Ce travail de thèse focalise sur le fonctionnement du réseau microbien de la lagune de Thau à travers une approche « Réseau » ayant permis l’étude simultanée de l’ensemble des groupes microbiens (21 groupes) des virus au microzooplancton. La croissance et la mortalité des micro-organismes ont été étudiées expérimentalement lors de plusieurs saisons puis d’une étude en mésocosme. Nous avons déterminé les proportions de mortalité dont sont responsables le microzooplancton et les virus au travers de la lyse virale. Un suivi in situ puis en mésocosme dans la lagune de Thau nous a permis d'observer la réponse des composantes du réseau microbien à un forçage typiquement Méditerranéen, la crue.Il apparait que les bactéries hétérotrophes ont les plus fortes croissances allant jusqu’à 2,18 jour-1. La croissance pour divers groupes pico- et nano-phytoplanctoniques était inférieure à 1,5 jour-1. La cause majeure de mortalité des différents groupes de micro-organismes étudiés est la prédation du microzooplancton (> 90% en moyenne), tandis que la lyse virale semble être un processus sporadique et nettement moins important. Le fait que les taux de prédation observés soient très proches des taux de croissance de différents micro-organismes suggère que le réseau microbien étudié présente une forte efficacité de transfert de la biomasse vers les niveaux trophiques supérieurs.Dans ce contexte, la crue provoque à court terme une diminution de la croissance microbienne et du broutage, alors qu’elle déclenche la lyse virale chez certains groupes. Cependant, la réactivité de ce réseau permet un rétablissement rapide indiquant une forte capacité de résilience de ce système. / The aims of this thesis work were to shed new lights on the functioning of the microbial food web (MFW) in the Thau coastal lagoon through a “global approach” that permit us to study simultaneously the entire MFW components (21 groups) from viruses to microzooplankton. Growth and mortality of microorganisms were studied experimentally along seasons and during a mesocosm experiment. We particularly focus on mortality due to microzooplankton (<200µm) grazing and viral lysis. Responses of the different components of the MFW under a typical Mediterranean forcing, flash flood, was also studied during an in situ monitoring and a mesocosm experiment in the Thau Lagoon.In conclusion, it appears that heterotrophic bacteria show the highest growth rates (until 2.18 day-1). Growth rates of pico- and nanophytolankton groups were always lower than 1.5 day-1. The major cause of mortality of the different group studied, reaching on average 90%, was due to the predation by the microzooplankton. Mortality due to viral lysis appeared to be a “sporadic processes”, less important than microzooplankton grazing indeed. In addition, the observed grazing rates or bacterivory were close to growth rates of microorganisms, suggesting an efficient trophic transfer of the microbial biomass towards higher trophic levels.River flash flood; an important forcing in the Mediterranean coastal zone; triggered on a short time scale, a decrease in growth and grazing rates of microorganisms whereas viral lysis was enhanced. However, the important dynamics of this studied MFW allowed the rapid reestablishment of growth and grazing rates, indicating a strong resilience capability of this system.

L'objectif de la thèse est d'évaluer l'impact de l'immersion des sédiments de dragage du Grand Port Maritime du Havre (GPMH) sur l'environnement faunistique et sédimentaire à proximité du site de clapage d'Octeville (baie de Seine Orientale), en proposant une démarche scientifique originale, apportant une vision intégrée par (1) l'utilisation de marqueurs géochimiques couplés à une étude sédimentaire (2) l'étude de la dynamique spatiale et temporelle de la macrofaune benthique en lien avec une expérimentation in situ (3) la mise en place d'un nouvel indicateur multicritères spécifique de la pression de clapage (4) l'étude de l'ensemble du réseau trophique via le développement d'un modèleECOPATH. D'une part, les résultats ont mis en évidence l'existence d'une zone à l'équilibre sédimentaire au nord-ouest, avec deux gradients opposés de COT, contrôlés par les courants de marée et de houle. De plus, il est possible d'identifier les sédiments portuaires grâce à leur composition chimique différente. La zone impactée par les clapages est relativement restreinte. D'autre part, la macrofaune benthique apparaît peu impactée par les clapages. La communauté est particulièrement bien inféodée à l'environnement bio-hydro-sédimentaire de la zone d'étude. Des variations d'abondances et de dominances ont été observées depuis 2003. De plus, le nouvel indicateur proposé permet de classer l'impact engendré par les dépôts de sédiments en mer. Le réseau trophique est actuellement stable sur la zone impactée comme sur celle non-impactée par le clapage. / The aim of this thesis is to assess the impact of dumping by Le Havre harbour on the faunistic and sedimentary environment near the Octeville dumping site (Eastern part of the bay of Seine). This thesis propose an original scientific approach, including an integrated view (1) by the use of geochemical markers coupled with a sedimentary study (2) a study of the spatial and temporal benthic macrofauna dynamics with an experimentation in situ (3) the creation of a new multicriteria specific indicator of the dumping pressure and (4) a study of the food web with the development of an ECOPATH model. On the one hand, the results showed the existence of a sedimentary equilibrium area in the north-west, with two opposite TOC gradients, controlled by tidal and swell. Harbour sediments can be identified by their different chemical compositions. The area impacted by the dumping is limited. On the other hand, the benthic macrofauna appears less impacted by the dumping. The community is adapted in the bio-hydro-sedimentary environment of the study area. Variations in abundance and dominance have been observed since 2003.In addition, a new indicator allows the classification of dumping impact. The food web is currently stable in both impacted and not impacted areas.

Shore zones of large rivers are hot spots of biodiversity and contribute significantly to riverine ecosystem functioning. Today, shore degradation and other structural impair-ments like river straightening and channelization are strong impact factors on river ecosystem health. However, we still lack a thorough understanding of how structural shore zone degradation affects benthic community composition and their inherent ecosystem functions. In this thesis I tested the influence of training structure induced environmental factors on benthic macroinvertebrate community composition and the share of non-native species. Moreover, I assessed the community-associated ecosystem functions in terms of secondary production and resource utilization. In the main channel, communities were composed of only a few specialized taxa with low abundances, which contributed little to riverine secondary production. This is probably due to the harsh conditions produced by constantly high flow velocities and relocation of the fine sandy sediment. Main channel habitats were hardly affected by the adjacent training structure. Hence, species compositions and productivities were similar at all investigated main channel sites. By contrast, each of the shore communities was diverse, highly abundant and productive in comparison to the main channel. However, variations between shore structure communities and their ecosystem functions were prominent. One particular training structure, i.e. the off-bankline revetment, bore the most diverse and by far most productive benthic community, which utilized vast total amounts of basal resources (1,323 g DM m-² y-1). Varying sediment compositions, availability of macrophytes and diverse flow velocities, including lentic conditions, were revealed as key factors for increasing biodiversity, secondary production and resource utilization. Allochthonous boulder habitats were generally highly prone to non-native species invasion. Neozoa proved less productive than many native community members and consumed minor relative and total amounts of the prevailing resource pelagic algae. The present quantitative comparison of shore type specific effects on biodiversity, biomass and productivity provides managers with a tool to improve the ecological attributes of large river ecosystems with an unchangeable, impaired macrostructure. In its entirety, this thesis constitutes a sound basis to increase the mechanistic understanding of the way in which shore zone manipulation can affect riverine benthic communities and their associated ecosystem functions. / Die Uferbereiche großer Flüsse sind für die Biodiversität und Funktion dieser Ökosys-teme von enormer Bedeutung. Uferdegradierung und Kanalisierung gehören zu wichti-gen Faktoren, die Flussökosysteme nachhaltig beeinträchtigen. Wie sich anthropogene Umstrukturierungen der Uferbereiche auf die Zusammensetzung benthischer Ge-meinschaften und deren Ökosystemfunktion auswirken ist jedoch weitestgehend unbe-kannt. In dieser Arbeit werden die Effekte von uferspezifischen Habitatfaktoren auf die Komposition des Makrozoobenthos und den Anteil an Neozoen getestet. Zudem wurden die gemeinschaftsassoziierten Ökosystemfunktionen in Bezug auf Sekundärproduktion und Ressourcennutzung erfasst und bewertet. Die benthische Gemeinschaft des Hauptstroms bestand lediglich aus wenigen spezialisierten Arten, welche nur geringfügig zur Gesamtsekundärproduktion des Flusses beitrugen. Dies war vermutlich auf die rauen Bedingungen im Hauptstrom (insbesondere hohe Strömungsgeschwindigkeiten und damit verbundener Sedimenttransport) zurückzuführen. Die Makrozoobenthosgemeinschaften des Hauptroms wurden von den jeweils angrenzenden Ufertypen nicht beeinflusst. Im Gegensatz zum Hauptstrom zeigte jeder der untersuchten Ufertypen hohe Dichten an benthischen Invertebraten wobei sich Zusammensetzung und Funktion der Artengemeinschaften zwischen den Ufertypen stark unterschieden. Dabei brachte das Parallelwerk die diverseste und produktivste Makroinvertebratenfauna hervor, welche enorme Mengen basaler Ressourcen ingestierte (1,323 g DM m-2y-1). Hauptfaktoren für eine Erhöhung von Biodiversität, Sekundärproduktion und Ressourcennutzung waren neben variablen Sedimentzusammensetzungen und Makrophytenbeständen sich oft ändernde Fließgeschwindigkeiten mit lentischen Phasen. Allochthone Steinhabitate waren generell anfällig für die Invasion nicht heimischer Arten. Diese Neozoen waren weniger produktiv als viele heimische Taxa und nutzten nur geringe Mengen pelagischer Algen, welche die meist verfügbare Ressource darstellten. Aus dem ökologischen Vergleich der verschiedenen Ufertypen lassen sich Managementempfehlungen zur Verbesserung des ökologischen Zustandes in Bezug auf Biodiversität und Ökosystemfunktionen ableiten, welche für große Flüsse mit degradierter und unveränderbarer Makrostruktur in Betracht gezogen werden können. In ihrer Gesamtheit liefert diese Arbeit ein fundiertes mechanistisches Verständnis über die Effekte von Ufermanipulationen auf benthische Gemeinschaften und deren assoziierte Ökosystemfunktionen in großen Flüssen.

No description available.

Nous pouvons trouver des propriétés structurelles similaires dans presque tous les réseaux trophiques (ensemble d’interactions de prédation). L'existence de ces invariants suggère qu’il serait possible, pour chaque réseau trophique, de déterminer des paramètres généraux qui décrivent sa structure. Il serait également possible de faire le cheminement inverse, soit à partir de paramètres généraux, d’obtenir une structure de réseau qui respecte ces invariants. C’est ainsi que fonctionnent les modèles génératifs, qui prédisent une structure à partir de paramètres généraux. Cependant, les modèles génératifs peuvent générer des structures de réseau qui diffèrent des données empiriques, parce qu'ils intègrent différentes hypothèses sur les mécanismes qui façonnent les réseaux trophiques, et donc sur les paramètres généraux qui doivent être utilisés. Dans ce mémoire, j’étudie l'effet de la pondération de la stabilité à l'aide du paramètre sigma (écart-type maximum des forces d’interactions qu’il ne faut pas dépasser si l’on veut que le réseau d’espèces reste stable) sur la distribution des propriétés de réseau obtenues par différents modèles génératifs. En effet, en donnant une plus grande importance aux réseaux dont la structure est a priori stable (potentiellement plus proche de celles retrouvées dans la nature) on pourrait corriger les prédictions des modèles en rapprochant leurs résultats des données empiriques. Le principe de correction fait ici référence à l’utilisation des probabilités par les modèles génératifs : la correction est la modification de ces probabilités en faveur des réseaux stables afin qu’ils soient sur-représentés dans les données générées. Notre hypothèse est donc que la pondération de la stabilité pourrait améliorer les prédictions des modèles génératifs. Les modèles génératifs étudiés ici sont les modèles de cascade, de niche et de hiérarchie emboîtée. Notre principale conclusion est que, de manière contre-intuitive, la pondération de la stabilité n’améliore pas la différence entre les structures de réseaux empiriques et celles des réseaux générés par les mo-dèles. Nos résultats montrent que pour les réseaux étudiés, la plus grande différence entre les réseaux trophiques modélisés par les modèles génératifs et les réseaux empiriques est la nature du modèle et non la correction par la pondération de la stabilité. Cela suggère que ces modèles prédisent la structure à partir d’un nombre de paramètres insuffisants, où de paramètres ne représentant qu’une fraction de la structure du réseau. Le modèle de niche présente la prédiction la plus proche des données empiriques, mais seulement pour les réseaux comptant jusqu'à 20 espèces. Cette étude souligne donc le long chemin qu'il nous reste à parcourir avant de pouvoir représenter les réseaux trophiques de façon réaliste à partir de modèles génératifs simples. / We can find similar structural properties in almost every food web. The existence of these invariants suggests that it could be possible for each food web to determine general parameters. The reverse case also works, i.e. from general parameters, to obtain a network structure. This is how generative models work, they predict a structure from general parameters. However, the network structures obtained from generative models differ from empirical data, because they incorporate different assumptions about the mechanisms that shape food webs and thus the gen-eral parameters used. In this study, I’ll investigate the effect of weighting stability using the sigma parameter (maximum standard deviation of interaction forces that should not be exceeded if the species network is to remain stable). I’m studying its effect on the distribution of network prop-erties obtained by different generative models. Indeed, by giving greater importance to networks whose structure is stable, one could correct the predictions of the models by bringing their results closer to the empirical data. The correction is the modification of these probabilities in favor of stable networks so that they are more easily chosen by the model. Our hypothesis is therefore that weighting stability could improve the predictions of the cascade, niche and nested hierarchy models. Our main conclusion is that stability weighting does not improve the difference between empirical and model-generated network structures. Our results show that for the networks stud-ied, the biggest difference between food webs modeled by generative models and empirical net-works is the nature of the model and not the correction by stability weighting. This suggests that these models predict structure from an insufficient number of parameters or from parameters that represent only a fraction of the network structure. The niche model shows the closest pre-diction to the empirical data, but only for networks with up to 20 species. This study highlights the long way to go before we can realistically represent food webs using generative models.

No description available.

Alterações no ecossistema marinho e nos estoques pesqueiros devido à pressão da pesca podem ser detectadas por meio de indicadores multiespecíficos. Geralmente, esses indicadores são aplicados a séries temporais de capturas aliados a dados bio-ecológicos dos recursos. Entretanto, abordagens alternativas baseadas em dados de comercialização do pescado podem ser utilizadas. Neste estudo foram aplicados vários indicadores multiespecíficos aos dados disponíveis da região Sudeste/Sul do Brasil, integrando aspectos ecológicos e econômicos de forma inédita para essa região. Para isto, utilizaram-se dados da estatística pesqueira e dados de comercialização de pescado entre 1968-2007, além de dados bio-ecológicos dos recursos (nível trófico, comprimento máximo, longevidade e profundidade). Foram analisadas as tendências desses parâmetros em relação aos desembarques, às quantidades comercializadas e aos preços de mercado. Os indicadores Índice Trófico Marinho, Fishing-in-Balance e Índice de Preço Relativo Logaritmizado também foram explorados. Foi realizada uma análise inferencial das tendências de preço e quantidade das principais categorias de mercado e de suas correlações. A avaliação ecológico-econômica evidencia uma tendência de escassez das espécies-alvo da pesca e de algumas espécies de nível trófico, longevidade e comprimento máximo altos, além do fenômeno \"pricing down the food web\". Portanto, a base de dados do mercado provou ser valiosa para compreender a dinâmica da pesca numa perspectiva ecossistêmica. / Changes in marine ecosystems and fisheries resources due to the fishing pressure can be detected by multispecies indicators. These are, usually, applied to catch or landing time series, jointly the resources bio-ecological data. However, there is an alternative approach, based on market data that could be used. In this study, several multispecies indicators were applied to data from Southeastern/Southern Brazil, integrating ecological and economics aspects to this region in an unprecedented way. Fishery landings and market values for the period 1968-2007 were used, besides bio-ecological classification of seafood categories (trophic level, longevity, maximum length and depth). Trends of these parameters by landings and market quantities and prices were analysed. The Marine Trophic Index, Fishing-in-Balance and the Logarithm Relative Price Index were also applied. Moreover, an inferential analysis of individual categories statistical trends in market prices and quantities and their correlations were done. The joint ecological-economic analysis provided evidence of the scarcity of most higher trophic level, longevity and maximum length categories and fisheries target species, besides the \"pricing down the food web\" phenomenon. Therefore, the market database proved to be priceless to understand the fishery dynamic in an ecosystem perspective.

Alterações no ecossistema marinho e nos estoques pesqueiros devido à pressão da pesca podem ser detectadas por meio de indicadores multiespecíficos. Geralmente, esses indicadores são aplicados a séries temporais de capturas aliados a dados bio-ecológicos dos recursos. Entretanto, abordagens alternativas baseadas em dados de comercialização do pescado podem ser utilizadas. Neste estudo foram aplicados vários indicadores multiespecíficos aos dados disponíveis da região Sudeste/Sul do Brasil, integrando aspectos ecológicos e econômicos de forma inédita para essa região. Para isto, utilizaram-se dados da estatística pesqueira e dados de comercialização de pescado entre 1968-2007, além de dados bio-ecológicos dos recursos (nível trófico, comprimento máximo, longevidade e profundidade). Foram analisadas as tendências desses parâmetros em relação aos desembarques, às quantidades comercializadas e aos preços de mercado. Os indicadores Índice Trófico Marinho, Fishing-in-Balance e Índice de Preço Relativo Logaritmizado também foram explorados. Foi realizada uma análise inferencial das tendências de preço e quantidade das principais categorias de mercado e de suas correlações. A avaliação ecológico-econômica evidencia uma tendência de escassez das espécies-alvo da pesca e de algumas espécies de nível trófico, longevidade e comprimento máximo altos, além do fenômeno \"pricing down the food web\". Portanto, a base de dados do mercado provou ser valiosa para compreender a dinâmica da pesca numa perspectiva ecossistêmica. / Changes in marine ecosystems and fisheries resources due to the fishing pressure can be detected by multispecies indicators. These are, usually, applied to catch or landing time series, jointly the resources bio-ecological data. However, there is an alternative approach, based on market data that could be used. In this study, several multispecies indicators were applied to data from Southeastern/Southern Brazil, integrating ecological and economics aspects to this region in an unprecedented way. Fishery landings and market values for the period 1968-2007 were used, besides bio-ecological classification of seafood categories (trophic level, longevity, maximum length and depth). Trends of these parameters by landings and market quantities and prices were analysed. The Marine Trophic Index, Fishing-in-Balance and the Logarithm Relative Price Index were also applied. Moreover, an inferential analysis of individual categories statistical trends in market prices and quantities and their correlations were done. The joint ecological-economic analysis provided evidence of the scarcity of most higher trophic level, longevity and maximum length categories and fisheries target species, besides the \"pricing down the food web\" phenomenon. Therefore, the market database proved to be priceless to understand the fishery dynamic in an ecosystem perspective.

We are currently faced with the global challenge of conserving biological diversity while also increasing food production to meet the demands of a growing human population. Land-use change, primarily resulting from conversion to production land, is currently the leading cause of biodiversity loss. This occurs through habitat loss, fragmentation of remaining natural habitats, and resulting edge effects. Land-sparing and land-sharing approaches have been discussed as alternative ways to engineer landscapes to mitigate biodiversity loss while meeting production objectives. However, these represent extremes on a continuum of real-world landscapes, and it will be important to understand the mechanisms by which adjacent land use affects natural remnant ecosystems in order to make local land-management decisions that achieve conservation, as well as production, objectives. This thesis investigates the impact of juxtaposing production and natural forest on the community-wide interactions between lepidopteran herbivores and their parasitoids, as mediated by parasitoid spillover between habitats. The first and overarching objective was to determine whether herbivore productivity drives asymmetrical spillover of predators and parasitoids, primarily from managed to natural habitats, and whether this spillover alters trophic interactions in the recipient habitat. The study of trophic interactions at a community level requires understanding of both direct and indirect interactions. However, community-level indirect interactions are generally difficult to predict and measure, and these have therefore remained understudied. Apparent competition is an indirect interaction mechanism thought to be very important in structuring host-parasitoid assemblages. However, this is known primarily from studies of single species pairs, and its community-wide impacts are less clear. Therefore, my second objective was to determine whether apparent competition could be predicted for all species pairs within an herbivore assemblage, based on a measure of parasitoid overlap. My third objective was to determine whether certain host or parasitoid species traits can predict the involvement of those species in apparent competition. My key findings were that there is a net spillover of generalist predators and parasitoids from plantation to native forest, and that for generalists, this depends on herbivore abundance in the plantation forest. Herbivore populations across the edge were linked by shared parasitoids in apparent competition. Consequently, an experimental reduction of herbivore density in the plantation forest changed parasitism rates in the natural forest, as predicted based on parasitoid overlap. Finally, several host and parasitoid traits were identified that can predict the degree to which host or parasitoid species will be involved in apparent competition, a finding which may have extensive application in biological control, as well as in predicting spillover edge effects. Overall, this work suggests that asymmetrical spillover between production and natural habitats occurs in relation to productivity differences, with greater movement of predators and parasitoids in the managed-to-natural forest direction. The degree to which this affected species interactions has implications for landscape design to achieve conservation objectives in production landscapes.

Les réseaux trophiques jouent un rôle primordial dans la régulation des flux de matière et d’énergie au sein des écosystèmes. Dans le cadre des pratiques de recharge artificielle des aquifères, les biocénoses souterraines sont pleinement sollicitées et leur capacité à dégrader les flux de matière organique de surface conditionne le maintien de la qualité des eaux souterraines. L’objectif de ce travail est de déterminer l’influence d’une augmentation des flux de carbone organique dissous sur l’intensité des interactions trophiques entre les communautés microbiennes et les assemblages d’invertébrés au toit des nappes phréatiques rechargées artificiellement avec des eaux de ruissellement pluvial. A travers une approche expérimentale de terrain et de laboratoire, ce travail permet d’évaluer l’intensité des relations existant entre les flux de carbone organique dissous, les conditions environnementales, l’activité et la diversité de communautés microbiennes et l’abondance des communautés d’invertébrés. / Food webs play a crucial role in regulating the fluxes of matter and energy within ecosystems. Artificial recharge of aquifers relies heavily on the ability of groundwater biocenoses to degrade organic matter fluxes that is a condition to maintain the quality of groundwater. The objective of this work is to determine the impact of increased dissolved organic carbon supply on the trophic interactions between the microbial communities and invertebrate assemblages at the upper layers of groundwater artificially recharged with stormwater. Through a combined field and laboratory experimental approach, this work allows ranking the strength of relationship between dissolved organic carbon fluxes, environmental conditions, activity and diversity of microbial communities and abundance of invertebrate assemblages