidade fitoplanctônica foi analisada a partir de medidas de clorofila a, biomassa, riqueza, diversidade de espécies, espécies descritoras e diversidade funcional. Cyanobacteria (ex. Chroococcus limneticus, Aphanocapsa conferta, Aphanothece smithii, Planktolyngbya contorta) foi o grupo mais representativo independente da região (sul, centro ou norte) ou zonas (litoral ou pelágica). Observou-se um claro padrão espacial em direção ao norte da lagoa, que apresentou maiores valores de biomassa total e clorofila. Contudo, a riqueza e as espécies descritoras não demonstraram padrão espacial nítido. A Análise de Redundância (RDA) evidenciou a forte organização temporal das espécies em função do cenário abiótico, indicando que o alto grau de variabilidade temporal devido à hidrodinâmica local foi o principal fator direcionador da estrutura da comunidade fitoplanctônica na Lagoa Mangueira no período de estudo. Os resultados da análise da diversidade funcional demonstraram que não houve organização espacial considerando-se as formas de vida e a estrutura de tamanho da comunidade fitoplanctônica no período estudado, embora os grupos funcionais fitoplanctônicos tenham respondido à variação nos recursos, especialmente aumentando sua variedade e contribuição nos meses de primavera e verão, segregando o norte da lagoa, independente das zonas estudadas (pelágica e litoral). Em curta escala de tempo a comunidade fitoplanctônica da região pelágica se mostrou mais equitativa do que a região litoral ao longo do tempo. A contribuição das espécies Chroococcus limneticus, Aphanocapsa conferta e Aphanothece smithii a partir do 9° dia na região pelágica e praticamente todo o período estudado na região litoral indicam que embora tenha se verificado a variação da precipitação e vento ao longo do tempo, estados de equilíbrio da comunidade fitoplanctônica em ambientes fortemente condicionados pela hidrodinâmica podem ocorrer. / The phytoplankton is formed by very different organisms of polyphyletic origin, composed mainly by autotrophic unicellular beings who are not able to overcome the current (FALKOVISK; RAVEN, 1997). The dynamics, distribution and structure of phytoplankton communities can be explained by a variety of biotic and abiotic factors related to environmental heterogeneity. The principal objective of the present study was evaluate the influence of spatial heterogeneity and the temporal, on the structure and dynamics of phytoplankton in a subtropical shallow lake (Mangueira Lagoon, RS). The study took place in the Mangueira Lagoon (southern Brazil), which is a shallow aquatic ecosystem (Zmax = 7 m) long (90 km long, 3-10 km wide), continuous hot polymictic, considered oligo-mesotrophic, under the direct influence of an adjacent wetland on the north and has its margins inhabited largely by aquatic macrophytes, especially in the south. Samples were taken in the subsurface of the water, quarterly, for two years, in 19 sites, including the pelagic and coastal zones and the southern, central and northern regions of the lagoon, for abiotic and biological analysis. Samples were also collected in short time intervals during 60 days in the pelagic and coastal zones in the south region. The structure of the phytoplankton community was analyzed by measures of chlorophyll a, biomass, richness, diversity of species, descriptors species and functional diversity. Cyanobacteria (e.g., Chroococcus limneticus, Aphanocapsa conferta, Aphanothece smithii, Planktolyngbya contorta) was the most representative group independently of region (southern, central or north) or zones (coastal or pelagic). It was observed a clear spatial pattern to the north of the lagoon, which showed higher values of total biomass and chlorophyll. However, richness and descriptors species showed no clear spatial pattern. The Redundancy Analysis (RDA) showed strong temporal organization of the species as a function of the abiotic scenario, indicating that the high degree of temporal variability due to the local hydrodynamics was the main determining factor of the structure of phytoplankton community in the Mangueira Lagoon during the period of study. The results of the analysis of functional diversity showed that there was no spatial organization considering the forms of life and the size structure of the phytoplankton community during the period of study, although the phytoplankton functional groups had responded to changes in resources, especially increasing its variety and contribution in the months of spring and summer, segregating the north of the lagoon, independently of the studied zones (pelagic and coastal). In short timescale the phytoplankton community from the pelagic area was more equitable than that from the coastal region over time. The contribution of the species Chroococcus limneticus, Aphanocapsa conferta and Aphanothece smithii from the 9th day in the pelagic region and practically the entire period studied in the coastal region indicate that despite the variation in precipitation and wind observed over time, steady-state of the phytoplankton community in environments strongly conditioned by hydrodynamics may occur.

Les mucilages pélagiques marins (MPM) sont des phénomènes mondiaux sporadiques et, dans certaines régions, chroniques dans les zones côtières. Ces agrégats gélatineux, enrichis en matière organique et en microorganismes, forment des écosystèmes marins autonomes transitoires allant de 0,5 cm à plusieurs kilomètres de long. Ils correspondent à des étapes évolutives de la neige marine non-sédimentée maintenue dans la zone photique. Durant les dernières décennies une intensification des apparitions des MPM ont été recensées. Ainsi, les MPM sont devenus un sujet de préoccupation pour les populations qui exploitent les ressources côtières et dans le contexte du fonctionnement global de l'écosystème. Malgré l’intérêt scientifique grandissant au cours des dernières décennies au sujet de ces phénomènes, notamment en mer Adriatique, les causes de formation, la dynamique et le rôle respectif des microorganismes dans de tels systèmes restent énigmatiques. La plupart des études réalisées sur les MPM étaient axées uniquement sur les communautés microbiennes eucaryotes par l’utilisation de techniques microscopiques. Or de nos jours, les méthodes moléculaires permettent de se concentrer également sur l'ensemble de la communauté, y compris les procaryotes. Afin d'approfondir notre compréhension de ces phénomènes nous avons étudié un type MPM qui est apparu de manière récurrente et abondante au cours de la dernière décennie dans le sud du Golfe de Gascogne (France), le «Liga». Dans un premier temps, nous avons étudié la formation de ce MPM au travers d’une année complète en suivant la dynamique des communautés archées, bactériennes et eucaryotes par la technique de T-RFLP, technique d’empreinte moléculaire ciblant la petite sous-unité du gène codant pour ARNr. Cette approche a révélé que les communautés microbiennes du Liga étaient différentes des communautés microbiennes marines pour les trois domaines du vivant, et que ces deux communautés étaient gouvernées par des paramètres environnementaux dont la variation était saisonnière. Les archées n’ayant pas pu être détectés dans le Liga, nous nous sommes focalisés sur la structure des communautés bactériennes et eucaryotes au moyen de technologies de séquençage à haut débit. Cette méthode a révélé que le Liga était principalement composé d'espèces marines, même si ces communautés étaient significativement différentes des espèces marines. Dans le Liga, les communautés eucaryotes étaient principalement composées de dinoflagellés, de zooplancton et de cnidaires. Les communautés bactériennes étaient principalement composées d’Alphaproteobacteria et de Gammaproteobacteria. La diversité fonctionnelle du Liga fraîchement formé a été également étudiée pendant les saisons d'apparition de ce phénomène, au printemps et à l'automne. Nous avons ainsi mis en évidence que les communautés microbiennes du Liga avaient potentiellement moins de capacités de résistance au stress et que ces communautés étaient potentiellement plus virulentes que les communautés microbiennes marines. / Marine pelagic mucilage (MPM) is worldwide phenomena occurring sporadically and, in certain regions, episodically in coastal areas. These gelatinous aggregates, enriched in organic matter and microorganisms, form autonomous transitory marine ecosystems ranging from 0.5 cm to several kilometers. They correspond to evolving stages originating from the non-settling early marine snow maintained in the photic zone. During the last decades intensification of MPM events have been noticed. They became a matter of concern both for populations exploiting coastal resources and in the context of global ecosystem functioning. Although increased scientific attention has been paid during last decades to these phenomena in specific areas such the Adriatic Sea, the causes of appearance, the dynamics, and the respective role of microorganisms in such systems remain enigmatic. Most of the studies performed on MPM focused on eukaryotic microbial communities using microscopic techniques. However molecular methods allow nowadays focusing also on the whole community including the prokaryotic part. In order to deeper our understanding of these phenomena we studied a MPM that occurred recurrently and more frequently during the last decade in the south of the Bay of Biscay (France), the “Liga”. In a first step we investigated the formation of this MPM through a complete year by following the dynamics of archaeal, bacterial and eukaryotic communities using T-RFLP fingerprinting targeting the small subunit of rRNA genes. This approach revealed that Liga’s microbial communities where different from marine microbial communities for the three domains of life and that both marine mucilage and marine communities were linked with seasonal patterns. As archaea were not found in the Liga, we focused on bacterial and eukaryotic communities’ structures through high throughput sequencing. The molecular composition revealed that the Liga was mainly composed of marine species although these communities were significantly different from marine species. In the Liga, eukaryotic communities were mainly composed of dinoflagellates, zooplankton and cnidarians species and bacterial communities were mainly composed of Alphaproteobacteria and Gammaproteobacteria. Functional diversity of freshly-formed Liga was targeted during its seasons of apparition, in spring and in autumn. We highlighted that Liga’s microbial communities had less potential capabilities to resist to stress conditions and that these communities were potentially more virulent than marine microbial communities.

Submitted by (edna.saturno@ufrpe.br) on 2017-02-09T15:04:24Z No. of bitstreams: 1 Diogo Martins Nunes.pdf: 540969 bytes, checksum: 969307884f3ced0bc71b0426a1a8882d (MD5) / Made available in DSpace on 2017-02-09T15:04:24Z (GMT). No. of bitstreams: 1 Diogo Martins Nunes.pdf: 540969 bytes, checksum: 969307884f3ced0bc71b0426a1a8882d (MD5) Previous issue date: 2011-02-11 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Circle hooks (15/0 and 17/0) were compared with traditional hooks (type "J" 10/0) and used "hook timers (HT)” to identify the time capture and time in which the fish remained in line until haulback. Survival rates ranged considerably between species and species groups, and between the types of hooks and hooking location. As example, mortality rates showed billfishes significantly lower in circle hooks in compared to the traditional. The swordfish, in turn, reported higher mortality regardless the type of hook and hooking location, unlike the blue shark, which showed high levels of survival. By moreover, species of tunas and billfihes analyzed showed a significant trend toward reduction in mortality of individuals captured externally, resulting in an association between hooking location and the condition of the animal (χ2 = 13:54, p = 0.00023; χ2 = 27.35, p = 1.697e-07, respectively). For target species had a trend of increased survival with increased length of individual fish, although the group of sharks that trend was only observed for the blue shark, with a marginally significant difference, while other shark species showed a pattern otherwise, although the difference was statistically significant only for the crocodile shark. A total of 431 HT were activated and retrieved with fish on the line, represented by 20 species, of which 13 were captured more frequently at night. Some species demonstrated endure long periods of capture surviving until the time of haulback. Results suggest that knowledge of factors affecting survival of pelagic fish caught in fishing longline can develop/adopt fishing methods that reduce mortality primarily by members of the bycatch and animals caught incidentally. / Durante os experimentos anzóis circulares (15/0 e 17/0) foram comparados com anzóis tipo “J” 10/0 e utilizados “hook timers” (HT) para identificação da hora de captura e do tempo em que o peixe permaneceu na linha até seu embarque. O espadarte apresentou altos índices de mortalidade, ao contrário do tubarão azul, que obteve altos índices de sobrevivência a despeito do tipo e local em que o anzol foi fisgado. Por outro lado, as espécies de albacoras e agulhões analisados apresentaram uma tendência significativa de redução da mortalidade em indivíduos capturados externamente, resultando em uma associação entre o local de fisga e a condição do animal (χ2=13.54 e p=0.00023; χ2=27.35 e p=1.697e-07, respectivamente). Houve uma tendência de elevação da sobrevivência com aumento do comprimento individual dos peixes, embora no grupo dos tubarões essa elevação apenas foi observada para o tubarão azul, com uma diferença marginalmente significativa, enquanto que outras espécies de tubarão apresentaram um padrão contrário, embora a diferença tenha sido estatisticamente significante apenas para o tubarão cachorro. Um total de 431 HT foram ativados, havendo um claro crescimento da taxa de mortalidade dos peixes capturados com o aumento do tempo decorrido entre a captura e o seu embarque, porém, algumas espécies demonstraram suportar longos períodos de captura sobrevivendo até o momento do embarque. Os resultados sugerem que através do conhecimento dos fatores que afetam a sobrevivência de peixes pelágicos capturados na pesca com espinhel pode-se desenvolver/adotar métodos de pesca que reduzam a mortalidade principalmente dos integrantes da fauna acompanhante e animais capturados incidentalmente.

Une forte contamination radioactive du milieu marin, notamment par le 137Cs, s'est produite dans le Pacifique nord-ouest suite à l'accident nucléaire de Fukushima Dai-ichi survenu le 11 mars 2011. Deux sources majeures ont été à l'origine de cette contamination, les retombées atmosphériques (sèches et humides) et les rejets liquides directement en mer. Cette radioactivité a été transférée aux organismes marins conduisant à la contamination de plusieurs espèces pélagiques et benthiques. Dans le cadre de l'étude des conséquences de cet accident sur le milieu marin, une première modélisation de la dispersion du 137Cs dans les eaux de la côte Pacifique du Japon a été réalisée par le groupe SIROCCO, permettant ainsi d'estimer l'évolution spatio-temporelle de la concentration de ce radionucléide dans l'eau et de déterminer son terme source, c'est-à-dire sa quantité globale rejetée en mer sous forme liquide. Ce travail de thèse s'inscrit dans la même démarche et vise, par une approche de modélisation, à étudier le transfert du 137Cs aux chaines trophiques pélagiques de la côte Est du Japon, composées par les populations planctoniques, les poissons planctonivores, et les poissons carnivores. Le couplage d'un modèle radioécologique, spécifiquement développé pour cette étude, à un modèle de l'écosystème composé d'un modèle NPZD (Nutrients-Phytoplankto-Zooplankton-Detritus) et d'un modèle de circulation régionale, s'est imposé comme la méthode la plus adaptée à l'étude de la contamination des populations planctoniques dans des conditions post-accidentelles. Les résultats de cette étude ont montré des niveaux de contamination assez élevés de ces populations notamment aux alentours de la centrale où les concentrations estimées sont environ 4 ordres de grandeur supérieures à celles observées avant l'accident. En dépit de ces concentrations élevées, le débit maximal de la dose absorbée reste largement au-dessous du débit de référence à partir duquel les effets sur les populations sont ressentis. Cette étude a aussi mis en évidence la prédominance de la voie trophique dans les processus d'accumulation du césium par ces espèces, ainsi que la présence d'une légère bioamplification chez les classes de taille de zooplancton. Le modèle radioécologique développé pour étudier la contamination des espèces nectoniques est structuré en taille. Chaque espèce est composé d'un ensemble de cohortes dont le nombre est fonction de la durée de vie de l'espèce et de sa fréquence de reproduction. Contrairement aux modèles classiques, le taux d'ingestion de la nourriture par l'organisme ainsi que son régime alimentaire ne sont pas constants dans le temps mais généralement variables en fonction de la taille de l'organisme. Dans cette approche le processus de prédation est considéré comme étant totalement opportuniste. Les résultats sont généralement satisfaisants et le modèle a été validé dans les conditions d'équilibre pré-accidentelles ainsi que dans les conditions post-accidentelles. L'importance de la prise en compte des mouvements migratoires de certaines espèces dans ce type de modèle a été mis en évidence notamment dans les conditions accidentelles caractérisées par une forte variabilité spatiale de la concentration du radionucléide dans la colonne d'eau. Les niveaux de contamination estimés pour les différentes espèces sont largement supérieurs à ceux observés avant l'accident, avec une tendance à l'augmentation lorsque la taille de l'individu augmente. / Huge amounts of radionuclides, espicially 137Cs, were released to the coastal northwestern Pacific ocean after the Fukushima nuclear power plant accident, that occurred on 11 March 2011. The resultant radiocesium contamination was quickly transferred to marine biota resulting in elevated cesium levels in various organisms. Using a modelling approach, this work aims to study the 137Cs transfer to the marine pelagic food chains, from plankton populations to the large piscivorous fishes. Coupling the radioecological model, developed in this study, with an ecosystem model comprising an NPZD biogeochemical model and a regional ocean circulation model, is appeared to be the most adapted tool for modelling of plankton populations contamination in this accidental situation. The results of this study showed high contamination levels in the plankton populations, especially in the vincity of the power plant, where the maximal concentrations are estimated to be about 4 orders of magnitude higher than those observed before the accident. In spite of these high contamination levels, the maximum 137Cs absorbed dose rates for phyto- and zooplankton populations were estimated to be well below the 10 Gy/h benchmark value, from which a measurable effect on the marine biota can be observed. This study has also highlighted the predominance of the cesium uptake from food and the presence of biomagnification potential at this trophic level. The radioecological model developed to study the nektonic species contamination is based on the individual size. In this approach, each species is represented by a set of cohorts. The number of these cohorts is a function of the species life span and reproduction frequency. Unlike traditional approaches, the organism ingestion rate and diet composition considered in this modelling approach are not constant, but vary over the time according to the size of the organism. The model results are in general satisfactory, and the validation is carried out in both equilibrium and accidental situations. This study highlighted the importance of the organism migratory movements in the radioecological modelling espicially in the accident situations caracterized by a very high spatial variability of radionuclides concentrations in the seawater. The detailed caracteristics of 137Cs concentration dynamics in the different species are discussed. The contamination levels estimated for the different species are significantly higher than those observed before the accident, with a clear tendency to increase with individual size.