The Eden Estuary is a small, coastal inlet situated in Fife between the Tay and Forth Estuaries on the east coast of Scotland. A multidisciplinary case study of the estuary was conducted over a three year period observing the dynamic responses of biotic and abiotic behaviour to long term patterns of climate variability. Historical Trend Analysis (HTA) was combined with autocorrelation and spectral density analysis to identify trends, patterns and periodicity in natural cycles. River flow and wind direction data were cross-correlated with the North Atlantic Oscillation Index (NAOI) to link local responses to patterns of northern hemisphere circulation, and with Wolfe Sunspot Numbers representing variable solar activity as a potential driving mechanism for climate driven change. Assessment of the current state of ‘estuary health' used a proxy analysis of ecosystem function, combining Bray-Curtis similarity nMDS of macrofaunal community diversity with species functional traits. The observed estuary responses were subsequently projected onto the forecasted climate change scenarios reported by the IPCCAR4, UKCIP09 and to modelled projections of solar activity to propose future trajectories of change for the estuary. Autocorrelation analysis of river flow and wind direction data identified significant (95%) correlations corresponding to solar, lunar, planetary and volcanic events. Spectral density analysis similarly identified significant (>95%) frequencies corresponding to known periods of solar activity, lunar cycles and Bruckner climatic cycles. Formal cross -correlation revealed significant (95%) relationships between both river flow and wind data with the NAOI, and using a longer times series, between river Thames annual flow and Wolfe sunspot numbers; correlating solar maximums with high flow. Periods consistent to Schwabe and Hale solar cycles were evident in the wind and river data however the NAOI only displayed Hale periodicity, inferring the river and wind data are not solely influenced (or potentially driven) by the NAO. No detrimental impact of estuary change was observed in the biotic responses inferring maintenance of estuary health. This study identifies potential driving mechanisms of estuary perturbation and whilst causal mechanisms can only be proposed, these observations form a baseline for future targeted modelling, monitoring and management.

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Coastal and estuarine systems worldwide are under threat from future global climate change, with potential consequences including increased penetration of tidal driven salt water into estuarine surface waters. In coastal climate change research this issue has been neglected, despite increases in salinity potentially detrimentally impacting upper estuarine and riverine ecosystem function worldwide. In this research the first direct attempt is made at predicting the impact of future climate-driven increases in saline penetration upon estuarine and riverine benthic macroinvertebrate communities through the acute salinity tolerances of selected species. Two study estuary-river systems were selected based upon their perceived susceptibility to future increases in saline penetration. These estuaries exhibited dynamic tide and salinity profiles with large salinity ranges recorded over a tidal cycle and significant differences in saline penetration extents between low (summer) and high (winter) freshwater river discharge conditions. Salinity was shown to be the dominant environmental variable driving benthic macroinvertebrate species distributions in both estuaries; however additional environmental factors were shown to have locally dominant effects (i.e. sediment grain size). Laboratory and field based salinity toxicity experiments suggested that the tolerance of euryhaline-marine and brackish water species to reductions in salinity corresponded well to tolerance values in published literature. In contrast limnic derived species exhibited greater salinity tolerance under laboratory and field tidal cycle conditions than those published. For all test species, actual field distributions did not reflect distributions anticipated by saline tolerances alone, likely due to the effects of additional biotic and abiotic factors experienced under field conditions. The macroinvertebrate species salinity tolerances did not account for actual field distributions with sufficient accuracy to allow for precise prediction of future distribution patterns under projected saline penetration profiles due to the influence of additional environmental factors. Under the high greenhouse gas emissions climate scenario (SRES A1FI) for the years 2020, 2050 and 2080, projected relative sea level rise was shown to result in an increase in both the upstream extent of saline penetration and gradient of maximum salinity zones in both estuaries. However these increases were moderate even under worst-case conditions (0.32 km and 0.15 km) and unlikely to result in large-scale changes to the benthic macroinvertebrate community. However, in addition to relative sea level rise, predicted changes to freshwater river discharge (climatic and anthropogenic induced) and channel morphology could result in significant increases in the upstream extent of saline penetration predicted for projected sea level rise alone. This could result in critical consequences for estuarine and riverine ecology and ecosystem function across all trophic levels. A conceptual model exploring the potential ecological effects of both increases in saline penetration and changes to the estuarine system (anthropogenic and climatic) was developed, and implications for the future management of estuarine and riverine environments were identified.

The Asian Summer Monsoon (ASM) is an important climate system, affecting over half of the global population. Understanding past ASM changes is therefore crucial for assessing potential impacts of future climate change in Asia. However, previous reconstructions of ASM precipitation intensity generally rely on the local-scale catchments of lake, cave and vegetation-based records. There is significant disparity between these records, possibly attributable to local microclimate responses overprinting the regional signal. This thesis reconstructs precipitation-driven river flux to the Pearl River Estuary (PRE), a major river system in China, to record monsoon variability over a more regional scale. A suite of biornarker-based ratios indicative of terrestrial organic matter (TOM) flux (the concentration ratio of terrestrial to marine n-fatty acids, n-alcohols and sterols, and the BIT Index), are analysed in contemporary grab samples and a sediment core from 6.5 ka to present. Additionally, carbon isotope (813C) values of leaf wax n-fatty acids are analysed from 6.5 ka to present to assess potential vegetation change. TOM input to the modem PRE generally decreases from river to ocean. Superimposed on this decrease, the biomarker distributions record a rapid decrease across the delta toe, indicating that organic matter (OM) burial is largely dictated by the sedimentary regime. From 6.5 ka to present, BIT indices show strong covariance with a precipitation record within the drainage basin, indicating that soil OM input to the PRE covaried with paleoprecipitation 6.5 ka to present. The other three biomarker ratios also record a general decrease in TOM. However, these ratios record some disparity at 5.5 ka, suggesting a change in vegetation OM input to the core. Leaf wax 813C values record a significant enrichment at 2 ka, consistent with a previously published bulk 813C record, suggesting an anthropogenically-driven shift to a greater C4 plant component with the onset of agriculture. 111.

L'influence de différents facteurs environnementaux sur le comportement natatoire des copépodes calanoïdes estuariens Eurytemora affinis et Pseudodiaptomus annandalei a été étudiée au moyen d'un système de suivi lagrangien en trois dimensions. Nous avons observé des changements marqués dans le comportement natatoire de P. annandalei en réponse à une augmentation graduelle de salinité. Nos résultats montrent une salinité optimale pour le comportement et peuvent être expliqués par une redirection de la dépense énergétique du mouvement à l'effort d'osmorégulation quand la salinité diverge de la zone optimale. Nous avons étudié les effets immédiats de concentrations non létales de trois polluants sur le comportement de nage d’E. affinis. Nonylphénol, cadmium et un mélange d’hydrocarbures aromatiques polycycliques ont provoqué une augmentation de la vitesse de nage chez les trois stades adultes. Dans la plupart des cas, les effets ont été observés pendant une courte période d’exposition et ont persisté ou diminué pendant une courte période de décontamination. Nos résultats montrent que la première réponse aux polluants semble indépendante de leurs propriétés toxiques et ressemble à une réaction de fuite visant à échapper à des conditions stressantes. Nous avons montré qu'une exposition brève à la toxine de diatomée 2(E), 4(E) decadienal provoque une hyper-activité dose-dépendante pour les trois stades adultes de P. annandalei et une diminution de la vitesse de nage. L’analyse multifractale de la norme du déplacement a révélé chez les trois stades adultes un mouvement plus brownien en présence de la toxine avec des effets moindres chez les femelles non ovigères. / The effects of environmental stressors on the dynamics of Eurytemora affinis and Pseudodiaptomus annandalei, two widespread species of estuarine calanoid copepods, were investigated by means of Three Dimensional Particle Tracking Velocimetry. We observed changes in the swimming behavior of P. annandalei in response to salinity variation. Results show an optimal salinity for swimming activity and highlight differences between adult states. Redirection of energy from swimming to osmoregulation when salinity diverges from the optimal range of the species is a possible explanation. We investigated the effects of sub-lethal concentrations of three commonly found contaminants on the behavior of E. affinis. Nonylphenol, cadmium and polycyclic aromatic hydrocarbons increased both swimming speed and activity. In most cases, effects were observable within 30 minutes of exposure and persisted or faded during a period of depuration of similar duration. Our results suggest that changes in behavior after a short-term exposure may be independent of the general mode of action of the chemicals. The increase in speed and activity resembles an escape reaction permitting copepods to evade stressful conditions. We investigated the effects of the diatom-derived aldehyde 2(E), 4(E) decadienal on the swimming behavior of P. annandalei. Short-term exposure to the toxin induced dose-dependent hyperactivity in the three adult states and a decrease in swimming speed. Multifractal analysis revealed differences in the statistical properties of the swimming behavior. Exposure to the toxin resulted in a more Brownian motion in males and ovigerous females, but had little effects on non-ovigerous females.

Studies of the effects of trace metal perturbation on microbial communities have, to date, concentrated on contaminated environments, single phylotypes or single metals. The effects of trace metals on bacterial communities in estuarine and marine environments have been largely overlooked. The aim of this research was to advance the scientific knowledge in this area by the implementation of incubation experiments. Experiments were designed to determine the effects of trace metal enrichment and aggregate formation on the structure and function of bacterial communities. Environmental samples included bacterioplankton from a pristine estuary (Erme, Devon), a moderately contaminated estuary (Tamar, Devon), a contaminated estuary (Fal, Cornwall), a coastal station (M1) and a truly marine station off the continental shelf (M2). Key factors influencing the response of bacterial communities to trace metal enrichment were identified. In marine communities the most influential factors were; environmental parameters, such as type and concentration of organic matter; initial community composition and ambient concentration of zinc. The addition of trace metals resulted in a decrease in diversity in the bacterial community from the Tamar Estuary, however, bacterial association with aggregates appeared to reduce this effect. Community dynamics of bacteria from a pristine estuary (Erme) demonstrated remarkable bacterial resilience under trace metal stress, particularly in samples dominated by bacteria from the Rhodobacteraceae. Some metals were shown to have a more profound effect on community dynamics than others, resulting in the division of trace metals into Type 1 and Type 2 categories as a function of bacterial response. RNA derived community fingerprints were more different between incubation conditions than DNA derived fingerprints, and were thus a more sensitive indication of response to trace metal enrichment. The wider implications of the effects of trace metals on bacterial communities in estuarine and marine environments are discussed, along with possible future research directions. Recommendations are made for future investigations of the effects of metal contamination in light of the results presented here.

Cette thèse cible les facteurs biotiques qui influent sur la toxicité des métaux chez les copépodes calanoïdes. Tout d'abord, la toxicité du cadmium (Cd) entre deux copépodes de l'ordre; calanoida Eurytemora affinis (Poppe 1880) d'une région tempérée (estuaire de la Seine, France) et Pseudodiaptomus annandalei (Sewell 1919) d'une région subtropicale (estuaire de Danshuei, Taiwan), ont été déterminés sur la base de leur sexe et de leur état de reproduction. Les résultats de cette étude ont révélé que les deux copépodes avaient des niveaux de sensibilité différents à la toxicité du cadmium et que leur sensibilité au cadmium était également fortement dépendante de leur sexe et de leur état de reproduction. En outre, une étude de la toxicité du cadmium dans les traits de vie du copépode a été testée en utilisant P. annandalei comme espèce modèle. Les résultats ont révélé que la toxicité du cadmium était également dépendante du stade de développement des copépodes. De plus, le Cd a eu un effet négatif sur la croissance, la reproduction et la durée de vie du copépode. Afin de comprendre la raison de la sensibilité au cadmium spécifique au sexe, la bioaccumulation du cadmium chez les deux sexes a été réalisée. De plus, dans les environnements naturels, les copépodes peuvent bioaccumuler les métaux via une voie directe dans l’eau ou via les aliments consommés. Dans un premier temps, des essais préliminaires ont été effectués pour identifier la cinétique de bioaccumulation des métaux chez les micro-algues utlisées pour nourrir les copépodes. L'accumulation du Cd dans les microalgues a été testée en exposant Pavlova lutheri dans différentes conditions de salinité et température. À la fin, il a été observé que l’augmentation de la température et la faible salinité favorisent l’absorption de Cd par les micro-algues. P. annandalei a ensuite été exposé au cadmium dans l'eau et par le biais de son régime alimentaire, en utilisant les informations fournies par les résultats ci-dessus. Cette expérience a révélé que l'absorption de Cd par P. annandalei provenait nettement plus d'eau que de la nourriture. Une hypothèse a été développée sur les raisons pour lesquelles l'absorption de Cd par l'eau par les copépodes était plus élevée que par l'exposition par Cd via l’aliment. En d’autres termes, l’absorption de métaux par l’eau est une voie plus importante dans la bioaccumulation des métaux que par la voie alimentaire en raison de l’absorption orale. L'hypothèse a été démontrée en exposant les copépodes à un colorant alimentaire et, à l'aide d'un microscope, il a été constaté que le colorant était entré dans l'intestin du copépode par l'ouverture de la bouche. L'absorption orale d'eau par le copépode a été confirmée par un test de bioaccumulation. Une étude moléculaire sur le test transcriptomique et l'expression différentielle spécifique au sexe du copépode de P. annandalei exposé au Cd a été réalisée. Les résultats ont montré que les copépodes de P. annandalei répondaient à la toxicité du cadmium de manière spécifique au sexe, et expliquaient pourquoi la femelle était moins sensible au cadmium que les copépodes mâles. De plus, l'exposition multigénérationnelle de P. annandalei au cadmium a montré un développement possible de l'adaptation, en particulier chez les copépodes femelles. Bien que les copépodes puissent développer des mécanismes adaptatifs pour tolérer les produits chimiques toxiques, une concentration croissante de métaux dans le milieu aquatique ainsi que des transferts de métaux par la mère sur plusieurs générations pourraient augmenter la concentration de copépodes. Une exposition à long terme pourrait réduire leur forme, compromettant ainsi la structure de la population de copépodes. Cette étude a montré que la mortalité, les traits d'histoire de vie et les réponses moléculaires des espèces modèles peuvent fournir d'importants bioindicateurs pour l'évaluation des risques environnementaux. / As a result of the growing concerns about the fate of copepod ecology in the face of increasing environmental pollutants, several studies are being carried out. This thesis focused on biotic factors that influences metal toxicity in calanoid copepods. Firstly, cadmium (Cd) toxicity between two copepods in the order; calanoida; Eurytemora affinis (Poppe 1880) from a temperate region (Seine Estuary, France) and Pseudodiaptomus annandalei (Sewell 1919) from a subtropical region (Danshuei Estuary, Taiwan), was determined based on their sex and reproductive states. Results from this investigation revealed that both copepods have different levels of sensitivity to cadmium toxicity and also, their sensitivity to cadmium was significantly dependent on their sexes and reproductive states. In addition, an investigation of cadmium toxicity in copepod life history traits were further tested using P. annandalei as a model specie. The results revealed that Cd toxicity was also dependent on the developmental stages of the copepods. In addition, Cd showed negative effect on the growth, reproduction and lifespan of the copepod. Furthermore, to understand the reason for sex-specific sensitivity to cadmium, an investigation on the bioaccumulation of Cd was carried out. Moreover, in the natural environments, copepods could bioaccumulate metals either directly from the water or indirectly from consumed diets. Before, both routes of metal uptake were tested, some preliminary test was carried out on the rate at which copepod diet (microalgae) take up metal. Microalgae accumulation of Cd was tested by exposing Pavlova lutheri to Cd under different conditions (salinity and temperature). At the end, it was observed that increased temperature and low salinity influenced the uptake of Cd in the algae. P. annandalei was then exposed to Cd in water and through their diets, using the information from the above results. This investigation revealed that P. annandalei uptake of Cd was significantly more from water than from the diets. A hypothesis was developed based on why copepod uptake of Cd from water was higher than from dietary Cd exposure. That is, metal uptake from water is a more important route in the bioaccumulation of metals than through dietary route because of oral intake. The hypothesis was demonstrated by exposing copepods to a dyed medium, and with the aid of a microscope, the dyed medium was observed to have entered inside the gut of the copepod through the mouth opening. Oral intake of water by copepod was confirmed by a bioaccumulation test. A molecular study on the transcriptomic assay and sex-specific differential expression of P. annandalei copepod exposed to Cd was carried out. The results showed that P. annandalei copepod responded to Cd toxicity in a sex-specific manner, and why female was less sensitive to Cd than male copepods were discussed. Moreover, multigenerational exposure of P. annandalei to Cd showed a possible development of adaptation, particularly in the female copepods. Although, copepods could develop adaptive mechanisms to tolerate toxic chemicals, however, an increasing concentration of metals in the aquatic environment in addition to maternal transfers of metals over several generations could increase the concentration in copepods. A long term exposure could reduce their fitness, thereby compromising copepod population structure. This study showed that mortality, life history traits and molecular responses of model species can provide important bio-indicators for environmental risk assessment.

Les intégrons sont des plateformes génétiques bactériennes de capture et d'expression de gènes. Les intégrons cliniques sont les principaux responsables de la forte augmentation récente des bactéries multirésistantes aux antibiotiques. Cependant, dans l’environnement, ils ne représentent qu’une part minime de l’importante diversité des intégrons. Ainsi, les objectifs de cette thèse étaient (i) d’évaluer l’étendue de la diversité des intégrons dans l’environnement, (ii) de comprendre les phénomènes responsables de la structuration du pool d’intégrons dans le compartiment sédimentaire d’un milieu estuarien anthropisé et (iii) de rechercher l’existence potentielle d’intégrons indicateurs du niveau de contamination chimique.Le suivi des intégrons de classes 1, 2 et 3 et des populations d’E. coli dans des sédiments du bassin versant de la Risle impactés par des sources de contamination fécale bien caractérisées ont montré qu’en étiage, les souches d’E. coli d’origine humaine se disséminaient sur de courtes distances. Les intégrons de classe 1 se disséminent sur des distances un peu plus importantes et se maintiennent dans les 12 premiers centimètres du compartiment sédimentaire au moins.Une méthode a été développée permettant, pour la première fois, l’analyse de la diversité des intégrons via séquençage haut-débit. L’application de cette méthode sur une carotte sédimentaire de 4,8 m de profondeur prélevée dans l’estuaire fluvial de la Seine a permis de mettre en évidence plusieurs milliers de classes d’intégrons dont de nombreuses intégrases encore jamais répertoriées. La diversité des intégrons chute fortement avec la profondeur. Les intégrons de classe 1, majoritaires dans les sédiments de surface, ont une abondance qui chute fortement avec la profondeur cependant ils répondent plutôt positivement à la contamination chimique renforçant l’idée de leur utilisation comme proxy de pollutions anthropiques récentes. Trois classes d’intégrons dominent dans la vase consolidée représentant 38% des séquences obtenues dans la carotte sédimentaire mais répondant plutôt négativement à la contamination chimique. Enfin, la structure du pool d’intégrons est fortement corrélée à celle de la communauté bactérienne mais semble en partie indépendante de la communauté bactérienne dans deux des fractions sédimentaires profondes avec la dominance d’une nouvelle classe d’intégrons qui semble sélectionnée par les HAP. / Integrons are bacterial genetic platforms allowing acquisition and expression of genes. Clinical integrons play a major role in the strong increase of antibiotic multi-resistant bacteria recently observed. However, in the environment, they represent only a tiny fraction of the large integron diversity. Therefore, the aims of this thesis were (i) estimating the extent of the integron diversity in the environment, (ii) understanding phenomena responsible for integron pool structure in anthropized estuarine sediments and (iii) looking for integrons potentially proxy of chemical pollution level. The research of class 1, 2 and 3 integrons and the analysis of E. coli populations in sediments from the Risle drainage basin impacted by well-characterized fecal contamination sources show that E. coli strains with human origins were spread on short distances during low water level periods. However, class 1 integrons are spread on slightly longer distances and remain present in the 12 first centimeters of sediments at least. A methodology was developed allowing, for the first time, the analysis of integron diversity by high-throughput sequencing. In this way, the analysis of a 4.8 meter core sediment from the fluvial Seine estuary highlighted several thousands integron classes including many new integrases absent from data bases. Integron diversity decreases along with depth. Class 1 integrons are the majority integrons in surface sediments but their abundance strongly decreases in deep sediments. Class 1 integron abundance rather responds positively to chemical pollutions accentuating the idea that class 1 integrons could be used as proxy of recent anthropogenic pollutions. In the sediment core, three integron classes outshine the whole dataset: they represent 38% of all the sequences from the sediment core. However, abundances of these three majority integron classes rather respond negatively to chemical pollution levels. Integron pool structure is highly correlated to bacterial community diversity but seems to be partially independent to bacterial community diversity within two deep fractions from the sediment core: in these two sediment fractions, a new integron class outshines the rest of integron classes and seems to be specific to these two sediment fractions. Furthermore, this new integron class seems to be selected by PAH.