Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous, toxic contaminants that are released to the environment from various petrogenic and pyrogenic sources. In an effort to more clearly identify and trace sources of PAHs in the environment, purification and compound specific isotope analysis methods were developed to accurately measure the stable carbon isotope ratio of individual PAHs. Development of the method included improving accuracy and precision of the isotopic measurement by producing highly pure extracts using various chromatographic techniques. The method was refined by improving compound separations using purification techniques and high resolution chromatographic columns. The purification method consists of alumina/silica gel column chromatography, gel permeation chromatography and thin layer chromatography. The mean recovery of PAHs after the purification procedure was approximately 80 %. Sample purities after purification were verified by GC/FID and full scan mass spectrometry. To better resolve peaks and provide more accurate stable carbon isotope measurements, various gas chromatographic conditions were evaluated. The precision of the method ranged between 0.08 and 0.43 . The analytical protocols were evaluated to confirm compositional and stable isotopic integrity during purification and stable isotopic analysis. To confirm the utility of the purification and isotope analysis methods, various environmental samples from marine, land and lacustrine environments were analyzed. The isolates were analyzed for the composition and the stable carbon isotope ratios of PAHs. The stable carbon isotope ratio was measured by GC/IRMS and the results, along with quantitative compound compositions, were used to characterize and identify the contaminant sources. The sources of the PAHs in the study areas were differentiated by PAH molecular ratios and confirmed by stable carbon isotope ratios. This study confirms that compound specific isotope analysis of pollutants by GC/IRMS can be used to identify PAH sources in environmental samples. The study also confirms that the purification and stable carbon isotope analysis methods that were developed can be used to accurately measure the stable carbon isotope ratios of PAHs in environmental samples for the purpose of source identification. GC/IRMS measurement of stable isotopic compositions can be an effective fingerprinting method when used in conjunction with traditional molecular composition methods.

Little is known about the enzyme-substrate interactions occurring during the dechlorination of chloroform (CF) and 1,1,1-trichloroethane (1,1,1-TCA) by the enrichment culture containing Dehalobacters, hereafter called DHB-CF/MEL. Compound specific isotope analysis (CSIA) is used to investigate the factors which may affect the isotope fractionation observed for CF and 1,1,1-TCA dechlorination. This thesis reports the first isotope enrichment factors observed for CF biodegradation at -27.5‰ ± 0.9‰, thus providing fundamental information for comparing isotope enrichment factors observed during trichlorinated alkane degradation by DHB-CF/MEL. The thesis also reports how the presence of CF and 1,1,1-TCA influences isotope fractionation and explores the possible influence of substrate inhibition on isotope fractionation during 1,1,1-TCA dechlorination. The data suggests that substrate inhibition during 1,1,1-TCA dechlorination by DHB-CF/MEL may not affect carbon isotope fractionation. The results suggest that CSIA is a promising monitoring tool even for the simultaneous biodegradation of CF and 1,1,1-TCA at different 1,1,1-TCA starting concentration.

Little is known about the enzyme-substrate interactions occurring during the dechlorination of chloroform (CF) and 1,1,1-trichloroethane (1,1,1-TCA) by the enrichment culture containing Dehalobacters, hereafter called DHB-CF/MEL. Compound specific isotope analysis (CSIA) is used to investigate the factors which may affect the isotope fractionation observed for CF and 1,1,1-TCA dechlorination. This thesis reports the first isotope enrichment factors observed for CF biodegradation at -27.5‰ ± 0.9‰, thus providing fundamental information for comparing isotope enrichment factors observed during trichlorinated alkane degradation by DHB-CF/MEL. The thesis also reports how the presence of CF and 1,1,1-TCA influences isotope fractionation and explores the possible influence of substrate inhibition on isotope fractionation during 1,1,1-TCA dechlorination. The data suggests that substrate inhibition during 1,1,1-TCA dechlorination by DHB-CF/MEL may not affect carbon isotope fractionation. The results suggest that CSIA is a promising monitoring tool even for the simultaneous biodegradation of CF and 1,1,1-TCA at different 1,1,1-TCA starting concentration.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous, toxic contaminants that are released to the environment from various petrogenic and pyrogenic sources. In an effort to more clearly identify and trace sources of PAHs in the environment, purification and compound specific isotope analysis methods were developed to accurately measure the stable carbon isotope ratio of individual PAHs. Development of the method included improving accuracy and precision of the isotopic measurement by producing highly pure extracts using various chromatographic techniques. The method was refined by improving compound separations using purification techniques and high resolution chromatographic columns. The purification method consists of alumina/silica gel column chromatography, gel permeation chromatography and thin layer chromatography. The mean recovery of PAHs after the purification procedure was approximately 80 %. Sample purities after purification were verified by GC/FID and full scan mass spectrometry. To better resolve peaks and provide more accurate stable carbon isotope measurements, various gas chromatographic conditions were evaluated. The precision of the method ranged between 0.08 and 0.43 . The analytical protocols were evaluated to confirm compositional and stable isotopic integrity during purification and stable isotopic analysis. To confirm the utility of the purification and isotope analysis methods, various environmental samples from marine, land and lacustrine environments were analyzed. The isolates were analyzed for the composition and the stable carbon isotope ratios of PAHs. The stable carbon isotope ratio was measured by GC/IRMS and the results, along with quantitative compound compositions, were used to characterize and identify the contaminant sources. The sources of the PAHs in the study areas were differentiated by PAH molecular ratios and confirmed by stable carbon isotope ratios. This study confirms that compound specific isotope analysis of pollutants by GC/IRMS can be used to identify PAH sources in environmental samples. The study also confirms that the purification and stable carbon isotope analysis methods that were developed can be used to accurately measure the stable carbon isotope ratios of PAHs in environmental samples for the purpose of source identification. GC/IRMS measurement of stable isotopic compositions can be an effective fingerprinting method when used in conjunction with traditional molecular composition methods.

Feeding experiments were conducted on Atlantic pollock (Pollachius virens) to examine the variability in tissue fatty acid (FA) composition and stable carbon isotope fractionation of FA during digestion, assimilation and mobilization of lipids. The FA profiles and compound-specific carbon isotopes of chylomicrons, liver, muscle and fasted serum were compared to diet. FA analysis demonstrated similarity among tissue groups despite differences in feeding states. The FA results indicate the blood of post-prandial fish may serve as an alternative to tissue biopsies for the estimation of marine fish diets with compound-specific isotope analysis (CSIA). Despite similarity among FA profiles, the carbon isotope discrimination factors of FA varied independently, which suggests that fractionation is influenced by the degree to which individual FA are oxidized. These results provide preliminary information that is necessary in order to use CSIA to estimate the effects of fish diets.

High Arctic permafrosted soils represent a massive sink in the global carbon cycle, accounting for twice as much carbon as what is currently stored as carbon dioxide in the atmosphere. However, with current warming trends this sink is in danger of thawing and potentially releasing large amounts of carbon as both carbon dioxide and methane into the atmosphere. It is difficult to make predictions about the future of this sink without knowing how it has reacted to past temperature and climate changes. This dissertation summarizes the results of the first study to look at long term, fine scale organic carbon delivery by the high-Arctic Colville River into Simpson’s Lagoon in the near-shore Beaufort Sea. Modern delivery of organic carbon to the Lagoon was determined to come from a variety of sources through the use of a three end-member mixing model and sediment biomarker concentrations. These sources include the Colville River in the western area of the Lagoon near the river mouth, marine sources in areas of the Lagoon without protective barrier islands, and coastal erosional sources and the Mackenzie River in the eastern area of the Lagoon. Downcore organic carbon delivery was measured on two cores in the Lagoon, one taken near the mouth of the Colville River (spans about 1800 years of history) and one taken on the eastern end of the Lagoon (spans about 600 years of history). Bulk organic parameters and biomarkers were measured in both cores and analyzed with Principle Component Analysis to determine long-term trends in organic carbon delivery. It was shown that at various times in the past, highly degraded organic carbon inputs of what is likely soil and peat carbon were delivered to the Lagoon. At other times, inputs of fresher, non-degraded, terrestrially-derived organic carbon inputs of what are likely higher amounts of plant and vegetative material was delivered to the Lagoon. Inputs of degraded soil carbon were also shown to correspond to higher temperatures on the North Slope of Alaska, likely indicating that warmer temperatures lead to a thawing of permafrost and in turn organic carbon mobilization to the coastal Beaufort Sea.

The Everglades is a sub-tropical coastal wetland characterized among others by its hydrological features and deposits of peat. Formation and preservation of organic matter in soils and sediments in this wetland ecosystem is critical for its sustainability and hydrological processes are important divers in the origin, transport and fate of organic matter. With this in mind, organic matter dynamics in the greater Florida Everglades was studied though various organic geochemistry techniques, especially biomarkers, bulk and compound specific δ13C and δD isotope analysis. The main objectives were focused on how different hydrological regimes in this ecosystem control organic matter dynamics, such as the mobilization of particulate organic matter (POM) in freshwater marshes and estuaries, and how organic geochemistry techniques can be applied to reconstruct Everglades paleo-hydrology. For this purpose organic matter in typical vegetation, floc, surface soils, soil cores, and estuarine suspended particulates were characterized in samples selected along hydrological gradients in the Water Conservation Area 3, Shark River Slough and Taylor Slough. This research focused on three general themes: (1) Assessment of the environmental dynamics and source-specific particulate organic carbon export in a mangrove-dominated estuary. (2) Assessment of the origin, transport and fate of organic matter in freshwater marsh. (3) Assessment of historical changes in hydrological conditions in the Everglades (paleo-hydrology) though biomarkes and compound specific isotope analyses. This study reports the first estimate of particulate organic carbon loss from mangrove ecosystems in the Everglades, provides evidence for particulate organic matter transport with regards to the formation of ridge and slough landscapes in the Everglades, and demonstrates the applicability of the combined biomarker and compound-specific stable isotope approach as a means to generate paleohydrological data in wetlands. The data suggests that: (1) Carbon loss from mangrove estuaries is roughly split 50/50 between dissolved and particulate carbon; (2) hydrological remobilization of particulate organic matter from slough to ridge environments may play an important role in the maintenance of the Everglades freshwater landscape; and (3) Historical changes in hydrology have resulted in significant vegetation shifts from historical slough type vegetation to present ridge type vegetation.

Le potentiel de biodégradation des éthènes chlorés (ECs) et du dichlorométhane (DCM) dans les eaux souterraines de l’ancien site industriel de Themeroil (Varennes-le-Grand, France) a été évalué par des études en microcosmes, à travers l’utilisation de biomarqueurs moléculaires, et par analyse isotopique spécifique au composé (compound specific isotope analysis, CSIA). L’objectif de ce travail a été d’évaluer i) la biodégradation de ces polluants et la diversité bactérienne associée dans les eaux du site, et ii) l’impact de mélanges de contaminants et des conditions rédox dans ce processus. L’implication majeure d’un taxon bactérien affilié à Dehalococcoides dans la dégradation du PCE dans les eaux du site, et son lien potentiel aux gènes de déshalogénase pceA et vcrA associés au processus de déchloration, ont été mises en évidence. La dégradation du DCM en présence d’ECs dans les eaux du site a ensuite été démontrée, et des souches bactériennes dégradant le DCM ont été isolées à partir d’eaux du site et caractérisées. La CSIA a révélé une forte biodégradation du DCM in situ. Des analyses des eaux du site, par qPCR ciblant les gènes dcmA et dhlA de la biodégradation bactérienne du DCM, et par séquençage haut-débit du gène de l’ARNr 16S, ont permis d’évaluer le rôle potentiel de différents taxa bactériens associés à la dégradation du DCM. Il a ainsi été montré que la répartition spatiale de ces taxa sur site dépend dans une large mesure des conditions rédox et du niveau de contamination. L’influence de ces paramètres sur la biodégradation, étudiée ensuite en microcosmes, a été confirmée par l’observation de différents profils de dégradation dans des conditions rédox et de co-contamination distinctes. Ceci suggère la participation de différents types de métabolisme à la biodégradation des éthènes et alcanes chlorés sur site. Les résultats obtenus confirment la pertinence d’études en microcosme pour évaluer le potentiel de biodégradation des polluants halogénés dans les sites contaminés, et pour orienter les traitements de dépollution à privilégier. / The biodegradation potential of chlorinated ethenes (CEs) and dichloromethane (DCM) in groundwater from the former industrial site of Themeroil (Varennes-le-Grand, France) was evaluated in microcosm studies, using molecular biomarkers and compound-specific isotope analysis (CSIA). The objective of this work was to evaluate i) the biodegradation of these pollutants and the associated bacterial diversity in site groundwater, and ii) the impact of contaminant mixtures and redox conditions on biodegradation. The major role of a taxon affiliated to Dehalococcoides in PCE degradation in site groundwater, and its potential link to dehalogenase genes pceA and vcrA associated with the process, were highlighted. Degradation of DCM in the presence of CEs in site groundwater was then demonstrated, and DCM-degrading strains were isolated from site groundwater and characterised. CSIA revealed a large extent of DCM biodegradation in situ. Analyses of groundwater from the site, targeting dcmA and dhlA genes for DCM biodegradation by qPCR, as well as by high-throughput sequencing of the 16S rRNA gene, allowed to evaluate the potential role of different bacterial taxa associated with DCM dehalogenation in DCM degradation on site. It was shown that the spatial distribution of these taxa on site depends significantly from redox conditions and contamination level. The influence of these parameters on biodegradation was also investigated in microcosms, and distinct degradation profiles were observed under different redox and co-contamination conditions. This suggests that different types of metabolism participate in biodegradation of chlorinated ethenes and alkanes on site. Obtained results confirm the relevance of microcosm studies in evaluating halogenated pollutants biodegradation potential on contaminated sites, and in guiding the choice of remediation approaches to be favoured.

No description available.

La méiofaune joue un rôle important dans le fonctionnement des habitats benthiques à substrat meuble (ex. flux de matière) en relation avec sa production élevée, sa position trophique intermédiaire et les importants transferts d’énergie vers les niveaux trophiques supérieurs qui y sont lié. Les relations trophiques et les flux de matière organique liés à la méiofaune restent néanmoins mal connus ou peu pris en compte. Afin de mieux appréhender le rôle de la méiofaune, la structure des communautés et les relations trophiques entre les sources de nourriture et ces consommateurs ont été déterminées dans cinq habitats à substrat meuble (i.e., vasière nue, herbier, zone à sables) de la baie de Marennes-Oléron, France, et de la baie de Sylt-Rømø, Allemagne, en tenant compte des variations temporelles. Le peuplement de méiofaune s’est trouvé être dominé par les nématodes et les copépodes benthiques. Les biomasses de microphytobenthos et de matière organique du sédiment sont apparues comme étant deux facteurs structurants pour les communautés. L’utilisation combinée de différents traceurs de la matière (i.e., isotopes stables, acides gras) a démontré que le microphytobenthos et les bactéries étaient les ressources trophiques majeures de la méiofaune dans les cinq habitats étudiés. Les mesures réalisées sur la structure des communautés et les données issues des traceurs de la matière ont été implémentées dans des modèles de réseaux trophiques. Dans tous les habitats, ces modèles ont mis en évidence que le flux de carbone dominant était issu du microphytobenthos, ceci démontrant les très faibles changements de comportements alimentaires malgré les importantes différences de sources trophiques en termes de disponibilité et de production des sources de nourriture entre ces différents habitats. Tous les groupes trophiques de nématodes, à l’exception des déposivores sélectifs, étaient particulièrement sélectifs et s’alimentaient majoritairement à partir de microphytobenthos, ceci étant à l’origine d’une forte production et d’un court temps de renouvellement de la méiofaune. En conclusion, cette thèse démontre le rôle important de la méiofaune dans les habitats à substrat meuble ainsi que l’importance de la relation trophique entre le microphytobenthos et la méiofaune dans le fonctionnement de ces réseaux trophiques. / Meiofauna play an important role in ecosystem processes in soft-bottom benthic habitats, e.g. food web dynamics, related to their highproduction, their intermediate trophic position and the energy they transfer towards higher trophic levels. The trophic linkages and flows of organic matter related to the meiofauna remain poorly known or taken into account. To better assess the role of meiofauna, the community structure and trophic relationships between food sources and meiofauna were determined in five intertidal soft-bottom habitats (i.e., mudflat, seagrass bed, sandflat) of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany, taking temporal variations into account. Meiofauna communities were dominated by nematodes and benthic copepods. Biomass of microphytobenthos and of sediment organic matter were two of the major drivers of community structure. The combination of trophic markers (i.e., stable isotopes, fatty acids) demonstrated that microphytobenthos and bacteria were the major food sources of meiofauna in the five habitats. Information from community structure assessments and trophic marker analyses were implemented in food web models. In all habitats, these models demonstrated that the main flow of carbon to meiofauna originated from microphytobenthos, highlighting negligible changes in meiofauna feeding behavior besides the large differences in availability and productivity of food sources between these habitats. All trophic groups of nematodes, except for selective deposit feeding nematodes, were highly selective and mainly fed on microphytobenthos, resulting in a high production and a short turn-over time of meiofauna. In conclusion, this thesis demonstrated the important role of meiofauna in soft-bottom habitats as well as the importance of the trophic pathway from microphytobenthos to meiofauna in the functioning of these food webs.