Previous work found significant differences in growth rates of native mussels at locations downstream from the regulated Walter’s Dam and the out-of-service, free-flowing Davy Crockett Dam. The purpose of this study is to investigate differences within the macroinvertebrate communities related to factors driving the differences in mussel growth between rivers. Macroinvertebrate samples were collected following the Tennessee Department of Environment and Conservation protocol for SQKICK collection and analyzed using the Tennessee Macroinvertebrate Index (TMI). There were no significant differences in TMI scores between the downstream sites of the rivers, but there were significant increases in chlorophylla, dissolved oxygen, and specific conductance downstream compared to upstream in both rivers. This suggests that these indices are suitable to identify pollution changes, but potentially not the productivity differences that impacted mussel growth.

The Arctic is a region undergoing unprecedented and unequivocal climate change. The seas of this extreme region form a major component of the oceanic thermohaline conveyor and natural carbon cycle. Using a combination of recent and historical datasets this study examines the distribution, diversity, photophysiology and primary productivity of phytoplankton in the Atlantic sector of the Arctic Ocean. CHEMTAX analysis reveals a diverse phytoplankton community structure in the Greenland Sea comprising six main phytoplankton groups. The influence of sea-ice and water column stratification are key factors in the presence or absence of groups such as haptophytes and prasinophytes. Group-specific differences are observed in spectral absorption and photophysiological parameters. However, the influence of environmental factors has a stronger influence than taxonomic composition on photophysiology. A clear division between the photoacclimatory response of algal communities beneath sea-ice and those of open-ocean stations is predominantly due to ‘E_k independent’ photoacclimation beneath sea-ice. This occurs due to the combined effect of sea-ice decreasing irradiance entering the water column and a positive correlation between P_m ^B and temperature. This variation in photophysiology is important for primary production models as a sensitivity analysis shows that errors in these parameters propagate to give the largest final errors in primary production values. The importance of other model parameters varies with the level of biomass in the water column and the presence or absence of sea ice. Accelerated ice-melt and an increase in open water due to climate change are likely to increase primary production in the Atlantic Arctic alongside an altered distribution of phytoplankton groups, with an increase in the importance of prasinophytes or haptophytes.

This dissertation includes 3 chapters which focus on algal bloom of the tidal fresh James River. The first chapter describes nutrient and light limitation assays performed on algal cultures and draw conclusions about long-term patterns in nutrient limitation by comparing results with a previous study . This chapter also describes the influence of riverine discharge upon nutrient limitation in a point-source dominated estuary. This chapter was published in Estuaries and Coasts (Wood and Bukaveckas 2014). The second chapter presents the first comprehensive assessment of the occurrence of the cyanotoxin Microcystin in water and biota of the James River. Data presented in this chapter show that bivalve grazing declines in the presence of Microcystin in the water. The chapter also describes feeding habits in fish as a predictor for inter-specific differences in Microcystin accumulation in their tissues. The work presented in this chapter was published in Environmental Science & Technology (Wood et al. 2014). The third chapter describes the fate of algal carbon in the James River Estuary and the importance of autochthonous and allochthonous sources of organic matter in supporting production of higher trophic levels. Here I draw upon ecosystem metabolism data (NPP and R), abundance and grazing estimates for primary consumers and estimates of advective losses of chlorophyll and external inputs of nitrogen to place ‘top-down’ effects in the broader context of factors influencing chlorophyll and nitrogen fluxes in the James. . This chapter also describes results from mesocosm experiments used to assess the influences of grazers on chlorophyll, nutrients and Microcystis. This work will be submitted in the summer of 2014 to the journal Ecosystems.

Les forêts de mangrove contribuent de manière significative au flux d'énergie, au cycle des nutriments et du carbone dans l'océan côtier, étant un puits pour le CO2 atmosphérique. Les forêts de mangroves sont très productives et stockent une quantité élevée de carbone à la fois dans leurs sols et dans leur biomasse.Au cours de la décomposition de la litière, les nutriments et le carbone peuvent être recyclés ou exportés vers les écosystèmes adjacents par l'action des marées. La mangrove de Can Gio (Ho Chi Minh Ville, Vietnam), dégradée par l'épandage de défoliants pendant la guerre du Vietnam, a pu être restaurée grâce à la replantation et à la régénération naturelle. À ce jour, la forêt de mangrove de Can Gio est la plus grande forêt de mangrove contiguë au Vietnam, et est devenue la première réserve biosphère UNESCO dans ce pays. L'objectif principal de cette thèse était de caractériser le cycle du carbone dans la forêt de mangrove tropicale.Les résultats de cette thèse ont permis de:- Développer des équations allométriques permettant d’estimer la biomasse aérienne de la forêt plantée de mangroves de l’espèceRhizophora apiculatadans le sud du Vietnam;- Calculer les stocks de carbone totaux dans différents peuplements de mangrove se développant sous le climat tropical du sud du Vietnam;- Caractériser les taux de décomposition de la litière et évaluer la dynamique des nutriments et des métaux traces au cours des processus de dégradation de la litière, ainsi que l'évolution de δ13C pendant la décomposition;- Déterminer la variabilité saisonnière des flux de CO2 à différentes interfaces: sol-air, eau-air et tronc-air, et caractériser les profils de concentration en CO2 dans la canopée. / Mangrove forests significantly contribute to energy flow, nutrient and carbon cycling in the coastal ocean, being a sink for atmospheric CO2. Mangroves forests are highly productive and store high amount of carbon both in their soils and in their biomass. During leaf litter decomposition, nutrients and carbon can be recycled or exported to adjacent ecosystems by the tidal action. Can Gio mangrove, degraded by the spraying of defoliants during the Vietnam War, successfully recovered through replantation and natural regeneration after 40 years. To date, the Can Gio mangrove forest is the largest contiguous mangrove forest in Vietnam, and became the first Mangrove Biosphere Reserve in this country. The main objective of this PhD thesis was to characterize carbon cycling within the Can Gio mangrove forest, which is a tropical one.The results of this PhD thesis allowed to: - Develop allometric equations and to estimate the aboveground biomass of Rhizophora apiculata Blume planted mangroves forest in Southern Vietnam; - Calculate the total carbon stocks in different mangrove stands developing under the tropical climate of Southern Vietnam; - Characterize the leaf litter decomposition rates, and assess nutrients and trace metals dynamics during litter decay processes, as well as the evolution of δ13C during decay; - Determine the seasonal variability CO2 fluxes at different interfaces: soil-air, water-air and trunk-air, and to characterize CO2 concentrations profiles in the canopy.

O objetivo principal desta pesquisa foi estudar a produção primária na Represa de Bariri, que é a segunda do sistema do Médio Tietê. Para atingirmos o objetivo proposto, as coletas foram realizadas em duas estações de amostragem M1, na zona limnética, e M2, na zona litorânea, nos meses de fevereiro, abril, julho e setembro de 1998. A produtividade primária da comunidade fitoplanctônica foi determinada através do método do oxigênio dissolvido. Os valores da produtividade primária líquida da comunidade fitoplanctônica na zona limnética variaram de 122 mgO2.m-2.h-1 (abril) a 2093 mgO2.m-2.h-1 (julho), enquanto que na zona litorânea, variaram entre 157 mgO2.m-2.h-1 (abril) a 861 mgO2.m-2.h-1 (fevereiro). A respiração na comunidade na zona limnética variou entre 18 a 376 mgO2.m-2.h-1 (fevereiro) e na zona litorânea, variou de 0 (abril) a 211 mgO2.m-2.h-1 (fevereiro). A menor produtividade primária, observada em abril, coincidiu com uma menor biomassa. Provavelmente, o fósforo foi o principal fator limitante da produtividade primária nos outros meses de estudos. A proliferação da S estrategista Microcystis spp em fevereiro, nas zonas limnética e litorânea e julho na zona limnética, foi associada à maior estabilidade da coluna d\'água desses períodos. Nas coletas de julho nas zonas litorâneas, abril e setembro, nas zonas limnética e litorânea, houve maior participação de espécies R e C estrategistas, como Rhodomonas lacustris, Auacoseira granulatagranulata, Chlamydomonas spp, Cryptomonas brasiliensis, Cryptomonas tetrapyrenoidosa, Anabaena spiroides e Anabaena circinalis. / Temporal and spacial variations of phytoplankton primary production in Bariri Reservoir (22º06\'S and 48º45\'W, São Paulo State, Brazil) were evaluated by in situ observations in two different areas: one in the limnetic zone (M1) and other in the littoral zone (M2) in February, April, July and September 1998. The phytoplankton primary productivity was determined by the dissolved oxigen method. The values of net primary productivity of the phytoplankton community in M1 varied from 122 mgO2.m-2.h-1 (April) to 2093 mgO2.m-2.h-1 (July), and M2, varied from 157 (April) to 861 mgO2.m-2.h-1 (February). The community respiration M1, varied from 18 (April) to 376 mgO2.m-2.h-1 (February) and M2, varied from zero (April) to 211 mgO2.m-2.h-1 (February).The lowest primary productivity, obtained in April, coincided with the lowest biomass. Probably, phosphorus was the main limitation of the primary productivity on the others study months. The bloom of Microcystis spp (S strategist) in February M1 and M2 and July M1 was related to water column more stable in these periods. In July M1, April M1 and M2 and September M1 and M2, the R and C strategists predominated, such as Rhodomonas lacustri, Aulacoseira granulata granulata, Chlamydomonas spp, Cryptomonas brasiliensis, Cryptomonas tetrapyrenoidosa, Anabaena spiroides and Anabaena circinalis.

The delivery of nutrients to the surface of marine algae can be controlled by the local hydrodynamic regime: in higher flow velocities, the Diffusive Boundary Layer (DBL) at the uptake surface is thinner, which can increase the flux of dissolved chemicals to the algal surface. If the primary productivity of an alga is controlled by the availability of a dissolved chemical, increased water flow should result in greater primary productivity due to increased chemical flux. To test the hypothesis that increased water flow will increase Photosystem II kinematics (PSII) in the green alga Caulerpa we used a Diving Pam Fluorometer to measure the maximum relative electron transport rate (Pmax), Saturation Irradiance (Ik), Non-photochemical quenching (NPQ), the light limited slope of photosynthesis vs. irradiance curve (α) and photo-chemical quenching (qP) and compared these measured values among treatments of varying flow speeds in a portable laboratory flume. We also measured the influence of water flow on values of Pmax, Ik, α , qP and NPQ in the field. Results showed that in C. racemosa collected from Tampa bay, and tested in a laboratory flume, values of Pmax and Ik were positively correlated to increase water flow, possibly indicating mass-transfer limitation. C. mexicana, collected from the Florida Keys, showed a decrease in values of Pmax, and Ik with increasing water velocity in flume experiments, indicating that the increased flow was resulting in physiological stress. This result was supported with field measurements for C. sertularioides, which showed a negative correlation between Pmax and flow velocity and Ik and flow velocity.

Primary production and carbon export connect biogeochemical cycles in the surface waters to the deep. Quantifying rates of production and carbon export are important to understanding the global carbon cycle. There are multiple productivity rate methods, but each measures a different fraction of production. The first type of method is in vitro methods that involve removing water samples from the environment and incubating with an isotopically labelled tracer, such as a nutrient. At the end of the incubation, the amount of enrichment in either the particulates (phytoplankton) or the dissolved oxygen are measured to determine productivity. The second type of method is in situ methods that measure the natural environmental parameters instead of incubations. In this study, the natural isotopic composition and the ratio of gases in the surface water are measured. Comparing in situ versus in vitro methods in the Arctic on a GEOTRACES cruise (July 2015), we identified five reasons to explain why methods do not agree: time of integration, depth of integration, recently shoaled mixed layer, mixing at the base of the mixed layer, and methodological issues. When comparing in vitro methods to each other, filter handling and some as yet unidentified bias causes differences. Comparing methods along Line P (over three years), we hypothesize that excretion of dissolved organic nitrogen, upwelling, bottle effects, mixing, and time of integration are the most important factors that cause disagreement between methods. End of bloom dynamics created an extreme case where method disagreement was most severe. Applying method comparison in the NE subarctic Pacific (August 2014 – June 2017) helps to understand what drives variability in primary production. Historical data show that chlorophyll-a is low and invariant offshore in the high nutrient low chlorophyll area (HNLC), where iron is limiting. We used satellites and models, which compare well with shipboard data, to expand our spatial and temporal coverage of the offshore HNLC area. Increased chlorophyll a is associated with higher production, higher salinity, and lower temperature. We hypothesize that iron can be supplied to surface waters by offshore fronts, using June 2015 and June 2016 as specific examples. Fronts are locations where temperature, salinity and/or density are rapidly changing, in this particular dissertation a 1°C change over 1/3 degree distance. We identified locations where fronts were located based on Mercator model sea surface temperatures and compared these features to satellite chlorophyll patterns. Our hypothesis is also supported by data from June 2017 where there were no fronts and chlorophyll was uniformly low. Future research should consider fronts as a possible mechanism for increasing productivity in the area. Identifying mechanisms that cause methods to disagree and then applying to biogeochemical regions allows for better understanding of carbon cycling. / Graduate / 2020-09-12

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.

<p>Riparian vegetation along streams and rivers affects the aquatic community in numerous ways and often operates as a link for energy flux between forest and streams. The studies presented in this licentiate thesis focus on light and terrestrial invertebrates, two factors influenced by riparian zone structure, which potentially affect stream ecosystems and thus also brown trout (Salmo trutta). Paper I is a laboratory experiment where I study size dependent foraging behavior on surface-drifting terrestrial invertebrates and benthic invertebrates by brown trout. The results show a size-dependent difference in foraging ability with large trout being better able to use terrestrial surface prey than small trout. I argue that such ontogenetic foraging differences are due to both morphological constraints (eg. gape limitation) and size dependent behavioral differences related to predation risk. Paper II consists of a 5 month-long 2x2 factorial design field experiment where my objective was to examine the effects of terrestrial invertebrate input and solar radiation (PAR) on different trophic levels in a boreal headwater stream. More specifically, I followed the effects of increased light and decreased terrestrial invertebrate subsidies on periphyton, benthic macroinvertebrates and two size classes of the top fish predator, brown trout. The results showed that the reduction of terrestrial invertebrate input had size- and seasonal-dependent effects on trout, where large trout had lower growth rates than small trout, mainly in summer. Diet analyses of trout supported growth differences in that large trout in unmanipulated enclosures consumed relatively more terrestrial prey than large trout living in enclosures with reduced terrestrial inputs. A higher reliance on terrestrial prey subsidies by large trout compared to small may be explained by ontogenetic differences in foraging and habitat choice. Despite a 2.5-fold increase in PAR, light did not have an effect on chlorophyll a biomass, nor was there an effect on the density or composition of benthic macroinvertebrates. The lack of effects on primary production may be explained by very low nutrient levels in the stream.</p>

Coccolithophores are unicellular microscopic algae (Haptophyta) surrounded by calcium carbonate plates that are produced during their life cycle. These species, whose contemporary contributor is Emiliania huxleyi, are mainly found in the sub-polar and temperate oceans, where they produce huge blooms visible from space. Coccolithophores are sensitive to ocean acidification that results from the ongoing accumulation of anthropogenic carbon dioxide (CO2) in the atmosphere. The response of these organisms to global change appears to be related to the reduction of their ability to produce calcium carbonate at the cellular level. At the community levels, one anticipates changes in the carbon fluxes associated to their blooms as calcification is reduced. However, the consequences of such environmental changes on this species are speculative and require improvements in the description of the mechanisms controlling the organic and inorganic carbon production and export. The first aspect of this work was to study the response of these organisms to artificially modified CO2 concentrations representative of the conditions occurring in the past (glacial) and those expected by the end of the century (2100). Two different levels were examined: the continuous monospecific cultures (chemostats) allowed us to work at the cellular level while the mesocosms gave light to the mechanisms taking place in an isolated fraction of the natural community. The second aspect of this work consisted of field studies carried out during four cruises (2002, 2003, 2004 and 2006) in the northern Bay of Biscay, where the occurrence of E. huxleyi blooms were observed in late spring and early summer. We describe the vertical profiles of biogeochemical variables (nutrients, chlorophyll-a, dissolved inorganic chemistry, particulate carbon, transparent exopolymer particles (TEP)) and study processes such as primary production, calcification and bacterial production. The properties of these blooms are compared with those reported in the literature and enriched with original measurements such as the abundance and concentration of TEP that could play an important role in carbon export to the deep ocean, modifying the properties of the settling ballasted aggregates.