World-wide coral reefs are in a state of decline as a result of many local and regional factors. Recent global mass mortalities of reef corals due to record warm sea temperatures have led researchers to consider global warming as one of the most significant threats to the persistence of coral reef ecosystems over the next 100 years. It is well established that elevated sea surface temperatures (SSTs) cause widespread coral bleaching, yet confusion lingers as to what facet of extreme temperatures is most important. Utilizing long-term in situ datasets, nine thermal stress indices were calculated and their effectiveness at segregating bleaching years a posteriori for multiple reefs on the Florida Reef Tract was tested. Simple bleaching thresholds based on deviations above the climatological maximum monthly SST were just as effective at identifying bleaching years as complex thermal stress indices. Near real-time bleaching alerts issued by NOAA's Integrated Coral Observing Network (ICON) are now based upon a running 30-day average SST, such that alerts are only issued when the running 30-day average SST exceeds the estimated bleaching threshold for a particular site. In addition to three widespread, mass-coral bleaching events, the Florida Reef Tract was impacted by three tropical storms and 12 hurricanes from 1997-2005. Sea surface cooling associated with the high frequency of hurricanes that impacted Florida in 2005 likely acted to ameliorate the severity and duration of bleaching. Nonetheless, hurricane-associated cooling is not expected to nullify the proposed effects of climate change on coral reefs. The role of thermal stress in coral bleaching has been extensively studied for eastern tropical Pacific (ETP) coral reefs. However, the ETP presents a unique opportunity as this region has sub-optimal conditions for coral reef development because of upwelling of carbon dioxide-enriched deep water along the shallow thermocline. This upwelling results in a depressed aragonite saturation state which is likely an additional factor in the poor reef development throughout the ETP. The highest aragonite saturation documented in this study occur in the Gulf of Chiriquí, which corresponds with the greatest reef development of the entire ETP. Seasonal upwelling had a significant effect on the carbonate chemistry of surface waters in Pacific Panamá. This regionally-depressed aragonite saturation state of the ETP appears to result in corals with a less dense skeleton. Density values of poritid corals from the Galápagos, where aragonite saturation was the lowest documented in this study, were significantly less dense relative to those from Panamá and the Great Barrier Reef. The density of non-living pocilloporid framework components were no different across the ETP aragonite saturation gradients. This could be a result of the activity of boring sponges removing the primary carbonate material within the dead coral skeleton, thus lowering density, albeit physical-chemical dissolution cannot be ruled out. These studies provide real-world examples of the ramifications of global climate change upon coral reef ecosystems.

This research supports development of aquatic resource management strategies to address acid deposition in the Great Smoky Mountain National Park (GRSM) by 1) developing relationships between baseflow and stormflow chemical constituents and examining effects of elevation, area, geology, soil, and vegetation on stream chemistry; 2) evaluating physiological condition in brook trout in relation to changes in stream chemistry during stream acidification episodes, and 3) evaluating brook trout metrics with respect to stream chemistry, basin characteristics, and ecologically relevant hydrologic parameters. (1) Stream chemistry was monitored in eight GRSM streams considering basin area, site elevation, Anakeesta geology, soil, and vegetation. Following precipitation events, pH was significantly reduced and aluminum concentrations increased, while the concentration response of ANC, nitrate, sulfate, and base cations varied. Higher pH and ANC concentrations were observed in large and low-elevation streams. (2) Caged brook trout were exposed to two acid episodes during in situ bioassays conducted in three GRSM streams. Stream pH decreased (>0.7 pH units) and total dissolved aluminum increased (>0.175 mg/L) at all three sites during acid episodes. Whole-body sodium concentrations were significantly reduced (10-20%) when preceding 24-h time weighted average pH values (4.88, 5.09, 4.87) and corresponding 24-h aluminum concentrations (210, 202, 202 µg/L). Lower whole-body sodium concentrations were correlated with elevated proton and aluminum concentrations indicating physiological distress. (3) Water chemistry, hydrology and physical basin factors influenced brook trout distributions and densities in 16 collocated fish and water quality sampling sites (1990-2009). Higher concentrations of ANC, pH, sodium, and soil cation exchange capacity, and higher fall flows were associated with the presence of brook trout. Trout densities were higher in streams with higher concentrations of sodium, suggesting that sodium may ameliorate the effects of acid toxicity. These relationships provide useful information where GRSM managers can prioritize conservation and restoration efforts.

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.

Previous hydrometric studies demonstrated the prevalence of overland flow as a hydrological pathway in the tropical rain forest catchment of South Creek, northeast Queensland. The purpose of this study was to consider this information in a mixing analysis with the aim of identifying sources of, and of estimating their contribution to, storm flow during two events in February 1993. K and acid-neutralizing capacity (ANC) were used as tracers because they provided the best separation of the potential sources, saturation overland flow, soil water from depths of 0.3, 0.6, and 1.2 m, and hillslope groundwater in a two-dimensional mixing plot. It was necessary to distinguish between saturation overland flow, generated at the soil surface and following unchanneled pathways, and overland flow in incised pathways. This latter type of overland flow was a mixture of saturation overland flow (event water) with high concentrations of K and a low ANC, soil water (preevent water) with low concentrations of K and a low ANC, and groundwater (preevent water) with low concentrations of K and a high ANC. The same sources explained the streamwater chemistry during the two events with strongly differing rainfall and antecedent moisture conditions. The contribution of saturation overland flow dominated the storm flow during the first, high-intensity, 178-mm event, while the contribution of soil water reached 50% during peak flow of the second, low-intensity, 44-mm event 5 days later. This latter result is remarkably similar to soil water contributions to storm flow in mountainous forested catchments of the southeastern United States. In terms of event and preevent water the storm flow hydrograph of the high-intensity event is dominated by event water and that of the low-intensity event by preevent water. This study highlights the problems of applying mixing analyses to overland flow-dominated catchments and soil environments with a poorly developed vertical chemical zonation and emphasizes the need for independent hydrometric information for a complete characterization of watershed hydrology and chemistry.

Using paleolimnological techniques, I have studied surface-water acidification and the effects of liming in Swedish lakes on a decadal to millennial time-scale. The overall objective was to contribute to the discussion on the fulfilment of goals within the Swedish liming program. One of the main goals of this program is to restore lakes to natural or nearly natural conditions, i.e. to a reference condition as termed in the EU Water Framework Directive. In this context, a key issue is to define reference conditions. This is a central theme of my thesis, as lake sediments offer a unique way to study past lake conditions. Past lake-water acidity of 12 reference lakes in the Swedish liming program (ISELAW) was determined using diatom analysis of sediment cores. Pollen, lead, and flyash from coal/oil combustion were used as indicators of impact from land use and atmospheric pollution. A general trend in these lakes is an initial decline in pH after lake formation due to natural soil processes, which was then followed by rather low pH values (pH 5.3-6.5). In six of the lakes pH increased as a result of expansion of agriculture (burning, forest grazing) 2000 to 1000 years ago. Local mining and long-range airborne pollution have also impacted the lakes since medieval time. These results show that the conditions of the study lakes were not natural prior to industrialization and recent (20th century) acidification. The ISELAW lakes were selected on the basis of representing typical limed lakes, and they have been limed and monitored since at least the 1980s. A comparison of chemical/biological monitoring data and the paleolimnological data gives somewhat diverging results. Most of the monitoring data suggest that the lakes were subjected to acidification during the 20th century, but the paleolimnological data can only identify clear evidence of acidification in five of the 12 lakes, hence, all lakes were probably not recently acidified. According to conclusions from monitoring the lakes have recovered following liming. The paleolimnological data give a more complex picture and three different responses have been identified: 1) a return to a diatom composition found in the lake one hundred to several thousand years ago; 2) very small shifts in the diatom composition; or 3) a diatom composition previously not found in the lake. The latter response raised the question whether liming can cause an unnatural diatom community. A comparison of diatoms in surface sediment samples of 31 limed lakes with pre-industrial reference samples from 291 lakes showed that liming does not create an unnatural diatom composition. These results illustrate that the goals for liming were not reached in all of the limed lakes, and that paleolimnology can play an important role for assessments of acidification and liming. The comparative study also highlights the importance of designing monitoring programs that can produce reliable and long data series. Given the results of the paleolimnological investigations, it is obvious that we cannot assume that the 19th century represented a natural or near natural state, and thus is a realistic reference conditions. Natural long-term lake development and previous land-use impacts need to be considered in defining reference conditions. Neither can we disregard the fact that humans always will impact nature. Although paleolimnological studies are time consuming, I believe that they could be simplified to the extent that paleolimnology could become a routine method for environmental management.

Animals experience variation in their environment because of natural changes. However, due to anthropogenic disturbance, the speed and severity of these changes have recently increased. This thesis investigates how reproductive behaviours may be affected by human induced environmental change. In specific, I investigate how visual and chemical changes in the aquatic environment, caused by eutrophication, affect mating systems and sexual selection in fish. Broad-nosed- and straight-nosed pipefish, which both have been studied in detail for a long period, were used as model organisms. These two species are particularly suitable model organisms since they perform complex courtship behaviours, including the advertisement of ornaments and a nuptial dance. Further, two distinct populations were studied, one on the Swedish west coast and one in the Baltic Sea, as these two locations vary in the degree and extent of environmental disturbance, in particular turbidity. I found that changes in the visual environment had no impact on the development of female sexual ornaments in these sex-role reversed pipefishes, but it hampered adaptive mate choice. Turbidity also had a negative effect on reproductive success in the Baltic Sea population. Changes in the chemical environment in the form of increased pH reduced the probability to mate, while hypoxia did not alter mating propensity. However, hypoxic water delayed the onset of both courting and mating. Hence, human induced change in aquatic environments may alter the processes of sexual selection and population dynamics.

A series of experiments were conducted to examine protein digestion in the young bird and the physiological changes that affect protein digestion as the bird matures. Trial one determined the effect of age on pH of the gastrointestinal tract. The results showed that the pH of the proventriculus and gizzard decreases with age suggesting that gastric acid secretion increases proportionally with age and this may impact protein digestion. Experiment two examined the effect of age on ileal amino acid (AA) digestibility of feed ingredients. AA digestibility increased from 5 to 21 d and the degree of improvement differed among ingredients and specific AA. This finding coupled with the low AA content of some ingredients demonstrates the importance of using appropriate nutrient digestibility values for young birds when formulating pre-starter and starter diets. Experiment three determined the acid binding capacity (ABC) of feed ingredients and the effect of formulating diets based on ABC on diet ABC, gastrointestinal pH and performance. The research confirmed dramatic differences in ABC among ingredients and that diets could be formulated on the basis of ingredient ABC. However, the range in diet ABC was less than predicted suggesting interactive effects among ingredients. Intestinal pH was reduced however broiler performance was not improved when diets low in ABC were fed. Experiment four examined the effect of diet acidification with HCl on diet ABC, gastrointestinal pH, ileal amino acid digestibility and broiler performance. Improvements in performance and reductions in mortality were observed when broilers were fed acidified diets. Adding acid to diets did not improve AA digestibility and therefore was not the reason for improved performance indicating an alternative mechanism of action. It is concluded that acid production by the proventriculus of young birds is low and increases with age however this does not impact protein digestion. Methods of improving performance of broiler chickens may include diet acidification however this is not the effect of remedying the low acid production by young birds. Therefore, alternative mechanisms are positively affecting broiler performance.

As human activities continue to generate accelerating levels of carbon dioxide emissions, the world’s oceanic resources are threatened by variability in seawater chemistry, known as ocean acidification. Recent increases in atmospheric carbon dioxide have resulted in decreased carbonate ion concentrations and ocean pH levels, leading to increasingly acidic waters. The exact consequences of these chemical changes on ecosystems and individual species are difficult to predict; however, research has shown that economically valuable calcifying species will experience reduced reproductive fitness and population declines. Ocean acidification, therefore, poses an immediate risk to both fish stocks and fishery industries. From a local perspective, individual regions will need to implement dynamic management strategies to prepare for anticipated economic consequences. In a global context, international cooperation is required for further research and collaborative efforts must be made to reduce future acidification.

Le processus de la rétroaction déshydratation-effet de serre (RDES) est une hypothèse pour tenter d'expliquer la tendance au refroidissement observé durant l'hiver arctique. Un forçage radiatif indirect des aérosols, tel que l'acide sulfurique sur les aérosols, aurait pour effet d'entraver les processus de nucléation des cristaux, pour ainsi diminuer la concentration de noyaux glaçogènes (IN) (Blanchet et Girard, 1994) Tel que durant la transformation des masses d'air continentales en masses d'air polaires par refroidissement radiatif, le développement de cristaux de plus grande taille est favorisé. Le taux de précipitation est ainsi augmenté et la masse d'air se déshydrate plus rapidement (Girard, 1998). Par conséquent, la basse atmosphère arctique est déshydratée et refroidie par réduction de l'effet de serre. Cette étude consiste à effectuer une étude de sensibilité du climat arctique à l'effet RDES selon: 1) deux types de circulations atmosphériques (OAN+ et OAN-), 2) une faible acidification des aérosols se traduisant par un faible facteur de réduction (0,08) de la concentration de noyaux de glaciation (IN) (Borys el al., 1989), 3) une grande plage de température puisque l'on simule le mois de février et mars (nouveauté). Le modèle NARCM 3D est utilisé pour effectuer les simulations puisqu'il contient le module CAM, qui simule les processus physiques, les émissions et le transport des aérosols (Gong el al., 2003). Les résultats obtenus montrent que l'hypothèse de la RDES n'est pas vérifiée pour les 4 mois simulés (février et mars 1985 et 1995). Les facteurs composant la suite logique menant à l'effet de refroidissement associé au processus de la RDES ne sont pas réunis dans les zones où l'anomalie de température est négative. Deux facteurs sont défavorables aux processus de la RDES, soit une circulation atmosphérique davantage latitudinale pour les deux types de circulation, créant un faible apport d'aérosols en Arctique central, et soit un petit facteur de réduction des IN, ayant un effet plus grand dans les régions chaudes du domaine. Ces facteurs favorisent une stagnation des concentrations importantes des aérosols sulfatés dans les régions des mers de Barents et Kara. Le transport des aérosols vers l'Arctique central n'est pas favorisé pour les 4 mois simulés. Toutefois, pour les quatre mois d'étude, la réduction de la concentration de IN modifie la phase des nuages en augmentant la proportion de glace au détriment des gouttelettes. La baisse modeste de IN imposée a un effet plus grand pour les nuages relativement chauds du fait qu'ils contiennent déjà peu de IN. La baisse de la concentration de IN génère une baisse du taux de déposition de la vapeur d'eau sur les cristaux. Donc, le rapport saturant par rapport à la glace augmente, suivie d'une hausse de la concentration des gouttelettes et des cristaux. Par la suite, le taux d'évaporation des gouttelettes s'intensifie, engendrant ainsi une augmentation du CES et une diminution du CEL. Les nuages optiquement plus minces sont les plus sensibles aux altérations du contenu en eau liquide et solide des nuages. Ce processus induit une perte de la quantité d'eau totale dans les nuages, de même qu'une réduction du forçage radiatif des nuages d'une valeur moyenne de -3,3 W/m². ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Aérosols, Arctique, Noyaux de glaciation, Acidification, Phase des nuages.

Abstract: Acidification was categorized as the main environmental problem in Scandinavia during the 1960’s. Fortunately for Sweden, as with other countries in Scandinavia, has shown a process of recovery from acidification, by emission control. Further Sweden has had an extended liming program to mitigate the effects from acidification. Regarding the acidification assessment of the EU Water Framework Directive, it requires that EU members attain a ‘good ecological status’ in their surface waters. The status is defined as a deviation from a reference value and this is achieved using a reference reflecting a preindustrial state. As the waters are recovering from acidification the liming program can be reduced. Hence, there is a need to develop tools that can be used for decisions to stop liming in single waters. This study states three approaches: the well known hydrochemical model MAGIC, a meta-MAGIC model which calibrates the reference value computed by MAGIC model and paleolimnology studies. The latter is the key because it is the one that measures the reference value by immediate samples insitu. However, all methods have advantages and disadvantages, which allowed the development of an additional tool called meta-paleo for the same purpose. This meta-paleo model is designed based on an 11 years mean of contemporary water chemistry and paleolimnology data of 71 lakes. This tool for acidification assessment enables to work with few parameters of water chemistry. However it is concluded that the model has uncertainties, which should be evaluated so it can be used as a tool for decision making.