During summer, the Baltic Sea is subjected to the world’s largest cyanobacterial blooms. These blooms are linked to eutrophication and raise many questions concerning their effects on the ecosystem. To understand their impacts on the food web dynamics, it is essential to assess growth responses of grazers to these cyanobacteria. In the northern Baltic proper, copepods are the most important herbivores providing an essential link between the primary producers and higher trophic levels. In this Thesis, Papers I &amp; II evaluate methods to estimate copepod growth in response to feeding conditions in situ. The most conspicuous diazotrophic filamentous cyanobacterium in the Baltic Sea is Nodularia spumigena, a producer of nodularin which is highly toxic to vertebrates, yet its ecological role is largely unknown. In Paper III, reciprocal interactions between cyanobacteria, sympatric algae and copepods are studied. The results suggest that nodularin is likely involved in allelopathic interactions, but it is not an inducible defense against grazers. Furthermore, the results of Papers IV &amp; V, indicate that natural assemblages of N. spumigena and Anabaena spp. may support copepod reproduction and that total diazotrophic filamentous cyanobacteria appear to provide a beneficial feeding environment for the feeding stages of copepod nauplii, most probably by stimulating the microbial communities that nauplii feed upon. Since cyanobacterial blooms are projected to increase due to global climate change, the combined effects of toxic cyanobacteria, ocean acidification and global warming predicted for year 2100 are further investigated on copepods in Paper IV. Taken together, these studies indicate that filamentous diazotrophic cyanobacteria contribute to sustaining secondary productivity and have potential implications of management practices with respect to combating eutrophication, global climate change and sustaining fish feeding conditions. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.</p>

Des approches traditionnelles en combinaison avec des méthodes moléculaires et biochimiques ont été utilisées pour étudier les communautés zooplanctoniques de la saline de Sfax. Une dizaine d'espèces ont été identifiées dans 4 bassins de salinité croissante. Les copépodes étaient la composante la plus représentative du compartiment zooplanctonique dans les bassins A5, A16 et C41. Le bassin M2 est monozoïque avec une présence exclusive d'Artemia salina.Nous avons montré le rôle crucial de la salinité dans la distribution des espèces mais nous avons souligné également l’influence, quoique plus faible, d’autres facteurs comme le ratio N:P qui pourrait être liée au mode de vie des animaux et directement aux phytoplancton. La composition en acides gras des copépodes et des Artemia est liée aux facteurs physico-chimiques et biologiques. Grâce à leur teneur en acides gras hautement insaturés, les copépodes et les Artemia peuvent être utilisés comme source alimentaire pour les poissons d'élevage. La phylogénie des copépodes est controversée puisque la structuration génétique de ce groupe n’est pas nettement identifiable. L’existence d’espèces cryptiques au sein des Paracartia grani est supposée mais reste à confirmer. Les facteurs abiotiques ne sont pas impliqués dans ces processus de divergence génétique. Chez Artemia salina, la forte teneur en sel, est un facteur de ségrégation des populations, l’adaptation des artémies à cette condition aboutit à des populations génétiquement distinctes. Un clivage génétique est repéré, il met en évidence une séparation entre les populations vivant dans de fortes teneurs en sel et celles en pleine mer. / Zooplankton community of solar saltern of Sfax. A dozen of species were identified in four ponds of increasing salinity. Copepods were the most abundant group in A5, A16 and C41. M2 is monozoic with an exclusive presence of Artemia salina. Salinity have a crucial role in species distribution, whereas, other factors such as N:P ratio have smaller influence. Fatty acids composition of copepods and Artemia depends on physico-chemical and biological parameters. Owing to their Highly unsaturated fatty acids (HUFAs) composition, copepods and Artemia of the saltern of Sfax can be used as food source for cultured fishes. Copepods phylogeny is controversial because their genetic structure is not clearly identifiable. The existence of cryptic species within Paracartia grani is assumed but should be confirmed. Abiotic factors are not involved in processes of genetic divergence. For Artemia salina, the high salinity, is a factor of population segregation, the adaptation of Artemia in such condition leads to distinct, genetically, population. A genetic divide was identified, it highlights a separation between population living in high salinity and those in the sea.

Les estuaires font partie des écosystèmes les plus productifs de la planète. Ils constituent une zone d'importants échanges de matières et jouent à ce titre un rôle capital pour les cycles biogéochimiques. Du fait de leur position à l'interface entre domaines continental et marin, ils sont également un lieu de passage obligatoire pour de nombreuses espèces de poissons migrateurs ou encore de nourricerie et de refuge. Ces systèmes sont contraints par de nombreuses pressions de natures diverses dont certaines en lien avec les activités humaines locales (p. ex. pêcheries, transport maritime, dragages, pollutions accrues, etc.). Ces altérations viennent s'ajouter à la variabilité intrinsèque de ces systèmes naturellement complexes (variabilité spatio-temporelle de différents facteurs environnementaux ; c.-à-d. température, salinité, turbidité, etc.). Toutefois, une intensification de ces d'altérations, dont une partie est associée à la composante climatique des changements globaux, est observée depuis ces dernières décennies. Ces modifications avérées et leurs incidences sur les communautés biologiques constituent un enjeu en matière de gestion des écosystèmes estuariens. Cependant, par manque de chroniques de données continues suffisamment longues, peu d'études sur l’évolution à long terme de systèmes estuariens ont été réalisées à ce jour. Pour mes travaux, j'ai eu à ma disposition un ensemble de chroniques uniques - acquises depuis 35 ans - associées à plusieurs suivis écologiques de l'estuaire de la Gironde (notre site atelier). L'objectif général de cette thèse est de caractériser l’évolution globale du système dans son ensemble (physico-chimie et biologie) et d'identifier les forçages impliqués. L’originalité de ces travaux, par rapport aux études spécifiques déjà menées, consiste à analyser l’évolution de l’ensemble des descripteurs caractéristiques du fonctionnement d'un système modèle et de qualifier la part relative aux forçages globaux. L'étude des séries chronologiques, via une approche end-to-end basée sur des analyses multivariées, permet d'identifier deux changements abrupts d'état de l'écosystème de l'estuaire de la Gironde, associés à des fluctuations hydroclimatiques à large échelle (bassin Atlantique nord) mais aussi à une échelle plus locale (estuaire). Des hypothèses relatives aux possibles mécanismes impliqués, reliant les altérations climatiques à large échelle aux altérations observées à l'échelle des communautés biologiques estuariennes, sont discutées. Un deuxième volet de la thèse, au travers d’une approche modélisatrice basée sur le concept de niche d'Hutchinson, permet d'identifier un changement de répartition spatiale, longitudinale, des populations de copépodes estuariennes en réponse au réchauffement des masses d'eau et à la marinisation de l'estuaire. Enfin un troisième volet de mes travaux s'est consacré à l'étude spécifique d'une espèce de copépode invasive : Acartia tonsa. Suivant une double approche modélisatrice permettant d'estimer à la fois les niches fondamentale et réalisée de l'espèce, ces travaux illustrent l'importance relative des changements climatiques qui ont facilité la colonisation et l'essor de cette espèce dans l'estuaire. / Estuaries are among the most productive ecosystems on Earth. They constitute important areas for materials exchanges and play therefore a crucial part in biogeochemical cycles. Because of their location at the interface between marine and continental realms, they are also a migratory path for different fish species and in some cases, a nursery or a refuge area. These systems are submitted to many pressures, some of them being related to anthropogenic activities (e.g fisheries, maritime traffic, dredging, rising pollutions, etc.). These changes are superimposed to the intrinsic variability of these naturally complex ecosystems (characterized by a spatio-temporal variability of different environmental factors; i.e., temperature, salinity, turbidity, etc.). However, since recent years, an intensification of these alterations, being partly linked to the climatic component of Global Change, is observed. These changes, already documented, and their incidence on biological communities, constitute a challenge for the future management of estuarine ecosystems. However, due to a lack of long-term continuous time series, for now few studies on the long-term evolutions of estuarine systems have been reported. In this work, I used a unique set of data (35 years) provided by an ecological monitoring of the Gironde estuary (the model of estuary used in the study). The main objective of this thesis is to characterize the evolution of the whole system (physico-chemistry and biology) over the last three decades and to identify the forcings involved. The originality of this work comes from a global analysis of the main estuarine descriptors and from the evaluation of the relative contribution of global forcings. A study based on multivariate analyses, through an end-to-end approach, reveals two abrupt shifts in the state of the ecosystem of the Gironde estuary. These two changes appear to be linked to hydroclimatic fluctuations at a regional scale (North Atlantic basin) and also at a local scale. Some hypotheses on the possible mechanisms involved, linking the large-scale climatic alterations to the changes observed on the biological estuarine communities are discussed. A second study that uses a modeling approach based on the ecological niche concept of Hutchinson, identifies a change in the spatial (longitudinal) distribution of estuarine copepod populations in response to warming and marinisation processes. Finally, a third work focuses on an invasive copepod species: Acartia tonsa. A double modeling approach estimates both the fundamental and realized niches of the species. The results highlight the relative importance of climate changes that facilitated the colonization of the estuary by A. tonsa.

O presente estudo avalia como a estrutura e a produção da comunidade de copépodes pelágicos da plataforma interna ao largo de Ubatuba (SP, Brasil) responderam às variações ambientais durante o período de julho de 2005 a junho de 2008. Durante estes três anos, a produção secundária dos copépodes foi estudada por meio da aplicação de modelos empíricos de crescimento e de estimativas de crescimento peso-específico obtidas através de experimentos de produção de ovos. Aspectos reprodutivos de 16 espécies de copépodes (9 calanóides, 3 ciclopóides e 4 harpacticóides) foram analisados neste período, através de experimentos de incubação e de métodos indiretos de obtenção de taxas de produção e viabilidade dos ovos. A comunidade de copépodes esteve representada por 70 espécies e foi caracterizada por altos valores de riqueza, diversidade e eqüitabilidade. Os copépodes apresentaram grande variabilidade nos valores médios de densidade (4726 ± 3711 ind. m-3) e de biomassa (7,42 ± 5,64 mg C m-3) e foram dominados por espécies de pequeno porte (< 1000 µm), destacando-se as fêmeas adultas de Oncaea waldemari e os copepoditos imaturos de paracalanídeos e clausocalanídeos. Quando comparada com outros ambientes tropicais e subtropicais, a região estudada apresentou valores elevados de densidade e biomassa. Da mesma maneira, a produção secundária média apresentou variabilidade temporal elevada (1,13 ± 1,11 mg C m-3 dia-1), com uma importante contribuição dos copepoditos imaturos de espécies dispersoras de ovos. No geral, os valores médios registrados foram considerados altos quando comparado com outros ambientes tropicais e subtropicais, embora a razão Produção/Biomassa média tenha sido similar às registradas nestes locais. A intrusão periódica da ACAS parece ter sido a principal responsável pelas alterações observadas na estrutura e produção da comunidade. A maioria dos meses não influenciados pela ACAS apresentou valores de densidade, biomassa e produção inferiores às respectivas médias. Entretanto, os resultados observados sugerem que as flutuações da comunidade de copépodes podem responder não apenas à intrusão da ACAS, mas também a uma complexa conjunção de fatores, incluindo as próprias relações inter e intra-específicas. Com relação à reprodução, as espécies dispersoras de ovos apresentaram taxas médias de produção de ovos similares às obtidas em outras regiões tropicais e subtropicais, enquanto que as retentoras apresentaram valores levemente inferiores. Entretanto, foram registrados picos ocasionais de produção destas últimas espécies, sugerindo que estes copépodes possuem estratégias que compensam os meses de baixa produtividade. A reprodução de algumas espécies analisadas parece ser associada a fatores intra-específicos, tais como o tamanho dos ovos e a razão entre machos e fêmeas. Além disso, as espécies dispersoras analisadas são provavelmente influenciadas pela temperatura e pelo alimento. A relação entre os tamanhos e pesos de fêmeas e ovos de 32 espécies de copépodes pelágicos mostrou que a variabilidade interespecífica observada nessas proporções é similar à tendência observada para espécies de altas latitudes. Comparando as taxas de produção estimadas a partir das equações empíricas com as obtidas experimentalmente, observa-se diferenças expressivas nas estimativas de produção secundária, o que sugere a influência de outras variáveis além daquelas consideradas pelos modelos. / The present study evaluates how the pelagic copepod community structure and production from the inner shelf off Ubatuba (SP, Brazil) responded to environmental variability from July 2005 to June 2008. During these three years copepod secondary production was studied by the application of growth empirical models and weight-specific growth estimates obtained through egg production experiments. Reproductive aspects of 17 copepod species (10 calanoid, 3 cyclopoid and 4 harpacticoid) were analyzed through incubation experiments and indirect methods to obtain production and egg hatching success rates. Copepod community was represented by 70 species and was characterized by high values of richness, diversity and evenness. Copepods had great variability in mean abundance values (4,726 ± 3,711 ind. m-3) and biomass (7.42 ± 5.64 mg C m-3) and were dominated by small size species (< 1,000 µm), especially Oncaea waldemari adult females and immature copepodites of paracalanids and clausocalanids. When compared to other tropical and subtropical environments, the copepod community in the study area had high average abundance and biomass. Mean secondary production rates had high temporal variability (1.13 ± 1.11 mg C m-3 day-1), with an important contribution from immature copepodites of broadcast spawner species. Production values were also high but mean Production/Biomass ratios were similar when compared to other tropical and subtropical environments. The periodic SACW (South Atlantic Central Water) intrusions seem to be the main responsible for the variability in community structure and production. Most months non-influenced by SACW had abundance, biomass and production values lower than the annual average. However, copepod community fluctuations may not have responded only to SACW intrusions, but also to inter- and intra-specific relations. Broadcast spawner species had mean egg production rates similar to the ones obtained in other tropical and subtropical regions, while sac spawners showed slightly lower values. Nevertheless, occasional production peaks were recorded for the latter, suggesting that these copepods have reproductive strategies to compensate for low productivity periods. Some species reproduction traits seem to be related to intra-specific factors, such as egg size and the male/female ratio. Besides, broadcast spawners were probably influenced by temperature and food. The relationship between female and egg size and weight from 32 pelagic copepod species showed that inter-specific variability observed in these proportions was similar to those observed for high-latitude species. When reproduction rates estimated from empirical equations with those obtained experimentally are compared, expressive differences in secondary production estimates emerge, which suggests the influence of other variables in addition to those accounted for by empirical models.

O presente estudo avalia como a estrutura e a produção da comunidade de copépodes pelágicos da plataforma interna ao largo de Ubatuba (SP, Brasil) responderam às variações ambientais durante o período de julho de 2005 a junho de 2008. Durante estes três anos, a produção secundária dos copépodes foi estudada por meio da aplicação de modelos empíricos de crescimento e de estimativas de crescimento peso-específico obtidas através de experimentos de produção de ovos. Aspectos reprodutivos de 16 espécies de copépodes (9 calanóides, 3 ciclopóides e 4 harpacticóides) foram analisados neste período, através de experimentos de incubação e de métodos indiretos de obtenção de taxas de produção e viabilidade dos ovos. A comunidade de copépodes esteve representada por 70 espécies e foi caracterizada por altos valores de riqueza, diversidade e eqüitabilidade. Os copépodes apresentaram grande variabilidade nos valores médios de densidade (4726 ± 3711 ind. m-3) e de biomassa (7,42 ± 5,64 mg C m-3) e foram dominados por espécies de pequeno porte (< 1000 µm), destacando-se as fêmeas adultas de Oncaea waldemari e os copepoditos imaturos de paracalanídeos e clausocalanídeos. Quando comparada com outros ambientes tropicais e subtropicais, a região estudada apresentou valores elevados de densidade e biomassa. Da mesma maneira, a produção secundária média apresentou variabilidade temporal elevada (1,13 ± 1,11 mg C m-3 dia-1), com uma importante contribuição dos copepoditos imaturos de espécies dispersoras de ovos. No geral, os valores médios registrados foram considerados altos quando comparado com outros ambientes tropicais e subtropicais, embora a razão Produção/Biomassa média tenha sido similar às registradas nestes locais. A intrusão periódica da ACAS parece ter sido a principal responsável pelas alterações observadas na estrutura e produção da comunidade. A maioria dos meses não influenciados pela ACAS apresentou valores de densidade, biomassa e produção inferiores às respectivas médias. Entretanto, os resultados observados sugerem que as flutuações da comunidade de copépodes podem responder não apenas à intrusão da ACAS, mas também a uma complexa conjunção de fatores, incluindo as próprias relações inter e intra-específicas. Com relação à reprodução, as espécies dispersoras de ovos apresentaram taxas médias de produção de ovos similares às obtidas em outras regiões tropicais e subtropicais, enquanto que as retentoras apresentaram valores levemente inferiores. Entretanto, foram registrados picos ocasionais de produção destas últimas espécies, sugerindo que estes copépodes possuem estratégias que compensam os meses de baixa produtividade. A reprodução de algumas espécies analisadas parece ser associada a fatores intra-específicos, tais como o tamanho dos ovos e a razão entre machos e fêmeas. Além disso, as espécies dispersoras analisadas são provavelmente influenciadas pela temperatura e pelo alimento. A relação entre os tamanhos e pesos de fêmeas e ovos de 32 espécies de copépodes pelágicos mostrou que a variabilidade interespecífica observada nessas proporções é similar à tendência observada para espécies de altas latitudes. Comparando as taxas de produção estimadas a partir das equações empíricas com as obtidas experimentalmente, observa-se diferenças expressivas nas estimativas de produção secundária, o que sugere a influência de outras variáveis além daquelas consideradas pelos modelos. / The present study evaluates how the pelagic copepod community structure and production from the inner shelf off Ubatuba (SP, Brazil) responded to environmental variability from July 2005 to June 2008. During these three years copepod secondary production was studied by the application of growth empirical models and weight-specific growth estimates obtained through egg production experiments. Reproductive aspects of 17 copepod species (10 calanoid, 3 cyclopoid and 4 harpacticoid) were analyzed through incubation experiments and indirect methods to obtain production and egg hatching success rates. Copepod community was represented by 70 species and was characterized by high values of richness, diversity and evenness. Copepods had great variability in mean abundance values (4,726 ± 3,711 ind. m-3) and biomass (7.42 ± 5.64 mg C m-3) and were dominated by small size species (< 1,000 µm), especially Oncaea waldemari adult females and immature copepodites of paracalanids and clausocalanids. When compared to other tropical and subtropical environments, the copepod community in the study area had high average abundance and biomass. Mean secondary production rates had high temporal variability (1.13 ± 1.11 mg C m-3 day-1), with an important contribution from immature copepodites of broadcast spawner species. Production values were also high but mean Production/Biomass ratios were similar when compared to other tropical and subtropical environments. The periodic SACW (South Atlantic Central Water) intrusions seem to be the main responsible for the variability in community structure and production. Most months non-influenced by SACW had abundance, biomass and production values lower than the annual average. However, copepod community fluctuations may not have responded only to SACW intrusions, but also to inter- and intra-specific relations. Broadcast spawner species had mean egg production rates similar to the ones obtained in other tropical and subtropical regions, while sac spawners showed slightly lower values. Nevertheless, occasional production peaks were recorded for the latter, suggesting that these copepods have reproductive strategies to compensate for low productivity periods. Some species reproduction traits seem to be related to intra-specific factors, such as egg size and the male/female ratio. Besides, broadcast spawners were probably influenced by temperature and food. The relationship between female and egg size and weight from 32 pelagic copepod species showed that inter-specific variability observed in these proportions was similar to those observed for high-latitude species. When reproduction rates estimated from empirical equations with those obtained experimentally are compared, expressive differences in secondary production estimates emerge, which suggests the influence of other variables in addition to those accounted for by empirical models.

Made available in DSpace on 2014-12-17T14:01:59Z (GMT). No. of bitstreams: 1 DanyheltonDFD.pdf: 1227676 bytes, checksum: c8754b4250e0bb6e5391c5ffbe8423a3 (MD5) Previous issue date: 2009-04-30 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Top-down (grazing) and bottom-up (nutrient, light) controls are important in freshwater ecosystems regulation. Relative importance of these factors could change in space and time, but in tropical lakes bottom-up regulation has to been appointed as more influent. Present study aimed to test the hypothesis that phytoplankton growths rate in Armando Ribeiro reservoir, a huge eutrophic reservoir in semi-arid region of Rio Grande do Norte state, is more limited by nutrient available then zooplankton grazing pressure. Bioassay was conduced monthly from September (2008) to August (2009) manipulating two levels of nutrients (with/without addition) and two level of grazers (with/without removal). Experimental design was factorial 2X2 with four treatments (X5), (i) control with water and zooplankton from natural spot ( C ), (ii) with nutrient addition ( +NP ), (iii) with zooplankton remove ( -Z ) and (iv) with zooplankton remove and nutrient addition ( -Z+NP ). For bioassay confection transparent plastic bottles (500ml) was incubate for 4 or 5 days in two different depths, Secchi`s depth (high luminosity) and 3 times Secchi`s depth (low luminosity). Water samples were collected from each bottle in begins and after incubates period for chlorophyll a concentration analysis and zoopalnktonic organisms density. Phytoplankton growths rates were calculated. Bifactorial ANOVA was performance to test if had a significant effect (p<0,005) of nutrient addition and grazers remove as well a significant interaction between factors on phytoplankton growths rates. Effect magnitude was calculated the relative importance of each process. Results show that phytoplankton growth was in generally stimulated by nutrient addition, as while zooplankton remove rarely stimulated phytoplankton growth. Some significant interactions happening between nutrient additions and grazers remove on phytoplankton growth. In conclusion this study suggests that in studied reservoir phytoplankton growth is more controlled by ascendent factors than descendent / A produ??o prim?ria dos ecossistemas aqu?ticos ? regulada por fatores ascendentes, (disponibilidade de luz e nutrientes), e por fatores descendentes (herbivoria). A import?ncia relativa desses fatores pode variar no tempo e no espa?o, mas em lagos tropicais tem sido sugerido que os fatores ascendentes s?o geralmente mais importantes. O presente estudo teve como principal objetivo testar a hip?tese de que o crescimento fitoplanct?nico no reservat?rio Armando Ribeiro Gon?alves, um grande reservat?rio eutr?fico na regi?o semi-?rida do Rio Grande do Norte, ? mais limitado pela disponibilidade de nutrientes do que pela press?o de herbivoria do zoopl?ncton. Bioensaios foram realizados mensalmente entre Setembro (2007) e Agosto (2008), manipulando-se dois n?veis de nutrientes (com/sem adi??o) e dois n?veis de herb?voros (com/sem remo??o). O desenho experimental foi do tipo fatorial 2X2 com quatro tratamentos (x5), (i) controle contendo a ?gua e o pl?ncton natural do ambiente ( C ), (ii) com adi??o de nutrientes ( +NP ), (iii) com remo??o de zoopl?ncton ( -Z ) e (iv) com remo??o de zoopl?ncton e adi??o de nutrientes ( -Z+NP ). Nos bioensaios foram incubadas garrafas pl?sticas transparentes de 500 mL por 4 ou 5 dias em duas profundidades distintas: na profundidade do disco de Secchi (alta luminosidade) e em uma profundidade 3x maior do que a anterior (baixa luminosidade). Amostras de ?gua foram coletadas de cada garrafa no inicio e ap?s o per?odo de incuba??o para an?lises das concentra??es de clorofila a e densidades de organismos zooplanct?nicos. Foi calculada a taxa de crescimento fitoplanct?nico. Uma ANOVA bifatorial foi realizada para testar se houve efeito significativo (p<0,05) da adi??o de nutrientes e da remo??o de herb?voros bem como uma intera??o significativa entre ambos os fatores sobre as taxa de crescimento do fitopl?ncton. A magnitude de cada efeito tamb?m foi calculada para quantificar a import?ncia relativa de cada processo. Os resultados mostram que o crescimento fitoplanct?nico foi geralmente estimulado pela adi??o de nutrientes enquanto a remo??o do zoopl?ncton raramente estimulou o crescimento fitoplanct?nico. Algumas intera??es significativas ocorreram entre os efeitos da adi??o de nutrientes e da remo??o de herb?voros sobre o crescimento fitoplanct?nico. Como conclus?o, esta pesquisa sugere que o crescimento fitoplanct?nico no reservat?rio estudado, ? mais fortemente controlado por fatores ascendentes do que por fatores descendentes

La méiofaune joue un rôle important dans le fonctionnement des habitats benthiques à substrat meuble (ex. flux de matière) en relation avec sa production élevée, sa position trophique intermédiaire et les importants transferts d’énergie vers les niveaux trophiques supérieurs qui y sont lié. Les relations trophiques et les flux de matière organique liés à la méiofaune restent néanmoins mal connus ou peu pris en compte. Afin de mieux appréhender le rôle de la méiofaune, la structure des communautés et les relations trophiques entre les sources de nourriture et ces consommateurs ont été déterminées dans cinq habitats à substrat meuble (i.e., vasière nue, herbier, zone à sables) de la baie de Marennes-Oléron, France, et de la baie de Sylt-Rømø, Allemagne, en tenant compte des variations temporelles. Le peuplement de méiofaune s’est trouvé être dominé par les nématodes et les copépodes benthiques. Les biomasses de microphytobenthos et de matière organique du sédiment sont apparues comme étant deux facteurs structurants pour les communautés. L’utilisation combinée de différents traceurs de la matière (i.e., isotopes stables, acides gras) a démontré que le microphytobenthos et les bactéries étaient les ressources trophiques majeures de la méiofaune dans les cinq habitats étudiés. Les mesures réalisées sur la structure des communautés et les données issues des traceurs de la matière ont été implémentées dans des modèles de réseaux trophiques. Dans tous les habitats, ces modèles ont mis en évidence que le flux de carbone dominant était issu du microphytobenthos, ceci démontrant les très faibles changements de comportements alimentaires malgré les importantes différences de sources trophiques en termes de disponibilité et de production des sources de nourriture entre ces différents habitats. Tous les groupes trophiques de nématodes, à l’exception des déposivores sélectifs, étaient particulièrement sélectifs et s’alimentaient majoritairement à partir de microphytobenthos, ceci étant à l’origine d’une forte production et d’un court temps de renouvellement de la méiofaune. En conclusion, cette thèse démontre le rôle important de la méiofaune dans les habitats à substrat meuble ainsi que l’importance de la relation trophique entre le microphytobenthos et la méiofaune dans le fonctionnement de ces réseaux trophiques. / Meiofauna play an important role in ecosystem processes in soft-bottom benthic habitats, e.g. food web dynamics, related to their highproduction, their intermediate trophic position and the energy they transfer towards higher trophic levels. The trophic linkages and flows of organic matter related to the meiofauna remain poorly known or taken into account. To better assess the role of meiofauna, the community structure and trophic relationships between food sources and meiofauna were determined in five intertidal soft-bottom habitats (i.e., mudflat, seagrass bed, sandflat) of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany, taking temporal variations into account. Meiofauna communities were dominated by nematodes and benthic copepods. Biomass of microphytobenthos and of sediment organic matter were two of the major drivers of community structure. The combination of trophic markers (i.e., stable isotopes, fatty acids) demonstrated that microphytobenthos and bacteria were the major food sources of meiofauna in the five habitats. Information from community structure assessments and trophic marker analyses were implemented in food web models. In all habitats, these models demonstrated that the main flow of carbon to meiofauna originated from microphytobenthos, highlighting negligible changes in meiofauna feeding behavior besides the large differences in availability and productivity of food sources between these habitats. All trophic groups of nematodes, except for selective deposit feeding nematodes, were highly selective and mainly fed on microphytobenthos, resulting in a high production and a short turn-over time of meiofauna. In conclusion, this thesis demonstrated the important role of meiofauna in soft-bottom habitats as well as the importance of the trophic pathway from microphytobenthos to meiofauna in the functioning of these food webs.