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Freshwater lakes provide many important ecosystem functions and services to support biodiversity and human well-being. Proximal and remote sensing methods represent an efficient approach to derive water quality indicators such as optically active substances (OAS). Measurements of above-ground remote and in situ proximal sensors, however, are limited to observations of the uppermost water layer. We tested a hyperspectral imaging system, customized for underwater applications, with the aim to assess concentrations of chlorophyll a (CHLa) and colored dissolved organic matter (CDOM) in the water columns of four freshwater lakes with different trophic conditions in Central Germany. We established a measurement protocol that allowed consistent reflectance retrievals at multiple depths within the water column independent of ambient illumination conditions. Imaging information from the camera proved beneficial for an optimized extraction of spectral information since low signal areas in the sensor’s field of view, e.g., due to non-uniform illumination, and other interfering elements, could be removed from the measured reflectance signal for each layer. Predictive hyperspectral models, based on the 470 nm–850 nm reflectance signal, yielded estimates of both water quality parameters (R² = 0.94, RMSE = 8.9 µg L−1 for CHLa; R² = 0.75, RMSE = 0.22 m−1 for CDOM) that were more accurate than commonly applied waveband indices (R² = 0.83, RMSE = 13.2 µg L−1 for CHLa; R² = 0.66, RMSE = 0.25 m−1 for CDOM). Underwater hyperspectral imaging could thus facilitate future water monitoring efforts through the acquisition of consistent spectral reflectance measurements or derived water quality parameters along the water column, which has the potential to improve the link between above-surface proximal and remote sensing observations and in situ point-based water probe measurements for ground truthing or to resolve the vertical distribution of OAS.

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<p>Dissolved organic matter (DOM) in natural waters is a heterogeneous mixture of organic molecules with direct and indirect influences on aquatic organisms. Although the influences are usually attributed to DOM quantity (quantified as Dissolved Organic Carbon, DOC), the role of quality (optical and binding characteristics obtained by absorbance and fluorescence spectroscopy and potentiometric titration, respectively) is not well-understood. Through an initial critical review of the literature, followed by experimental geochemical, toxicological, and physiological investigations, a number of conclusions were reached that improve our knowledge in this area. Freshwater DOM sources exhibit source-dependent protection against metal toxicity, in particular copper (Cu). Generally, for this indirect effect, optically-dark terrestrially-derived or allochthonous DOMs offer better protection than microbially-derived or autochthonous sources. Linear regressions revealed that the better ameliorative effect is principally related to a higher aromatic composition (specific absorption coefficient, SAC₃₄₀) and a greater humic-like fluorescent component as quantified by parallel factor analysis (PARAFAC). In addition, the allochthonous DOMs were shown to have relatively higher magnitudes of titration index (TI), a new summary of chemical reactivity of DOM molecules obtained by titration analysis, and closely related to optical properties. TI was strongly correlated with SAC₃₄₀, suggesting greater binding capacities for DOM molecules with higher SAC₃₄₀. Consequently, a method for incorporation of SAC₃₄₀ as a DOM quality measure into the Biotic Ligand Model (BLM) was developed which improved Cu toxicity predictions in experimental tests with natural DOMs. For direct effects, two basic physiological functions (Na⁺ metabolism and nitrogen excretion) of the adult water flea (<em>Daphnia magna</em>, a cladoceran crustacean) and the zebrafish (<em>Danio </em><em>rerio</em>, a teleost fish) were investigated at circumneutral and acidic pH (≥ 7 and ~ 5, respectively). Three previously characterized, chemically-distinct natural DOM sources as well as a commercial humic acid (AHA) were examined. Regardless of the pH conditions, while Na⁺ regulation of <em>D</em>. <em>magna </em>remained unaffected by the presence of all DOMs, the passive diffusive efflux of Na⁺ in zebrafish was attenuated, indicating ameliorative action against unidirectional Na⁺ loss. In addition, only a distinct allochthonous-autochthonous DOM source stimulated the Na⁺ uptake rate of zebrafish at low pH. Ammonia excretion rates of <em>D</em>. <em>magna </em>were reduced at circumneutral pH by the most highly coloured, allochthonous DOM, and at low pH by all three natural DOMs. Both in <em>D. magna </em>and in <em>D. rerio</em>, urea excretion rates at both pH conditions were not influenced by the presence of the various DOMs, and the same was true for ammonia excretion in the zebrafish. A commercially prepared humic acid (Aldrich humic acid, AHA) exerted anomalous actions relative to those of natural DOMs, and does not appear to be representative of their normal effects. In contrast to the actions of DOM in detoxifying metals, these direct effects of DOMs on freshwater organisms appeared highly unpredictable with variable dependencies on the source, pH and species. This thesis has advanced our understanding of the relationships between DOM quality and its indirect and direct effects on aquatic organisms, and points to new directions for future work.</p> / Doctor of Philosophy (PhD)

Landfilling is the most widely used method for the disposal of municipal solid wastes (MSW) in the United States due to its simplicity and low cost. According to the 2014 report on Advancing Sustainable Materials Management by the USEPA, only 34% of the total MSW generated in the US was recycled, while 13% was combusted for energy recovery. In 2014, 53% of the MSW generated, (i.e. 136 million tons) in the US was landfilled. The treatment of landfill leachates, generated by percolation of water through the landfill, primarily due to precipitation, has been found to be one of the major challenges associated with landfill operation and management. Currently, leachates from most landfills are discharged into wastewater treatment plants, where they get treated along with domestic sewage. Issues associated with treatment of landfill leachates due to their high nitrogen and heavy metal content have been widely studied. Recently, it has been observed that the organic carbon in landfill leachates, specifically humic and fulvic acids (together referred to as "humic substances") contain aromatic groups that can absorb large amounts of ultraviolet (UV) light, greatly reducing the UV transmissivity in wastewater plants using UV disinfection as the final treatment step. This interference with UV disinfection is observed even when landfill leachates constitute a very small fraction (of the order of 1%) of the total volumetric flow into wastewater treatment plants. Humic substances are present as dissolved organic matter (DOM) and typically show very low biodegradability. Removing these substances using chemical treatment or membrane processes is an expensive proposition. However, the concentrations of humic substances are found to be reduced in leachates from landfill cells that have aged for several years, suggesting that these substances may be degraded under the conditions of long-term landfilling. The primary objective of this research was to use a two-stage process employing thermophilic pretreatment followed by a mesophilic anaerobic membrane bioreactor (AnMBR) to mimic the conditions of long-term landfilling. The AnMBR was designed to keep biomass inside the reactor and accelerate degradation of biologically recalcitrant organic carbon such as humic substances. The treatment goal was to reduce UV absorbance in raw landfill leachates, potentially providing landfills with an innovative on-site biological treatment option prior to discharging leachates into wastewater treatment plants. The system was operated over 14 months, during which time over 50% of UV-quenching organic carbon and 45% of UV absorbance was consistently removed. To the best of our knowledge, these removal values are higher than any reported using biological treatment in the literature. Comparative studies were also performed to evaluate the performance of this system in treating young leachates versus aged leachates. Next-generation DNA sequencing and quantitative PCR (qPCR) were used to characterize the microbial community in raw landfill leachates and the bioreactors treating landfill leachate. Analysis of microbial community structure and function revealed the presence of known degraders of humic substances in raw as well as treated landfill leachates. The total number of organisms in the bioreactors were found to be higher than in raw leachate. Gene markers corresponding to pathogenic bacteria and a variety of antibiotic resistance genes (ARGs) were detected in raw landfill leachates and the also in the reactors treating leachate, which makes it necessary to compare these ARG levels with wastewater treatment in order to determine if leachates can act as sources of ARG addition into wastewater treatment plants. In addition, the high UV absorbance of leachates could hinder the removal of ARBs and ARGs by UV disinfection, allowing their release into surface water bodies and aiding their proliferation in natural and engineered systems. / Ph. D.

Les Argiles de Boom ont été identifiées par le SCK-CEN comme un éventuel site de stockage de déchets nucléaires en couche géologique profonde : elles font l’objet d’études dans le laboratoire souterrain de Mol (Belgique). Dans ce contexte, il est important d’évaluer les conséquences du creusement de galeries sur les propriétés de ces Argiles. Ce travail de thèse cible plus particulièrement les effets d’oxydation à l’air et de biodégradation anaérobie sur la MO fossile. Les expériences d’oxydation ont combiné des suivis expérimentaux (série artificielle) et des études sur des échantillons altérés in situ (série naturelle) dans les galeries du laboratoire. Elles ont ciblé le kérogène, la MOE et MOD. La confrontation des données des deux séries révèle que nos simulations expérimentales sont représentatives des processus ayant lieu dans les galeries. Ces travaux démontrent aussi que l’oxydation induit (i) une augmentation importante de la quantité de MOD et (ii) une modification majeure de la chimie de la MOE et de la MOD caractérisée par la formation de molécules oxygénées de faible poids moléculaire. Par ailleurs, l’étude comparative des eaux issues des échantillons altérés avec celles prélevées dans les piézomètres du site démontre que ces dernières ne sont pas affectées par des processus d’oxydation et sont comparables aux eaux issues des échantillons sains. Des expériences de biodégradation menées sur des argiles saines et préalablement oxydées artificiellement n’ont montré aucune évolution significative de la MO fossile (MOE et MOD); la biodégradation anaérobie n’est donc pas un processus dominant dans le contexte des perturbations induites par les excavations / The Boom Clay was focused because it is identified by SCK-CEN as a possible radioactive waste storage in the geological disposal site and in situ experiments are performed in the underground laboratory of Mol (Belgium). In this context, it is important to assess the consequences of galleries excavation on the properties of the Boom Clay. The particular focus of this study is the effects of air oxidation and anaerobic biodegradation on the OM. The experiments dealing with the effects of air oxidation have combined studies of artificial oxidized samples (artificial series) and samples altered in the gallery of the underground laboratory (natural series). These experiments focus on the Kerogen, the EOM and the DOM. The comparison of data from artificial and natural series shows firstly that our experimental simulations are the representative of processes taking place in the galleries. These studies show that air oxidation induced (i) a significant increase in the amount of DOM and (ii) a major change in the chemistry of the EOM and DOM characterized by the formation of low molecular weight oxygenated molecules. Moreover, comparison between water extracted from altered samples and piezometers shows that the water of the site is not affected by oxidation processes. The piezometer water samples are similar to that extracted from non-altered samples. Biodegradation experiments conducted on non altered and artificially oxidized clay did not show significant changes of fossil and dissolved organic matter. It seems that anaerobic biodegradation is not a major process in the context of disturbances induced by the excavation

Ce doctorat s’intègre dans le projet ANR BIOMET (JC05_59809) et a eu pour vocation d’améliorer les connaissances actuelles sur l’influence de la matière organique dissoute sur la spéciation et la biodisponibilité des métaux particulièrement dans le cas de système sous forte pression urbaine tel que la Seine. La compréhension de l’influence de la MOD sur la spéciation et la biodisponibilité des métaux suppose en outre que l’on connaisse précisément sa composition chimique ou plus exactement ses groupements fonctionnels. C’est pourquoi une partie de ces travaux est consacrée à l’extraction et la caractérisation de la matière organique dissoutes d’origine naturelle et urbaine. La caractérisation des fractions de MOD a été réalisée de manière originale par une approche multidimensionnelle à l’aide d’un véritable éventail de techniques analytiques (analyses élémentaires; isotopiques; fonctionnelles et moléculaires) permettant ainsi de mieux aborder l’influence de la MOD sur la spéciation et la biodisponibilité du cuivre et du plomb. Parallèlement à l’étude de caractérisation de la MOD, ce travail s’attache à mieux cerner le rôle de la MOD d’origine urbaine en particulier de la MOD hydrophile sur la spéciation et la biodisponibilité du cuivre et du plomb. Dans cet objectif, les techniques : potentiométrique à l’aide d’électrode ionique spécifique et la récente technique électrochimique AGNES ainsi que des biotests de toxicité aiguë (Daphnia magna) et de bioaccumulation (Fontinalis antipyretica) ont permis : - d’étudier la complexation du cuivre et du plomb par les fractions de MOD obtenues afin notamment de fournir des paramètres de complexations des MOD hydrophiles peu connues jusqu’à présent et ainsi mieux prédire le transport des métaux en milieu urbain. - d’évaluer le rôle protecteur de la MOD d’origine urbaine sur la biodisponibilité du cuivre. Les résultats ont montré que la MOD issue des effluents de station d’épuration et rejetée dans le milieu récepteur présente des caractéristiques originales à savoir un fort pourcentage de MOD hydrophile, c’est à dire une faible hydrophobicité et un degré d’aromaticité peu marqué soulignant le caractère peu réfractaire de cette MOD. En revanche une plus grande diversité fonctionnelle de la MOD d’origine urbaine par rapport à la MOD naturelle a été mise en évidence notamment par un taux de structures protéiques très important. Les résultats obtenus ici pour la première fois vis-à-vis des MOD hydrophiles d’origine urbaine ont montré une réactivité particulière vis-à-vis du cuivre. En effet les fractions HPI et plus généralement les fractions issues des effluents de station d’épuration ont montré une teneur en sites complexants plus élevée que ce qu’il avait été déjà observé pour des matières organiques naturelles. Les valeurs des constantes ne semblent pas varier d’une fraction à l’autre et assez peu suivant l’origine de la MOD. Le rôle particulier de l’azote dans la complexation du cuivre notamment sous la forme de groupements amines a été mis en évidence. Les approches utilisées pour évaluer la biodisponibilité du cuivre ont révélé pour l’ensemble des fractions de MOD un effet protecteur vis-à-vis du cuivre sur les organismes vivants. Néanmoins cet effet protecteur ne se trouve pas à la hauteur de celui pouvant être prédit par le modèle de l’ion libre principalement dû à une biodisponibilité de certains complexes organiques. Ceci peut être expliqué par l’important taux de structures protéiques dans ces MOD, les protéines étant connues pour jouer un rôle important dans les mécanismes de transports des métaux au sein des organismes. Par ailleurs, l’outil DGT (Diffusive gradient in thin films) a montré son efficacité pour évaluer la fraction biodisponible du cuivre / This thesis was carried out on the framework of the ANR BIOMET research project (JC05_59809). The main objectives were to improve the current knowledge on the influence of dissolved organic matter (DOM) on metal speciation and bioavailability in urban aquatic system. The understanding of the influence of DOM on trace metal speciation and bioavailability required that the chemical composition of DOM, more exactly its binding sites should be well understood. Therefore, one part of this research focused on the isolation and characterization of DOM. The characterization of DOM, with a multidimensional approach was realized with a lot of various techniques (such as elemental, isotopic, functional and molecular) that were of prime importance to better understand the influence of DOM on trace metal speciation and bioavailability. To accomplish these objectives, the techniques such as potentiometry with ionic selective electrode and the recent electroanalytical technique AGNES and bioassays such as a bioaccumulation test (Fontinalis antipyretica) and an acute toxicity test (Daphnia magna) were performed in order to: - study the copper and lead binding by isolated DOM fractions in order to give some binding parameters of hydrophilic DOM and to better predict the fate of the trace metal. - evaluate the protective role of urban DOM on copper bioavailability. Results showed some particular characteristics of DOM from wastewater effluent such as a high proportion of hydrophilic DOM, i.e. a low hydrophobicity and a low degree of aromaticity underlying the low refractory character of urban DOM. Nevertheless a higher content of various functional groups was determined in urban DOM than in natural DOM. A very high content of proteinaceous structures was particularly identified in urban DOM. Binding experiments revealed for the first time on urban hydrophilic DOM, a higher content of binding sites than in natural DOM and these sites are strongly correlated to amino groups. The values of binding constant seem to not vary according to the nature of the fraction or the origin. The different approaches used to evaluate copper bioavailability depicted a protective role of DOM to the organisms Daphnia magna and Fontinalis antipyretica. Nevertheless this protective effect is hardly explained by the free ion concentration due to a bioavailability of some organic complexes. This feature could be explain with the high content of proteinaceous structures in these DOM fractions, since proteins are well know to play an important role in the transport mechanisms of trace metals into the organisms. Moreover, the DGT device (diffusive gradient in thin films) shows a good efficiency to assess the bioavailable copper

Dans cette thèse, nous nous focalisons sur le problème de la décomposition polyadique minimale de tenseurs de dimension trois, problème auquel on se réfère généralement sous différentes terminologies : « Polyadique Canonique » (CP en anglais), « CanDecomp », ou encore « Parafac ». Cette décomposition s'avère très utile dans un très large panel d'applications. Cependant, nous nous concentrons ici sur la spectroscopie de fluorescence appliquée à des données environnementales particulières de type échantillons d'eau qui pourront avoir été collectés en divers endroits ou différents moments. Ils contiennent un mélange de plusieurs molécules organiques et l'objectif des traitements numériques mis en œuvre est de parvenir à séparer et à ré-estimer ces composés présents dans les échantillons étudiés. Par ailleurs, dans plusieurs applications comme l'imagerie hyperspectrale ou justement, la chimiométrie, il est intéressant de contraindre les matrices de facteurs recherchées à être réelles et non négatives car elles sont représentatives de quantités physiques réelles non négatives (spectres, fractions d'abondance, concentrations, ...etc.). C'est pourquoi tous les algorithmes développés durant cette thèse l'ont été dans ce cadre (l'avantage majeur de cette contrainte étant de rendre le problème d'approximation considéré bien posé). Certains de ces algorithmes reposent sur l'utilisation de méthodes proches des fonctions barrières, d'autres approches consistent à paramétrer directement les matrices de facteurs recherchées par des carrés. / In this manuscript, we focus on the minimal polyadic decomposition of third order tensors, which is often referred to: “Canonical Polyadic” (CP), “CanDecomp”, or “Parafac”. This decomposition is useful in a very wide panel of applications. However, here, we only address the problem of fluorescence spectroscopy applied to environment data collected in different locations or times. They contain a mixing of several organic components and the goal of the used processing is to separate and estimate these components present in the considered samples. Moreover, in some applications like hyperspectral unmixing or chemometrics, it is useful to constrain the wanted loading matrices to be real and nonnegative, because they represent nonnegative physical data (spectra, abundance fractions, concentrations, etc...). That is the reason why all the algorithms developed here take into account this constraint (the main advantage is to turn the approximation problem into a well-posed one). Some of them rely on methods close to barrier functions, others consist in a parameterization of the loading matrices with the help of squares. Many optimization algorithms were considered: gradient approaches, nonlinear conjugate gradient, that fits well with big dimension problems, Quasi-Newton (BGFS and DFP) and finally Levenberg-Marquardt. Two versions of these algorithms have been considered: “Enhanced Line Search” version (ELS, enabling to escape from local minima) and the “backtracking” version (alternating with ELS).

Dissolved organic matter (DOM) is the largest pool of organic carbon in aquatic systems and an important component of the global carbon cycle. Large amounts of DOM are decomposed within lakes, resulting in fluxes of CO2 and CH4 to the atmosphere. Therefore, there is a considerable interest in understanding the controls of DOM decomposition in freshwaters. There is evidence that in lakes intrinsic controls related to DOM composition are of primary importance, yet our knowledge about molecular drivers of DOM degradation is limited. This thesis addresses the link between chemical composition and reactivity of lake DOM by applying an experimental approach, molecular-level DOM characterization, and kinetic modeling of DOM decay. The first study shows that photoinduced transformations and partial removal of colored aromatic components of DOM have profound effects on DOM degradation kinetics, mediated by the shifts in the relative share of rapidly and slowly degrading DOM fractions. Two following studies estimate exponential decay coefficients for each individual molecular formula identified within bulk DOM. A continuous distribution of exponential decay coefficients is found within bulk DOM, which directly corroborates the central and previously empirically untested assumption behind the reactivity continuum model of DOM decay. Further, individual decay rates are evaluated in connection to specific molecular properties. On average, highly unsaturated and phenolic compounds appear to be more persistent than compounds with higher aromatic content (plant polyphenols and polycondensed aromatics), and aliphatic compounds demonstrate the highest decay rates. The reactivity of aromatics additionally increases with increasing nominal oxidation state of carbon. Molecular analysis further indicates that increasing reactivity of DOM after UV exposure is caused by disintegration of supramolecular complexes. Study IV shows that changes in relative proportion of terrestrial versus algal DOM control degradability of DOM through seasons. Under ice, when algal-derived DOM is maximally depleted, DOM degradation potential converges to similarly low levels, regardless of lake type (productive or humic), and bacterial respiration primarily relies on terrestrial carbon. This suggests a general pattern of baseline metabolism across boreal lakes. I conclude that DOM is a dynamic reactivity continuum and a tight link exists between DOM behavior and compositional properties.