Climate change and fisheries have affected marine environments worldwide leading to impacts on ecosystem structure and functioning. However there is clear evidence of spatial variability in the response of these impacts both within and among marine ecosystems. Although several studies have tried to explain the effect of these impacts on marine food webs, it is unclear how they interact, and how they may affect marine ecosystems remains an important unanswered question. This suggests the urgent need for multiple-trophic level and ecosystem-based management approaches to account for both fisheries and climate change impacts at ocean basins across the globe. Marine apex predators, such as seabirds, are vulnerable to the effects of both climate and fishing impacts, and can be used as reliable and sensitive bio-indicators of the status of the marine ecosystem. The Celtic Sea ecosystem is a productive shelf region in the Northeast Atlantic. It is characterized by high fish and invertebrate biodiversity. In addition, internationally important numbers of seabirds, such as Northern gannet Morus bassanus (L.), Manx shearwater Puffinus puffinus (B.), Common guillemot Uria aalge (P.) and Black-legged kittiwake Rissa tridactyla (L.), breed along the Celtic Sea coasts. In recent years, fisheries from across Europe have intensively exploited the Celtic Sea, leading to changes in stock structure. Moreover, the increase in annual average Sea Surface Temperature by 0.67 oC over the past two decades has altered the composition of plankton communities. These impacts, independently and in tandem, are likely to have had dramatic effects upon the Celtic Sea food web emphasizing the need to enhance our understanding of this important marine ecosystem. In this thesis the effects of climate change and fisheries on the Celtic Sea pelagic food web are evaluated, in particular focussing on the response of seabird populations. This is in part because of recent declines in the breeding success of many seabird colonies in the northeast Atlantic, particularly around the North Sea. Long-term data across four trophic levels (phytoplankton, zooplankton, mid-trophic level fish and seabirds) and different modelling approaches are used to determine factors influencing seabird productivity at different geographical scales. First, I review the direct and indirect effects of climate change and fisheries upon marine ecosystems, as well as their impacts upon marine birds. Second, I use data collected during 1986-2007 from a single seabird colony, across four trophic levels, to investigate long-term direct and indirect climate effects. The results suggest only a weak climate signal in the Celtic Sea, and this is only evident between mid-trophic level fish and certain species of seabird. Third, a similar multi-trophic level approach across three nearby regions in the southwest UK (Irish Sea, Celtic Sea, and English Channel) reveal no evidence of a bottom-up signal during the period 1991-2007. These findings are in contrast with the nearby North Sea region, where a strong bottom-up effect was found to affect seabird populations, highlighting the importance of regional-based studies across multiple trophic levels. Finally, to provide a more complete picture of the Celtic Sea, and how it might respond to changes in fisheries management and climatic variation, I use the complex tropho-dynamic ecosystem model Ecopath with Ecosim. The main focus is on how seabird biomass changes in response to the application of different fisheries regimes likely to be implemented under forthcoming reforms to the Common Fisheries Policy (e.g. the application of quotas and discard bans), as well as future climate change scenarios, in order to provide guideline support for resource management and seabird conservation in the Celtic Sea. The results suggest that some seabird guilds (gulls and some other scavengers) may be negatively affected by a reduction in discards, while other species (offshore divers) will benefit from a decrease in the fishing of pelagic fish species. Climate change is likely to have a negative impact across all trophic levels with a strong negative impact upon seabird populations. Therefore seabirds are likely to show species-specific responses to both climate variation (bottom-up effect) and changes in fishing practices, in particular our findings suggest that for some species climate may outweigh the fisheries impacts even when fisheries pressure is reduced by 50%. In summary, this study suggests that despite the generally negative impact of climate described for some regions in the Northeast Atlantic, the Celtic Sea ecosystem seems to be more resilient. However, both climate and fisheries and the interactions between these factors should be taken into account in the formulation of future management plans for the Celtic Sea ecosystem. The use of multiple-trophic level and ecosystem-based approaches over multiple spatial and temporal scales has helped to elucidate possible trophic mechanisms that are the response to future fishing and climate impacts in the Celtic Sea. The results of this study could have implications for both management plans and conservation policy.

Les microorganismes jouent un rôle prépondérant dans le fonctionnement des écosystèmes aquatiques, où ils sont à la base de la minéralisation et du recyclage de la matière organique. Les« vrais » champignons, ou Eumycètes, font partie de ces microorganismes hétérotrophes qui permettent le renouvellement de la matière organique dans les écosystèmes. Pourtant, la diversité et l’importance quantitative et fonctionnelle des champignons restent très largement méconnues dans les milieux pélagiques. Récemment, l’utilisation de méthodes moléculaires pour étudier la diversité des picoeucaryotes (de taille < 5 μm) lacustres a mis en évidence l’importance des champignons microscopiques avec, notamment, la présence de chytridiomycètes (chytrides). Cette découverte, en conjonction avec le rôle important connu des Eumycètes dans d’autres écosystèmes naturels, nous a amené à poser l’hypothèse d’une diversité et d’un rôle fonctionnel importants des champignons dans les écosystèmes pélagiques. Ce travail vise à préciser la diversité globale, la structure génétique et l’importance quantitative des différentes divisions du règne des Eumycota dans les écosystèmes pélagiques lacustres, et à proposer des outils méthodologiques pour l’étude écologique de ces peuplements. La diversité phylogénétique et l’importance des champignons de taille comprise entre 0,6 et 150 μm ont été analysées dans trois milieux pélagiques différents. Une étude de clonage-séquençage de l’ADNr 18S et de l’ITS a été réalisée au printemps 2007 dans les lacs Pavin (oligomésotrophe), Aydat (eutrophe) et Vassivière (mésotrophe, humique). L’affiliation phylogénétique des séquences a permis, non seulement de confirmer la présence d’une importante diversité de chytridiomycètes parasites du phytoplancton, mais aussi de mettre en évidence la présence non négligeable d’ascomycètes et de basidiomycètes, potentiellement saprophytes. L’étude de la dynamique saisonnière de la structure des peuplements (par TRFLP) et de l’importance quantitative de différentes divisions (par PCR quantitative) de la communauté fongique ont permis de déceler des différences en fonction des saisons et de l’écosystème. Ces différences ont été reliées à la dynamique des peuplements phytoplanctoniques, avec une influence des apports allochtones, principalement dans le lac eutrophe d’Aydat. De plus, les séquences moléculaires générées au cours de ces dernières années ont permis l’élaboration d’amorces ciblant des clades de champignons microscopiques d’intérêt, pour une étude écologique de la dynamique des peuplements, par des approches PCR à temps réel et FISH (fluorescent in situ hybridization). Enfin, nous considérons que l’acquisition de données complémentaires permettra d’intégrer les champignons saprophytes et parasites dans les flux de matière et d’énergie qui transitent par les écosystèmes pélagiques et les cycles biogéochimiques associés. / Microorganisms play major roles in aquatic ecosystems, primarily as the main actors for organic matter mineralization and recycling. “True” fungi (i.e. Eumycota) are among heterotrophic microorganisms that are highly efficient in recycling organic materials in natural ecosystems. However, the overall diversity of fungi and their quantitative and functional importance remain largely unknown in typical pelagic ecosystems. Environmental 18S rDNA surveys have recently highlighted the importance of microscopic fungi in the diversity of picoeukaryotes (size < 5 μm) in lake ecosystems, including particularly the members of chytridiomycetes (i.e. chytrids) as the dominant phyla. These studies and the known major roles of fungi in natural ecosystems such as soils have leaded us to venture the hypothesis that fungal diversity and functional roles are important structuring factors in pelagic ecosystems. The main aims of the thesis were to examine the overall diversity, genetic structure and quantitative importance of various phyla belonging to the Kingdom Fungi in freshwater pelagic ecosystems. Methodological tools were also developed for ecological investigations of fungal populations of interest. Phylogenetic diversity and quantitative importance of fungi (size classe: 0.6 and 150 μm) were analysed in three contrasting pelagic lakes. Environmental 18S and ITS rDNA surveys were performed during spring 2007 in the oligomesotrophic Lake Pavin, the eutrophic Lake Aydat, and the mesotrophic and humic Lake Vassivière, all located in the French Massif Central. Phylogenetic affiliation of sequences confirmed the presence and the substantial diversity of chytridiomycetes, known as parasites of primarily phytoplankton. We also have unveiled a sizeable number of sequences belonging to the fungal lineages of ascomycetes and basidiomycetes, mainly known as saprophytes. The seasonal dynamics of fungal community structure (essayed by TRFLP),and the quantitative importance of various taxonomic divisions (estimates by real time quantitative PCR or qPCR), revealed significant differences with seasons and with ecosystems. These differences were linked to phytoplankton composition and population successions, with at times the influence of allochthonous inputs, primarily for the eutrophic Lake Aydat. Finally, molecular sequences obtained during the few past years allowed the development of primers for targeting microscopic fungal lineages of interest, and the ecological study of their in situ dynamics using qPCR and FISH (fluorescent in situ hybridization) approaches. Overall, we consider that the acquisition of complementary data is necessary to allow the inclusion of fungi and their main functions (i.e. saprophytisms and parasitism) in the energy and matter fluxes in pelagics ecosystems, and the related biogeochemical cycling.

The thesis combines laboratory experiments and field expeditions to study production, transfer and consumption of non-enzymatic antioxidants and thiamine in an aquatic food web. In particular, I (1) documented spatial and seasonal variation of tocopherols and carotenoids in the Baltic Sea pelagic food web, and (2) examined the effects of abiotic and biotic factors on tocopherol, carotenoid and thiamine concentrations in phytoplankton, zooplankton and fish. Moderate differences in temperature and salinity affected α-tocopherol, β-carotene and thiamine production in microalgae. Furthermore, the results suggest that acute stress favors the expression of non-enzymatic antioxidants rather than enzymatic antioxidants. Because production of α-tocopherol, β-carotene and thiamine differ markedly between microalgae, the availability of non-enzymatic antioxidants and thiamine is likely to be highly variable in the Baltic Sea and is difficult to predict. The transfer of non-enzymatic antioxidants from phytoplankton to zooplankton was biomass dependent. The field expeditions revealed that phytoplankton biomass was negatively associated with α-tocopherol concentration in mesozooplankton. Thus, increased eutrophication of the Baltic Sea followed by an increase in phytoplankton biomass could decrease the transfer of essential biochemicals to higher levels in the pelagic food web. This could lead to deficiency syndromes, of the kind already observed in the Baltic Sea. Astaxanthin is synthesized from precursors provided by the phytoplankton community. Thus biomass dependent transfer of astaxanthin precursors from phytoplankton to zooplankton could be responsible for astaxanthin deficiency in zooplanktivorous herring. Astaxanthin in herring consists mostly of all-Z-isomers, which are characterized by low bioavailability. Therefore, astaxanthin deficiency in salmon could be explained by the low concentration of this substance and its isomeric composition in herring.