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Hazard assessment of pesticides in aquatic environments requires accurate predictions of persistence and compartmentalization. A strategy for developing confidence in predictive fate models, such as the Exposure Analysis Modeling System (EXAMS) and the Simplified Lake and Stream Analysis model (SLSA), is to test the models using carefully chosen chemicals in semi-controlled and field situations. An objective of this approach would be to isolate the variability in a particular fate process and thereby assess the ability of an algorithm to model the process. For example, endothall, a relatively watersoluble aquatic herbicide, has essentially a sole fate process, biotransformation. Endothall was used to test the predictive capabilities of EXAMS and SLSA and to identify sources of variance in those predictions.

La gestion de l’eau douce est un problème majeur partout dans le monde. Les activités anthropiques liées à l’industrie, à l’agriculture et à l’implantation humaine sont les principales sources de pollutions de l’eau. Afin mettre en place des politique de prévention de la pollution, de réhabilitation des environnements aquatiques ou de recyclage des eaux usées, il est nécessaire d’acquérir des données massives sur la qualité de l’eau. Or, les méthodes actuelles de suivi des contaminants présentent des coûts élevés et de faibles débits de mesure du fait de leur incompatibilité avec un déploiement sur le terrain. Ces deux freins majeurs ne permettent pas de suivre les concentrations en polluant et notamment en métaux lourds dans les milieux aquatiques à des échelles spatiales et temporelles pertinentes. Plusieurs organisations internationales, dont l’ONU, ont de ce fait recommandé le développement de nouvelles méthodes analytiques plus performantes. Nous proposons ici une technique de mesure des contaminants métalliques lourds basée sur la diffusion Raman exaltée de surface (SERS). Le SERS présente de nombreux avantages pour l’analyse environnementale dont la sensibilité, la spécificité,la rapidité de mesure, l’adaptabilité aux matrices complexes ainsi que le coût modéré d’un instrument portable. Nous détaillerons donc la construction de la sonde SERS dédiée à la quantification de l’ion métallique lourd cible Zn2+, ainsi que les traitements de données nécessaire à l’établissement d’une quantification. Puis, nous examinerons la robustesse de la méthode de quantification vis-à-vis des sources de variabilités qui seront inévitablement rencontrées dans les eaux naturelles. / Freshwater management is a major problem all over the world. Anthropogenic activities related to industry, agriculture and human settlements are the main sources of water pollution. In order to makes policies for pollution prevention, rehabilitation of aquatic environments or waste water recycling, it is necessary to acquire massive data on water quality. Current contaminant monitoring methods have high costs and low frequency of measurement due to the incompatibility with field deployment. These two major brakes do not make it possible to monitor pollutant and especially heavy metal concentrations in aquatic environments at relevant spatial and temporal scales. Several international organizations, including the United Nations, have therefore recommended the development of new and better analytical methods.We propose here a technique for measuring heavy metal contaminants based on Surface Enhanced Raman Spectroscopy (SERS), which would allow a large scale deployment in the field.SERS has many advantages for environmental analysis including sensitivity, specificity, speed of measurement, adaptability to complex matrix and the moderate cost of portable instrument. We will therefore detail the construction of the SERS probe dedicated to the quantification of the target heavy metal ion Zn2+, which is a geochemical marker of anthropogenic contamination, as well as the data processing necessary for the establishment of quantification. Then, we will examine the robustness of the method of quantification with respect to the sources of variability that will inevitably be encountered in natural waters, when used directly in the field

O aumento na população humana mundial e nos padrões per capita de consumo criaram uma forte demanda por comida, fibras e biocombustíveis que apenas um modelo industrial de produção agrícola poderá atender. Porém, a agricultura é uma atividade que resulta em sérios impactos sobre o meio ambiente e a biodiversidade. Esta dissertação teve como objetivo testar a hipótese de que o uso e manejo da terra para a produção intensiva de soja resultam numa redução significativa no desempenho de organismos aquáticos conforme indicado por sobrevivência, crescimento e/ou desenvolvimento. Para tanto conduzimos experimentos em campo e em laboratório expondo populações de larvas de libélulas e girinos a ambientes de poças temporárias distribuídas ao longo de um gradiente de degradação ambiental compreendendo cerrados, pastagens e plantações. O desempenho de larvas de libélulas foi significativamente influenciado pelo uso e manejo da terra. Se por um lado a mortalidade de larvas de libélulas transplantadas para ambientes de cerrado e de pastagens variou entre 50 e 60%, larvas de libélulas em plantações de soja foram rapidamente erradicadas. A sincronia entre eventos de aplicação de pesticidas e os padrões temporais de mortalidade sugere que pesticidas são o principal vetor de alteração ambiental impedindo a colonização efetiva de campos agrícolas por libélulas. O desempenho de girinos de Physalaemus cuvieri também foi significativamente influenciado pelo uso e manejo da terra. Porém, as respostas de girinos foram em geral menos fortes e menos consistentes que aquelas observadas para libélulas. Girinos transplantados para ambiente de soja de 10 dias (primeiro experimento) e de 55 dias de idade (segundo experimento) tiveram desempenho tão bom ou superior àquele observado em ambientes de referência; em contraste, girinos transplantados para ambiente de soja de 50 dias (primeiro experimento) tiveram mortalidade total. Portanto práticas específicas de manejo aparentam modular o desempenho de P. cuvieri ao longo do ciclo de plantio. Ambientes de pastagem sempre foram relativamente favoráveis à sobrevivência, ao crescimento e ao desenvolvimento de girinos. Estes resultados têm importantes implicações para nossa conceptualização da permeabilidade de paisagens agroindustriais para a fauna aquática e semiaquática e, portanto, para a conservação da biodiversidade em paisagens agroindustriais. Ao menos no que diz respeito ao hábitat larval, pastagens se mostraram ambientes de alta permeabilidade para a colonização tanto de girinos como de libélulas. Por sua vez, plantações de soja aparentam ser completamente impermeáveis para o desenvolvimento das larvas de libélulas, mas temporalmente permeáveis para o desenvolvimento de girinos / The global increase in human population and in per capita consumption patterns has created a strong demand for food, fiber and biofuels that only an industrial model of agricultural production can meet. However, industrial agriculture has serious impacts on biodiversity and on the environment. This thesis aimed at testing the hypothesis that land use and land management for the intensive production of soybeans results in a significant reduction in the performance of freshwater organisms, as indicated by survivorship, growth and/or development. This hypothesis was tested by means of field and lab experiments exposing dragonfly larvae and tadpoles to conditions of temporary ponds distributed across a gradient in environmental degradation comprising cerrado, pastures and sugarcane fields. The performance of dragonfly larvae was significantly influenced by land use and land management. Whereas dragonfly survivorship in cerrado and pastures ranged between 50 and 60%, dragonflies transplanted to soybean fields were rapidly eradicated. The synchrony between pesticide application and temporal patterns in mortality strongly suggests that pesticides are the main driver of environmental change precluding the effective colonization of soybean fields by dragonflies. The performance of tadpoles of Physalaemus cuvieri was also significantly influenced by land use and land management. However, tadpole responses were in general less strong and less consistent than those of dragonflies. Tadpoles transplanted to 10-day old soybean fields (first experiment) and 55-day old soybean fields (second experiment) performed as well or better than tadpoles transplanted to reference sites; in strong contrast, tadpoles transplanted to 50-day old soybean fields (second experiment) suffered 100% mortality. Therefore, specific land management practices mediate P. cuvieri performance along the crop cycle. Pastures were always relatively favorable to tadpole survivorship, growth and development. These results have important implications to our conceptualization of the permeability of the agricultural matrix to aquatic and semiaquatic fauna and, therefore, to the conservation of biodiversity in agroindustrial landscapes. In regards to larval habitat, pastures have shown to be highly permeable to the colonization of tadpoles and dragonflies. In turn, soybean plantations appeared to be impermeable to dragonfly development, but temporally permeable to the development of tadpoles

O aumento na população humana mundial e nos padrões per capita de consumo criaram uma forte demanda por comida, fibras e biocombustíveis que apenas um modelo industrial de produção agrícola poderá atender. Porém, a agricultura é uma atividade que resulta em sérios impactos sobre o meio ambiente e a biodiversidade. Esta dissertação teve como objetivo testar a hipótese de que o uso e manejo da terra para a produção intensiva de soja resultam numa redução significativa no desempenho de organismos aquáticos conforme indicado por sobrevivência, crescimento e/ou desenvolvimento. Para tanto conduzimos experimentos em campo e em laboratório expondo populações de larvas de libélulas e girinos a ambientes de poças temporárias distribuídas ao longo de um gradiente de degradação ambiental compreendendo cerrados, pastagens e plantações. O desempenho de larvas de libélulas foi significativamente influenciado pelo uso e manejo da terra. Se por um lado a mortalidade de larvas de libélulas transplantadas para ambientes de cerrado e de pastagens variou entre 50 e 60%, larvas de libélulas em plantações de soja foram rapidamente erradicadas. A sincronia entre eventos de aplicação de pesticidas e os padrões temporais de mortalidade sugere que pesticidas são o principal vetor de alteração ambiental impedindo a colonização efetiva de campos agrícolas por libélulas. O desempenho de girinos de Physalaemus cuvieri também foi significativamente influenciado pelo uso e manejo da terra. Porém, as respostas de girinos foram em geral menos fortes e menos consistentes que aquelas observadas para libélulas. Girinos transplantados para ambiente de soja de 10 dias (primeiro experimento) e de 55 dias de idade (segundo experimento) tiveram desempenho tão bom ou superior àquele observado em ambientes de referência; em contraste, girinos transplantados para ambiente de soja de 50 dias (primeiro experimento) tiveram mortalidade total. Portanto práticas específicas de manejo aparentam modular o desempenho de P. cuvieri ao longo do ciclo de plantio. Ambientes de pastagem sempre foram relativamente favoráveis à sobrevivência, ao crescimento e ao desenvolvimento de girinos. Estes resultados têm importantes implicações para nossa conceptualização da permeabilidade de paisagens agroindustriais para a fauna aquática e semiaquática e, portanto, para a conservação da biodiversidade em paisagens agroindustriais. Ao menos no que diz respeito ao hábitat larval, pastagens se mostraram ambientes de alta permeabilidade para a colonização tanto de girinos como de libélulas. Por sua vez, plantações de soja aparentam ser completamente impermeáveis para o desenvolvimento das larvas de libélulas, mas temporalmente permeáveis para o desenvolvimento de girinos / The global increase in human population and in per capita consumption patterns has created a strong demand for food, fiber and biofuels that only an industrial model of agricultural production can meet. However, industrial agriculture has serious impacts on biodiversity and on the environment. This thesis aimed at testing the hypothesis that land use and land management for the intensive production of soybeans results in a significant reduction in the performance of freshwater organisms, as indicated by survivorship, growth and/or development. This hypothesis was tested by means of field and lab experiments exposing dragonfly larvae and tadpoles to conditions of temporary ponds distributed across a gradient in environmental degradation comprising cerrado, pastures and sugarcane fields. The performance of dragonfly larvae was significantly influenced by land use and land management. Whereas dragonfly survivorship in cerrado and pastures ranged between 50 and 60%, dragonflies transplanted to soybean fields were rapidly eradicated. The synchrony between pesticide application and temporal patterns in mortality strongly suggests that pesticides are the main driver of environmental change precluding the effective colonization of soybean fields by dragonflies. The performance of tadpoles of Physalaemus cuvieri was also significantly influenced by land use and land management. However, tadpole responses were in general less strong and less consistent than those of dragonflies. Tadpoles transplanted to 10-day old soybean fields (first experiment) and 55-day old soybean fields (second experiment) performed as well or better than tadpoles transplanted to reference sites; in strong contrast, tadpoles transplanted to 50-day old soybean fields (second experiment) suffered 100% mortality. Therefore, specific land management practices mediate P. cuvieri performance along the crop cycle. Pastures were always relatively favorable to tadpole survivorship, growth and development. These results have important implications to our conceptualization of the permeability of the agricultural matrix to aquatic and semiaquatic fauna and, therefore, to the conservation of biodiversity in agroindustrial landscapes. In regards to larval habitat, pastures have shown to be highly permeable to the colonization of tadpoles and dragonflies. In turn, soybean plantations appeared to be impermeable to dragonfly development, but temporally permeable to the development of tadpoles

Many antibiotic resistance genes (ARGs) conferring resistance to a broad range of antibiotics have often been detected in aquatic environments such as untreated and treated wastewater, river and surface water. ARG proliferation in the aquatic environment could depend upon various factors such as geospatial variations, the type of aquatic body, and the type of wastewater (untreated or treated) discharged into these aquatic environments. Likewise, the strong interconnectivity of aquatic systems may accelerate the spread of ARGs through them. Hence a comparative and a holistic study of different aquatic environments is required to appropriately comprehend the problem of antibiotic resistance. Many studies approach this issue using molecular techniques such as metagenomic sequencing and metagenomic data analysis. Such analyses compare the broad spectrum of ARGs in water and wastewater samples, but these studies use comparisons which are limited to similarity/dissimilarity analyses. However, in such analyses, the discriminatory ARGs (associated ARGs driving such similarity/ dissimilarity measures) may not be identified. Consequentially, the reason which drives the dissimilarities among the samples would not be identified and the reason for antibiotic resistance proliferation may not be clearly understood. In this study, an effective methodology, using Extremely Randomized Trees (ET) Algorithm, was formulated and demonstrated to capture such ARG variations and identify discriminatory ARGs among environmentally derived metagenomes. In this study, data were grouped by: geographic location (to understand the spread of ARGs globally), untreated vs. treated wastewater (to see the effectiveness of WWTPs in removing ARGs), and different aquatic habitats (to understand the impact and spread within aquatic habitats). It was observed that there were certain ARGs which were specific to wastewater samples from certain locations suggesting that site-specific factors can have a certain effect in shaping ARG profiles. Comparing untreated and treated wastewater samples from different WWTPs revealed that biological treatments have a definite impact on shaping the ARG profile. While there were several ARGs which got removed after the treatment, there were some ARGs which showed an increase in relative abundance irrespective of location and treatment plant specific variables. On comparing different aquatic environments, the algorithm identified ARGs which were specific to certain environments. The algorithm captured certain ARGs which were specific to hospital discharges when compared with other aquatic environments. It was determined that the proposed method was efficient in identifying the discriminatory ARGs which could classify the samples according to their groups. Further, it was also effective in capturing low-level variations which generally get over-shadowed in the analysis due to highly abundant genes. The results of this study suggest that the proposed method is an effective method for comprehensive analyses and can provide valuable information to better understand antibiotic resistance. / MS / Antibiotic resistance is a natural and primordial process that predates the use of antibiotics in humans for disease treatment and occurs when a bacterium evolves to render the drugs, chemicals, or other agents meant to cure or prevent infections ineffective. Antibiotic resistance genes (ARGs) conferring resistance to a wide range of antibiotics have been widely found in rivers, surface waters, and hospital and farm wastewater discharges. Even treated wastewater from treatment plants is a concern as ARGs have frequently been detected in effluent discharges which poses questions on the effectiveness of treatment plants in removing ARGs. Since, these systems are interconnected there’s a possibility of dissemination and proliferation of ARGs which may pose serious threat to human health. Hence, it is desirable to perform comparative studies among these aquatic habitats. In previous studies, researchers compared different habitats which tells how similar and dissimilar the environments are in terms of ARGs present in these samples. While these analyses are important, it doesn’t tell which ARGs are unique or which ARGs are responsible to create those similarities or dissimilarities. This information is crucial in order to understand the water environments in terms of occurrence and presence of ARGs, the risk posed by them, and in identifying factors responsible for resistance gene proliferation. In this research, a methodology was developed which could capture such ARG variations in the environmental samples, using data analysis algorithms. Further the developed methodology was demonstrated using environmental samples such as wastewater samples from different geographical locations (to understand the spread of ARGs globally), untreated vs treated wastewater (to understand the effectiveness of treatment plants in removing ARGs), and different aquatic habitats (to understand the impact and spread of ARGs within these habitats). It was determined that the proposed method was efficient in differentiating samples and identifying discriminatory ARGs. The comparison between environmental samples showed that the samples from different locations have specific ARGs which were unique to wastewater samples from certain locations suggesting that site-specific factors can have certain effect in shaping the ARG profiles. Comparing untreated and treated samples revealed that treatment plants were able to remove certain ARGs but it was also observed v that some ARGs proliferated after the treatment irrespective of location and treatment plant specific variables. Analyzing different environments, the approach was able to identify certain ARGs which were specific to certain environments. The results of this study suggest that the proposed method is an effective method for comprehensive analyses and can provide valuable information to better understand antibiotic resistance. In essence, it is a valuable addition for improved surveillance of antibiotic resistance pollution and for the framing of best management practices.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第25342号 / 農博第2608号 / 新制||農||1107(附属図書館) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 吉田 天士, 教授 澤山 茂樹, 准教授 神川 龍馬 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Au cours des dix dernières années, les gouvernements de l'Union Européenne ont été encouragés à collecter des données sur le volume et la qualité de tous les effluents d'eaux urbaines ayant un impact environnemental significatif sur les milieux aquatiques récepteurs. Les méthodes de surveillance de ces flux nécessitent des améliorations, en particulier pour les déversoirs d’orage, structures complexes responsables en grande partie de la dégradation de la qualité des milieux récepteurs. Le DSM-flux (Dispositif pour la surveillance et maîtrise des flux d'eaux et polluants des réseaux d'eaux pluviales et unitaires) est un nouveau dispositif préfabriqué et pré-étalonné qui garantit les conditions hydrauliques appropriées permettant de mesurer les débits et volumes déversés ainsi que les concentrations et masses de polluants qui y sont transportés. Dans cette thèse, une relation permettant de mesurer le débit au passage du DSM-flux a été construite grâce à une étude expérimentale sur modèle physique réduit, puis validée pour plusieurs configurations d'écoulement à l'amont du dispositif. Quelles que soient les conditions hydrauliques en amont, les incertitudes relatives sont inférieures à 15% et 2% pour les débits et les volumes étudiés, respectivement, ce qui reste équivalent, voire mieux, par rapport aux incertitudes des méthodes actuelles les plus fiables. La méthode de mesure a été validée in situ sur un dispositif à grande échelle construit sur le terrain et fonctionnant en conditions réelles, ce qui montre la robustesse de la méthode. De plus, grâce à sa conception originale, le DSM-flux favorise l'interception d'une fraction des polluants particulaires. L’hydrodynamique de ce dispositif de mesure a été analysée ainsi que les conditions qui engendrent la décantation des polluants particulaires. En fonction des conditions d'écoulement, ce dispositif peut retenir 50% de la masse totale des matières solides fines en suspension transitant par le dispositif, mais pour des écoulements à débits élevés, cette efficacité est significativement réduite. Sa capacité de rétention a été aussi observée sur le terrain et une méthodologie a été élaborée pour quantifier son efficacité de rétention lors d'études futures. Mise à part sa performance hydraulique, du point de vue opérationnel, le dispositif présente d’autres avantages par rapport à d’autres dispositifs existants : (i) il est pré-étalonné et peut être installé à l’aval de déversoirs d’orage déjà existants, (ii) il peut s’insérer directement au sein du canal de décharge (installation d’un regard de visite équipé d’un DSM), (iii) sa performance hydraulique est indépendante des conditions de l’écoulement à l’amont et (iv) il s’agit d’un dispositif intégré de mesure de débits et de leur qualité simultanément, en plus d’intercepter une partie de polluants particulaires. / Over the past decade, European Union governments have encouraged to collect data on the volume and quality of all urban water effluents with a significant environmental impact on receiving aquatic environments. Methods for monitoring these flows require improvements, particularly for combined sewer overflows, which are complex flows that contribute in significant proportion to the degradation of the quality of the receiving waters. The DSM-flux (Device for Stormwater and combined sewer flows Monitoring and the control of pollutant fluxes) is a new pre-calibrated and pre-designed device that guarantees the appropriate hydraulic conditions for measuring discharged flows and volumes as well as the concentrations and mass loads of pollutants carried in suspension by the flow. In this PhD work, a relationship allowing to measure the flow rates conveying through the DSM-flux was determined thanks to an experimental study on a small-scale physical model, and then validated for several flow configurations upstream of the device. Whatever the upstream hydraulic conditions are, the relative uncertainties are less than 15% and 2% for the flow rates and volumes studied, respectively, which is equivalent to the uncertainties of the most reliable current methods. The monitoring methodology was validated in situ in a large-scale device installed at the field and operating in real conditions, which shows the robustness of the method. Moreover, thanks to its original design, the DSM-flux allows the interception of a fraction of particulate pollutants. The hydrodynamics of this monitoring device were analysed as well as the conditions that cause the settling of particulate pollutants. Depending on the flow conditions, this device can retain 50% of the total mass of fine suspended solid matter transiting through the device, but for flows at high discharge rates, this efficiency is significantly reduced. Its retention capacity has also been observed in the field and a methodology has been developed to quantify its retention efficiency in future studies. Apart from its performance, from an operational point of view, the device has other advantages compared to other current devices: (i) it is pre-calibrated and can be installed downstream from existing combined sewer overflows, (ii) it can be directly installed through a manhole in the discharge channel, (iii) its hydraulic performance is independent from the flow conditions upstream, and (iv) it is an integrated monitoring device, measuring flow rates and their quality simultaneously, in addition to intercepting a part of the particulate pollutants.

Although the societies that lived in Egypt during the interlude of Pharaonic Period can be defined by the way of life intrinsically linked to the aquatic environment, whether for subsistence, socializing or in a symbolic way, the archaeological sites are analyzed only from point of view of land, ignoring your surroundings. Consequently, the areas of oasis, located in the Western Desert, are also ignored about this type of research. The suggestion of this research is to propose the observation of societies Egyptian oasis of a aquatic viewpoint, independent of the Nile or the lakes of Libyan Desert, but not observed only as a place to collect resources, but a place used for socializing and inspiration to culture material. To understand the populations of oasis is necessary in first understand the populations of the Nile and his speeches, especially those related to its vision over what was the desert environment and consequently its inhabitants and how this implies in material culture, especially those related to aquatic territories. / Embora as sociedades que viveram no Egito ao longo do intervalo de tempo que constitui o chamado Período Faraônico possam ser definidas pelo modo de vida ligado ao ambiente aquático, seja para a subsistência, socialização ou de uma forma simbólica, os sítios são analisados do ponto de vista somente da terra, ignorando o seu entorno. Consequentemente, as áreas de oásis, que se encontram no Deserto Ocidental, também não raramente são postas de lado no que diz respeito a este tipo de pesquisa. Desta forma, a sugestão é propor a observação das sociedades egípcias dos oásis de um ponto de vista aquista em que todos os ambientes aquáticos, seja o rio Nilo ou as regiões lacustres do Deserto Líbio, devem ser levantados, ou seja, não observados somente como um local para captação de recursos, e sim um espaço utilizado para a socialização e inspiração para a cultura material. Para se compreender as populações de oásis é necessário primeiramente entender as populações do Nilo e seus discursos, principalmente aqueles relacionados à sua visão em relação ao que era o ambiente desértico e consequentemente seus habitantes e de que forma isto implica na cultura material, especialmente aquelas ligadas aos territórios aquáticos.