Terrestrial organic matter (TOM) constitutes an important source of energy in many aquatic environments (streams, lakes, wetlands). This is the first study to examine the role of TOM in food webs of the rocky intertidal zone. We compared the consumption of red alder leaves (Alnus rubra) to common marine sources of drifting detritus along the southern Oregon coast (Nereocystis luetkeana, Phyllospadix spp., and Fucus gardneri). We used short term (hours to days) and long term (months) feeding experiments to compare the rate of consumption among each plant species during the Spring and Fall of 2014 and 2015. In addition, we quantified the amount of TOM in beach wrack and in the drift of two streams that flowed directly to the rocky intertidal zone. We also measured the food quality of each plant species (C:N and polyphenolic concentrations). On average, the two small streams in this study transported 1,113.6 kg AFDM/m3 of TOM per day during Fall leaf abscission to the rocky intertidal zone. Also, the biomass of terrestrial leaves in beach wrack varied from negligible (2.1 g AFDM) to the dominant source of detritus (60.7 g AFDM) depending on if it was the dominant riparian plant growing along the edges of the shore. Consistent with previous research, N. luetkeana was a high quality food (C:N = 15:1; polyphenolics = 418 mg/ml), whereas F. gardneri (C:N = 22:1; polyphenolics = 8098 mg/ml) was more recalcitrant. Phyllospadix spp. was puzzling because it had low concentrations of polyphenolics (800 mg/ml) but was not consumed. Alnus rubra had a high concentration of structural compounds (C:N = 33:1) and intermediate levels of polyphenolics (3,415 mg/ml after leaching). Both short term and long term experiments showed that the rates of consumption of Spring-shed, green leaves and freshly fallen brown leaves of A. rubra were intermediate between N. luetkeana and the less palatable marine species (F. gardneri and Phyllospadix spp.). Thus, A. rubra was eaten by common intertidal consumers and may constitute an important source of energy between brief inputs of more nutritious marine resources (e.g. N. luetkeana).

Nanoparticles have gained growing attention of the scientific community over the past few decades due to their high potential to be used in diverse industrial applications. Nanoparticles often possess superior characteristics, such as catalytic activity, photochemical activity, and mechanical strength, compared to their bulk counterparts, making them more desirable in different industrial applications. During the past few decades, the use of the nanoparticles in various industries has been increased. With increasing usage release of nanoparticles into the environment has also increased. There is a growing concern about the nanoparticle toxicity and numerous studies have shown the toxic effects of different nanoparticles on various plants, animals, and microorganisms in the environment. Toxicity of nanoparticles is often attributed to their morphology and their ability to undergo different transformations in the environment. These transformations include aggregation, dissolution, and surface adsorption. Natural organic matter (NOM) are the most abundant natural ligands in the environment which include Humic acid and Fulvic acid. These high molecular weight organic molecules have complex structures and contain many different functional groups such as carboxylic acid groups, hydroxyl, amino and phenolic groups that can interact with the nanoparticle surface. The nature and the intensity of the interaction are dependent on several factors including the size and the surface functionality of nanoparticles and pH of the medium. The smaller the nanoparticle, the higher the adsorption of NOM due to the high surface to volume ratio of smaller particles. Functional groups on the surface dictate the surface charge of the nanoparticles in water depending on the acidity. The higher the acidity, higher the adsorption of NOM due to increased electrostatic attractions between positively charged nanoparticles and the negatively charged NOM molecules. Adsorbed NOM on nanoparticles affect the other transformations such as aggregation and dissolution and can in turn alter the reactivity and toxicity of the nanoparticles. Therefore, effect of NOM is an important factor that should be considered in environmental toxicity related studies of nanoparticles.

Carbon isotope studies are commonly used to provide a proxy for past vegetation communities and for evaluating environmental change. Original studies suggested carbon isotope ratios of soil organic matter (SOM) faithfully preserved the isotopic composition of standing vegetation with little or no modification in the pedogenic and shallow burial environment. Recent studies of modern soils and laboratory experiments suggest that this may not necessarily be the case and that degradation of SOM in the burial environment may alter the original C-isotope ratio of bulk SOM. A first step in addressing the issue is to begin to understand the transformations of SOM in the burial environment; of particular interest in this study are transformations involving microbial residues. Sedimentary sequences with stacked buried soils afford the opportunity to study the changes that may occur through time and are especially useful if numerical ages and other environmental proxies are present. The objective of this study is to thoroughly investigate the composition and quantity of organic matter that has been preserved in the surface and buried soils at the Claussen site, using Fourier Transform Infrared Spectroscopy (FTIR), which provides an estimate for the abundance of organic matter components preserved in each paleosol's SOM. We can trace the fate of bioavailable OM and determine the magnitude of preferential decay of SOM with time by first comparing the composition of bulk SOM to the composition of physically protected carbon, located in soil microaggregates (Christensen, 1992) of the stacked buried soils. The results of this project suggest differences in the composition of paleosol and surface soil SOM that could impact paleovegetation interpretations derived from δ13C values.

Zinc deficient soils, or soils with low Zn bioavailability, are widespread, which exacerbates Zn deficiency in human as crops grown on these soils have low Zn content. Often crop yields are also compromised. Fertilizers based on soluble Zn salts often have limited efficacy in such soils. In this research, we evaluate the performance of polymer coated and bare ZnO nanoparticles (NPs) in an attempt to overcome limitations of soluble Zn salts in alkaline soils. We first synthesized 20-30 nm bare ZnO NPs with different surface chemistries to impart colloidal stability to the particles. Bare ZnO were treated in phosphate solution under certain conditions leading to the formation of a core made of ZnO NPs that is covered by a shell of amorphous Zn3(PO4)2 (core-shell NPs). This confers a negative charge to the particles over a wide pH range. The addition of nonionic (neutral dextran) and polyelectrolyte (negatively charged dextran sulfate (DEX(SO4)) during the synthesis resulted in the formation of DEX and DEX(SO4) ZnO NPs. Dextran has a minimal effect on the surface charge of ZnO but dextran sulfate confers a net negative charge. Bare and core-shell ZnO NPs were both electrostatically stabilized whereas DEX and DEX(SO4) ZnO NPs were sterically and electrosterically stabilized, respectively. We investigated the effect of treating seeds with ZnO NPs on the growth and accumulation of Zn in wheat (Triticum aestivum) seedlings in comparison to ZnSO4. All ZnO NPs stimulated seedling growth. Seedlings accumulated higher Zn concentrations when treated with ZnO NPs than with ZnSO4. Zinc sulfate was toxic even at the lower exposure concentrations, which was demonstrated by significantly lower germination success and seedling growth. In the second experiment, we investigated the effect of pH on the attachment and dissolution of ZnO NPs in soil, as compared to ZnSO4. Soil pH was adjusted to 6 and 8, then the soil was spiked with 100 mg Zn/kg soil in the form of ZnSO4, bare, DEX, DEX(SO4), and core-shell ZnO NPs. The results showed that DEX and core-shell ZnO NPs had significantly higher total Zn in soil solution compared to ZnSO4 at pH 8, with little dissolution. Dissolved Zn was similar among treatments except ZnSO4 at pH 6, indicating little dissolution of the ZnO NPs at either pH value. We also found that the engineered coatings dictate the behavior of the particles in simple aqueous systems, but their properties are altered in natural soil solutions because of the dominant effect of natural organic matter (NOM) on their surface chemistry. Based on the outcomes of the previous two experiments, we selected DEX and bare ZnO NPs to test the efficacy of ZnO NPs in delivering Zn to the grain of wheat under greenhouse conditions. We performed two independent studies where seeds were either treated with the NPs or grown in a soil spiked with Zn at pH 6 and 8 and spiked with Zn treatments (nano and ionic). We found that treating seeds with bare ZnO NPs significantly enhanced grain Zn concentrations as compared to the control, DEX-ZnO NPs, and ZnSO4. There were no differences in grain Zn concentration of plants treated with ionic or nano Zn treatments regardless of the soil pH. This work has elucidated important principles which will help carry forward efforts at developing effective ZnO NP-based fertilizers. It also suggests that treatment of seeds with ZnO NPs is more effective than amending soil or treating seeds with ZnSO4.

Black carbon (BC) is an organic residue formed primarily from biomass burning (e.g., wildfires) and fossil fuel combustion. Until recently, it was understood that BC was highly recalcitrant and stabilized in soils over millennial scales. However, a fraction of the material can be solubilized and transported in fluvial systems as dissolved BC (DBC), which represents on average 10% of the global export of dissolved organic carbon (DOC) from rivers to coastal systems. The composition of DBC controls its reactivity, and it has been linked with a variety of in-stream processes that induce both carbon sequestration and evasion of CO₂ from aquatic systems, which suggest DBC may have a significant contribution within the global carbon cycle. The primary objectives for the thesis were to elucidate environmental factors that control the fate and transport of DBC in fluvial systems. Ultra-high resolution mass spectrometry was used to characterize DBC on a molecular scale whereas benzenepolycarboxylic acids were used to quantify and characterize BC in both dissolved and particulate phases (PBC). Sinks for polycondensed DBC were linked to a series of in-stream biogeochemical processes (e.g., photodegradation, metal interactions); whereas photooxidation of particulate charcoal led to production of DBC, suggesting photodissolution as a previously unrecognized source of DBC to fluvial systems. Coupling of DBC with PBC, however, was hydrologically constrained with sources varying over temporal scales and land use regimes. For DBC in particular, an enrichment of heteroatomic functionality was observed as a function of anthropogenic land use. Furthermore, land use coupled with stream order (a proxy for in-stream processing as defined by the River Continuum Concept) could explain significant spatial variability in organic matter (e.g., DOC) composition within an anthropogenically impacted system. With an increase in wildfire frequency projected with on-going climate change trends, parallel projections for increases in BC production are also expected. Furthermore, conversion of natural landscapes for urban and agricultural practices is also expected to continue in the coming decades. Thus, it is imperative to reach a comprehensive understanding of processes regulating the transport of DBC in fluvial systems with efforts to constrain future BC budgets and climate change models.

The association between natural organic matter (NOM) and iron (Fe) minerals was widely found in soil and sediments and has been shown to impact the fate of Fe minerals and NOM. Ferrihydrite, a ubiquitous Fe mineral, serves as important sink for NOM and rapidly transforms to secondary Fe minerals in the presence of Fe(II). The associated NOM has been found to influence the Fe(II)-catalyzed ferrihydrite transformation pathway, but it remains unclear how various NOM affects this transformation and the implication. This study specifically investigates how different species of NOM affect Fe(II)-catalyzed ferrihydrite transformation under different C/Fe ratios. A series of Fe isotope tracer experiments were conducted to measure Fe atom exchange and electron transfer between aqueous Fe(II) and ferrihydrite in the presence of diverse NOM species. The fate of Ni during Fe(II)-catalyzed transformation of NOM-Fh coprecipitate was also investigated. Ferrihydrite was found less susceptible to Fe(II)-catalyzed transformation with increasing C/Fe ratio and fulvic acids and Suwannee River NOM (SRNOM) in the coprecipitates need lower C/Fe ratio than humic acids to completely inhibit formation of secondary Fe minerals. At C/Fe ratios where ferrihydrite transformed to secondary minerals, goethite was dominant in ferrihydrite coprecipitated with humic acids, whereas lepidocrocite was favored in ferrihydrite coprecipitated with fulvic acids and SRNOM. Adsorbed SRNOM may be more inhibitive than coprecipitated SRNOM on Fe(II)-catalyzed ferrihydrite transformation under similar C/Fe ratios. Despite no secondary mineral transformation at high C/Fe ratios, Mössbauer spectra indicated electron transfer still occurred between Fe(II) and ferrihydrite coprecipitated with fulvic acid and SRNOM. In addition, isotope tracer experiments revealed that a significant fraction of structural Fe(III) in the ferrihydrite mixed with the aqueous phase Fe(II) (~85%). After reaction with Fe(II), Mössbauer spectroscopy indicated some subtle changes in the crystallinity, particle size or particle interactions in the coprecipitate. The effect of coprecipitated SRNOM on Ni(II) distribution during Fe(II)-catalyzed ferrihydrite transformation was investigated with adsorbed Ni(II) and coprecipitated Ni(II). Ni(II) adsorbed on ferrihydrite was more resistant to acid extraction after Fe(II)-catalyzed transformation and suggested that structural incorporation of Ni into secondary Fe minerals occurred. With coprecipitated SRNOM, ferrihydrite did not transform to secondary minerals in the presence of Fe(II) but extensive Fe atom exchange between aqueous Fe(II) and structural Fe(III) still occurred. Limited change in Ni stability was observed, suggesting there was only small portion of Ni redistributed in the presence of Fe(II). Pre-incorporated Ni(II) in Ni-SRNOM-Fh coprecipitate was partially released (6-8 %) in the presence of Fe(II), but the distribution of remaining Ni(II) in the solid did not change measurably. Our observation suggests that the presence of SRNOM limited the redistribution of Ni most likely because of limited transformation of ferrihydrite to secondary minerals.

Soil organic matter consists of a heterogenous mixture of plant, animal, and microbial material in various stages of decomposition. It possesses characteristics which at present are not very well known. Careful studies have been directed towards the behavior of organic matter as it affects plants directly and man indirectly. Consequently, much tire is devoted to its study from the point of metal inactivation and chelation, the earlier investigations failed to produce results worthy of the efforts expended, so a loss of interest in the continued pursuit of knowledge resulted, about two decades ago when it was learned that many polyvalent metals in the soil exist as insoluble metallo-organic complexes, an interest was renewed in the study of soil organic matter interaction and chelation.

Coarse particulate organic matter (CPOM) is an essential part of the food chain in aquatic ecosystems because it represents a readily available carbon and energy source. The process by which it decomposes in rivers has been well studied and documented. However, the rate and extent of biodegradability of various CPOM components (i.e., twigs, leaves, grass, etc.) in storm drains is not well understood. The Jordan River TMDL study identified storm water generated CPOM as a likely cause of low dissolved oxygen levels in the lower Jordan River, but recent investigations have suggested that dissolved organic matter generated from this CPOM in storm drains and culverts entering into the Jordan River, rather than the CPOM itself, is the main driver of oxygen impairment. The degradability of CPOM components transported and stored in the storm drain system was studied to understand its relative impact on dissolved oxygen and nutrient status in the Jordan River. Results indicate the generation of highly degradable organic material is a function of the starting CPOM, and oxygen consumption is associated with the dissolved portion of organic material leached from CPOM in water. Leaves and grass produced the highest levels of all parameters studied. Between 93% to 95% of total oxygen demand is generated within the first 1 to 3 hours of the 24 hour test. Chemical oxygen demand and dissolved organic carbon proved to be the best indicator of biochemical oxygen demand. By using the results of the leaching study an estimate of water quality indicator levels in the Jordan River was made, and was compared to levels in samples collected from the Jordan River. The estimate proved accurate for dissolved organic carbon but not for total or volatile suspended solids. Results of this study were used to discuss possible solutions to reduce oxygen demand in the Jordan River.

A method is presented, using calculations of the underwater light field, to examine viability of phytoplankton at depth. For this study, viability is defined as the ability of phytoplankton to harvest, and efficiently convert enough photons into primary production to overcome metabolic demands. How the available light field influences the production environment is examined. Changes in water column constituents, such as chlorophyll and colored dissolved organic matter (CDOM) concentration, alter the spectral quality and quantity of the light field at depth. Certain species with specialized survival strategies, such as assemblages of photoprotective and light-harvesting accessory pigments, may be better-suited to 'making a living' at depth in response to the spectral quality of the underwater light field. Stations for study were identified from various cruises off the West Florida Shelf that exhibited variations in chlorophyll and/or CDOM concentration, including an optically complex, red-tide station. Optical and water column constituent measurements from these stations were used to develop input parameters to Hydrolight 4.1, a radiative transfer theory model, to simulate the underwater light field and to calculate absorbed radiation by phytoplankton (ARP). Values for respiration and quantum yield from the literature were used to calculate comparative values of net photosynthesis at these stations. The effect of differences in spectral light harvesting (pigmentation), photosynthetic efficiency rates, and respiration, on viability through the water column was examined.

Les foraminifères benthiques sont largement utilisés en océanographie comme bio-indicateurs paléoclimatiques et paléoenvironnementaux du fait de leur présence dans tous les milieux marins, leur sensibilité aux changements environnementaux et leur grande capacité de fossilisation. Néanmoins, leur utilisation nécessite une connaissance approfondie de leur écologie et des paramètres contrôlant leur distribution. Si les connaissances sur l’écologie des foraminifères benthiques sont de plus en plus complètes, elles demeurent très sporadiques dans la zone arctique, système complexe caractérisé par des interactions multiples entre l'atmosphère, l'océan et la cryosphère, pourtant au coeur du changement climatique global. L'amplification polaire du changement climatique conduit les régions des hautes latitudes à se réchauffer près de deux fois plus vite que les régions tempérées. Dans ce contexte, cette thèse s'attache à mieux comprendre l'écologie des foraminifères benthiques vivants dans plusieurs régions arctiques et définir l'importance du contrôle des paramètres environnementaux sur les faunes tels que les propriétés des masses d'eau, la productivité primaire et le flux de matière organique ainsi que la dynamique de la glace de mer. Les foraminifères benthiques vivants ont été analysés dans les premiers centimètres de sédiment de 21 carottes d’interfaces prélevées dans trois régions arctiques durant les étés 2014 et 2015 : la mer de Barents, la baie de Baffin et la mer de Chukchi. Ces trois régions présentent des particularités en termes de couvert de banquise, de circulation des masses d’eau ou de dynamique de la production primaire. Nos résultats montrent que ces facteurs influencent la distribution des foraminifères benthiques. Le flux de matière organique qui résulte de la forte productivité primaire printanière aux abords des fronts polaires hydrographiques, des bordures de glace de mer (zones marginales de glace) et dans la polynie des eaux du nord (baie de Baffin) impacte la densité et la diversité des faunes et favorise le développement de certaines espèces. Nonionellina labradorica dans les eaux arctiques froides et Cassidulina neoteretis associée aux eaux atlantiques répondent aux apports de matière organique fraîche tandis que Melonis barleeanus s’accommode des milieux riches en matière organique plus dégradée. Dans les environnements oligotrophes plus profonds, Oridorsalis tenerus est une espèce ubiquiste. Cette espèce est associée à Cibicidoides wuellerstorfi sur la marge ouest de la mer de Barents et Ioanella tumidula dans le bassin plus profond au nord de la mer de Chukchi. Les propriétés physiques et chimiques des masses d’eau contraignent également la distribution faunistique. En baie de Baffin et sur le plateau de la mer de Chukchi, les eaux corrosives engendrent la dissolution des carbonates, favorisant la dominance des espèces agglutinées. Les études menées dans le cadre de cette thèse permettent de calibrer l'outil foraminifère benthique dans l'actuel et d'affiner leur utilisation en tant que proxy paléoclimatique et paléoenvironnemental en Arctique. Enfin, une étude préliminaire sur les foraminifères benthiques fossiles de trois carottes de la mer de Barents a permis de montrer les variations des conditions paléoenvironnementales au cours des deux derniers siècles. / Benthic foraminifera are widely used in oceanography as paleoclimate and paleoenvironmental bio-indicators due to their presence in all marine environments, their sensitivity to environmental changes and their great capacity to fossilize. However, the use of benthic foraminifera as paleoenvironmental proxies requires a good knowledge of the ecological conditions and the parameters controlling species distribution. Although knowledges about the ecology of benthic foraminifera are improving, they remain sporadic in Arctic area, a complex ecosystem characterized by multiple interactions between the atmosphere, the ocean and the cryosphere and particularly sensitive to change and vulnerable to global warming. Temperatures in the Arctic have risen twice as fast as the global average over the past decades, a phenomenon that has been dubbed the “polar amplification of global warming”. In this context, this thesis aims at better understanding the ecology of living benthic foraminifera in Arctic regions and at defining the importance of environmental controls on fauna such as water mass properties, primary productivity, organic matter flux as well as sea-ice dynamics. Living benthic foraminifera were identified in the first centimetres of 21 surface sediment cores collected in three Arctic areas during summer in 2014 and 2015: Baffin Bay and the Barents and Chukchi Seas. These three regions present specific characteristics in terms of sea-ice cover, water mass circulation or primary productivity. Our results suggest that these factors influence the distribution of benthic foraminifera. The flux of organic matter resulting from primary productivity intensified during spring and summer periods near hydrographic polar fronts, sea-ice edges (marginal ice zones) and in the north water polynya (Baffin Bay) increases the fauna’s densities and diversity and favours the development of specific species. Nonionellina labradorica in cold Arctic waters and Cassidulina neoteretis associated with Atlantic waters respond to fresh supply of organic matter while Melonis barleeanus is found in environment rich in degraded organic matter. In deeper oligotrophic environments, Oridorsalis tenerus is a ubiquitous species associated with Cibicidoides wuellerstorfi on the west continental margin of Barents Sea and Ioanella tumidula in the deeper basin in the north of the Chukchi Sea. Physical and chemical water mass properties also affect the distribution of living benthic foraminifera. In the Baffin Bay and the continental shelf of the Chukchi Sea, corrosive waters lead to carbonate dissolution, favouring the dominance of agglutinated species. This thesis hence contributes to calibrate the benthic foraminifera to their environment and to improve their application as paleoclimate and paleoenvironmental proxies in the Arctic. Finally, a preliminary study about fossil benthic foraminifera in three cores of Barents Sea allowed to show variations of environmental conditions during the last two centuries.