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The purpose of this study was to determine the impact of key process parameters on the flow properties of a novel High Protein Dairy Food (HPDF). HPDF was manufactured by an approach similar to that of manufacture of Halloumi cheese (a semi hard cheese originally from Cyprus). The effect of pasteurization condition, pH of acidification and homogenization were investigated on flowability, composition and texture of the HPDF. The study consisted of three different stages. After each stage of experimentation, the HPDF was analyzed for compositional, textural (by texture profile analysis) and flow properties during heating by microwave, oven and hot water was measured by Schreiber melt test. The first stage of experimentation screened 18 batches of HPDF under three levels of pasteurization conditions (191°F/16 sec, 175°F/16 sec and 161°F/16 sec), three levels of pH of acidification (5.8,6.2 and 6.6) and two levels of homogenization conditions (two stage homogenization (2000 psi/500 psi) and no homogenization). Based on the results of the first stage, a statistically powerful second stage of experiment was designed in which two levels of pasteurization condition (191°F/16 sec and 161°F/16 sec) and three levels of pH of acidification (5.8, 6.2 and 6.6) were employed in duplicate to manufacture HPDF. The third stage of experimental design was to investigate the effect of two-stage homogenization treatment (2000 psi/500 psi) with two levels (homogenization and no homogenization). The results of all three stages of experimentation proved that HPDF made from milk pasteurized under higher pasteurization condition (191°F/16 sec) had significantly higher flow resistance under all three heating conditions. There was significant interaction between pH of coagulation of milk and pasteurization condition on flow properties of HPDF with pH of coagulation 5.8 restriction flow of HPDF under all three heating conditions. The role of homogenization in restricting flow of HPDF was not significant, although the mean flow of HPDF, made from homogenized milk, decreased. The mean protein content and mean moisture content of HPDF was significantly affected by all three processing conditions, although the mean fat content of HPDF was not influenced by any of these conditions. The mean fat, protein and moisture content of HPDF were in the range of 10.5-11, 26-34 and 47-54 percent respectively. The primary textural properties affected significantly by the processing condition were hardness, chewiness and gumminess. Particularly, hardness was influenced by higher pasteurization condition and lower pH of acidification. Further, to judge the consumer acceptability of HPDF, various recipes made out of HPDF with different heating applications (baking, stir-frying and soup) were served to 12 panelists of DPTC. Their opinions were collected and analyzed statistically. The analysis of limited focus group survey showed that consumer liking for HPDF recipe was significantly influenced by prior familiarity with the recipe, although there was some preference for HPDF over tofu due to its ‘dairy’ flavor. When the texture of HPDF manufactured from milk pasteurized at 191°F/16 sec and pH of acidification 5.8 and 6.2 were compared with various commercial protein sources, the hardness of the HPDF was very close to extra firm tofu. All the other textural properties of HPDF were significantly different from firm, silken, baked or reduced fat tofu. From this project, it is evident that a high protein food, which can be part of day-to-day human diet and potential tofu alternative, can be obtained using halloumi approach by optimizing pasteurization condition (191°F/16 sec) and pH of coagulation (5.8).

Cold-water corals act as critical foundation species in the deep sea by creating extensive three-dimensional habitat structures that support biodiversity hotspots. There is currently a paucity of data concerning the environmental requirements and physiology of cold-water corals, severely limiting our ability to predict how resilient they will be to future environmental change. Cold-water corals are expected to be particularly vulnerable to the effects of ocean acidification, the reduction in seawater pH and associated changes to the carbonate system caused by anthropogenic CO2 emissions. Here, the ecological niche and physiology of the cold-water coral Lophelia pertusa is explored to predict its sensitivity to ocean acidification. Species distribution models were generated in order to quantify L. pertusa’s niche in the Gulf of Mexico with regard to parameters including seafloor topography, the carbonate system, and the availability of hard substrate. A robust oceanographic assessment of the Gulf of Mexico was conducted in order to characterize the current environmental conditions at benthic sites, with a focus on establishing the baseline carbonate system in L. pertusa habitats. Finally, an experimental approach was used to test the physiological response of biogeographically separated L. pertusa populations from the Gulf of Mexico and the Norwegian coast to ocean acidification. Based on my findings, it appears that L. pertusa already persists near the edge of its viable niche space in some locations, and therefore may be highly vulnerable to environmental change. However, experimental results suggest that some populations may be surprisingly resilient to ocean acidification, yielding broad implications for the continued persistence of cold-water corals in future oceans. / Biology

Deep-water or cold-water corals are abundant and highly diverse, greatly increase habitat heterogeneity and species richness, thereby forming one of the most significant ecosystems in the deep sea. Despite this remote location, they are not removed from the different anthropogenic disturbances that commonly impact their shallow-water counterparts. The global decrease in seawater pH due to increases in atmospheric CO2 are changing the chemical properties of the seawater, decreasing the concentration of carbonate ions that are important elements for different physiological and ecological processes. Predictive models forecast a shoaling of the carbonate saturation in the water column due to OA, and suggest that cold-water corals are at high risk, since large areas of suitable habitat will experience suboptimal conditions by the end of the century. The main objective of this study was to explore the fate of the deep-water coral community in time of environmental change. To better understand the impact of climate change this study focused in two of the most important elements of deep-sea coral habitat, the reef forming coral Lophelia pertusa and the octocoral community, particularly the gorgonian Callogorgia delta. By means of controlled experiments, I examined the effects of long- and short-term exposures to seawater simulating future scenarios of ocean acidification on calcification and feeding efficiency. Finally In order to understand how the environment influences the community assembly, and ultimately how species cope with particular ecological filters, I integrated different aspects of biology such functional diversity and ecology into a more evolutionary context in the face of changing environment. My results suggest that I) deep-water corals responds negatively to future OA by lowering the calcification rates, II) not all individuals respond in the same way to OA with high intra-specific variability providing a potential for adaptation in the long-term III) there is a disruption in the balance between accretion and dissolution that in the long term can shift from net accretion to net dissolution, and IV) there is an evolutionary implication for certain morphological features in the coral community that can give an advantage under stresfull conditions. Nevertheless, the suboptimal conditions that deep-water corals will experience by the end of the century could potentially threaten their persistence, with potentially negative consequences for the future stability of this already fragile ecosystem. / Biology

Ocean acidification is the reduction in seawater pH due to the absorption of anthropogenic carbon dioxide by the oceans. Reductions in seawater pH can inhibit the precipitation of aragonite, a calcium carbonate mineral used by marine calcifiers such as corals. Lophelia pertusa is a cold-water coral that forms large reef structures which enhance local biodiversity on the seafloor, and is found commonly from 300-600 meters on hard substrata in the Gulf of Mexico. The present study sought to investigate the potential impacts of ocean acidification on L. pertusa in the Gulf of Mexico through combined field and laboratory analyses. A field component characterized the carbonate chemistry of L. pertusa habitats in the Gulf of Mexico, an important step in establishing a baseline from which future changes in seawater pH can be measured, in addition to collecting in situ data for the design and execution of perturbation experiments in the laboratory. A series of recirculating aquaria were designed and constructed for the present study, and support the maintenance and experimentation of live L. pertusa in the laboratory. Finally, experiments testing L. pertusa's mortality and growth responses to ocean acidification were conducted in the laboratory, which identified thresholds for calcification and a range of sensitivities to ocean acidification by individual genotype. The results of this study permit the monitoring of ongoing ocean acidification in the deep Gulf of Mexico, and show that ocean acidfication's impacts may not be consistent across individuals within populations of L. pertusa. / Biology

Acid deposition (AD) results largely from the combustion of fossil fuels, and has been found to negatively impact forest ecosystems. AD may acidify soils through base cation leaching or Al mobilization, may cause accumulation of nitrates and sulfates in soils, and in some cases has been related to forest decline. The Monongahela National Forest (MNF) lies downwind from many sources of AD pollution, and average deposition pH is around 4.4. Therefore, managers are concerned about the possible deleterious effects of AD on the forest ecosystem. During the 2006 Forest Plan revision, evaluation of site sensitivity to acidification was specifically stated as a step in the Forest's adaptive management process. To meet this management objective, forest practitioners must understand the effects AD has on the forest, prescribe appropriate practices, and be able to monitor for future changes. To address the needs of MNF managers we used Forest Inventory and Analysis (FIA) sites to evaluate forest growth patterns on the Forest and determined the relationship between growth and key indicators of soil acidity. Furthermore, we used those relationships to create a map of site resistance to acidification across the MNF. To further develop a monitoring scheme we assessed two soil sampling protocols and two soil analysis methods for their suitability for monitoring AD-related changes in soil chemistry. Additionally, we evaluated the utility of dendrochronological and foliar sampling as AD-specific monitoring methods. Across all FIA sites on the MNF periodic mean annual volume increment (PMAVI) ranged from -9.5 m³ha⁻¹yr¹ to 11.8 m³ha⁻¹yr¹, suggesting lower-than-expected growth on two-thirds of the sites. Growth was compared to soil indicators of acidity on 30 FIA sites. In the surface horizon, effective base saturation (+), Ca concentration (+), base saturation (+), K concentration (+), Fe concentration (-), Ca/Al molar ratio (+), and Mg/Al molar ratio (+), were correlated with PMAVI (p ≤ 0.1). In the subsurface horizon pH_(w) (+), effective base saturation (+), Al concentration (-), and K concentration (-) were correlated with PMAVI. Site resistance to acidification was mapped based on site parent material, aspect, elevation, soil depth, and soil texture. There was a significant (p ≤ 0.1) positive correlation between PMAVI and a resistance index developed using five soil and site factors. Resistance was also compared with key soil indicators of AD-induced decline on 28 sites across the forest, and pH, effective base saturation, and Al content were found to be the best indicators related to resistance index. Resistance index was used to create a map of the MNF, of which 14% was highly resistant (RI ≥ 0.7), 57% was moderately resistant (0.7 > RI > 0.45) and 29% was slightly resistant (RI ≤ 0.45). The first of our monitoring program evaluations compared soil sampling and analysis methods on 30 FIA plots. Analyses of variance showed that soil pH, effective base saturation, Ca/Al molar ratio, and sum of bases varied significantly with sampling protocol. We also compared lab analyses methods and found that if sampling by horizon, a linear relationship can be used to estimate Ca/Al_SrCl₂ ratio using NH₄Cl extractions. The second monitoring approach evaluated the utility of a northern red oak (Quercus rubra L.) dendrochronology on two FIA plots. This analysis suggests that pollution on the MNF caused a decrease in growth rate during the 50-year period from 1940 to 1990. There were no differences among ring width increment and basal area increment between the two sites. From 1900 to 2007 the two sites showed 58.5% similarity in growth trends, but these could not be attributed to a dissimilar influence of AD. The third monitoring approach evaluated the relationship between foliar and soil chemical indicators. Across FIA plots, nutrient concentrations varied by tree species. The first year results from a potted-seedling study suggest that soil acidity influences growth, and foliar concentrations are related to growth rates. This evaluation of the effects of AD on the MNF can be used to develop adaptive management plans and a monitoring program that will meet the AD-related objectives of the 2006 Forest Management plan. / Master of Science

Les changements globaux ont le potentiel d'altérer les cycles biogéochimiques entraînant des répercussions pour tout le réseau alimentaire. Puisque l'azote est généralement l'élément limitant en milieu estuarien, une altération de son cycle pourrait influencer l'ampleur et le type de production primaire ainsi que la composition de la communauté phytoplanctonique qui l'effectue. Il en va de même pour la composition de la matière organique qui peut affecter la valeur nutritive des algues pour les consommateurs de même que l'efficacité de la pompe biologique. Actuellement, aucune étude portant sur les impacts combinés de l'acidification et du réchauffement des eaux de l'estuaire maritime du Saint-Laurent n'a été réalisée. L'objectif de ce projet de maîtrise fut d'évaluer expérimentalement, à l'aide de mésocosme, les impacts cumulés que ces changements pourraient avoir sur la dynamique des nutriments et de l'azote en particulier ainsi que sur la composition élémentaire de la matière organique. Une combinaison factorielle de six pH (7,2; 7,4; 7,6; 7,8; 8,0 et un pH sans contrôle) et de deux températures (10 et 15°C) fut employée. Les résultats de l'expérience suggèrent que les organismes responsables des processus à l'étude sont tolérants à une diminution considérable du pH. Ceux-ci furent toutefois affectés par la hausse de température, qui entraîna une diminution du ratio N:P de consommation des nutriments, accéléra le développement de la floraison phytoplanctonique et l'épuisement des nutriments, puis mena à un changement taxonomique en fin d'expérience. Ce changement est possiblement responsable des différences observées dans la composition de la matière organique particulaire (POM) lors du déclin de la floraison planctonique (diminution des ratios POC:PON, POC:POP, POC:BSi et hausse du ratio BSi:PON). Ces résultats suggèrent que pour l'estuaire maritime du Saint-Laurent, le réchauffement pourrait entraîner des changements stœchiométriques au sein de la POM avec des conséquences probables pour les niveaux trophiques supérieurs et la pompe biologique.

Le recours à des épandages d'amendements calco-magnésiens dans les forêts acidifiées peut représenter une alternative intéressante pour corriger l'acidification des sols et la perte d'éléments nutritifs engendrés par des décennies de dépôts atmosphériques acides. Dans ce contexte, les objectifs de cette thèse sont d'évaluer les effets d'amendements calco-magnésiens sur (i) la diversité taxonomique et la structure des communautés des macroinvertébrés de sol forestier et sur (ii) deux processus fonctionnels associés notamment à l'activité des vers de terre, tels que la structuration du sol et l'évolution des humus. Au cours de nos travaux, trois sites localisés dans les Vosges (nord-est, France) ont été étudiés : deux massifs forestiers (sur grès et granite) en moyenne montagne, ayant fait l'objet d'amendements aériens en 2003 et la forêt domaniale de Humont située dans les collines sous-vosgiennes, où des amendements en 1991 et 2008 ont été réalisés. Les résultats montrent que 4 ans après amendement sur les bassins versants en moyenne montagne, l'abondance totale de la communauté de macrofaune a diminué, alors que les richesses spécifiques sont similaires. Cependant, la composition des communautés diffère avec moins de 50 % d'espèces communes aux sites amendés et témoins. Une diminution de l'abondance des prédateurs a également été observée alors que la plupart des détritivores ont été favorisés par l'amendement. Les études in vitro montrent également son effet positif sur les activités de structuration du sol par les vers de terre (production de turricules et construction de galeries). En forêt de Humont, les amendements ont eu un effet majeur à moyen terme (4 ans) et à long terme (20 ans) sur la population d'Aporrectodea velox, espèce endémique des Vosges. De part sa biomasse importante, cette augmentation de densité favorise l'amélioration des caractéristiques physico-chimiques du sol forestier tels que la structuration des sols et la morphologie des humus. / The use of liming (Ca-Mg) on acidified forest can be interesting to counteract soil acidification and loss of nutrients caused by decades of acid atmospheric deposition. In this context, the aims of this work were to assess liming effect on (i) taxonomical diversity and community structure of soil macro-invertebrates and on (ii) two associated functional processes related to earthworms: soil structuration and humus evolution. The PhD project was realised in three sites from the Vosges mountains (North-eastern, France): two forest mountain catchments (one lying on sandstone and the other on granite) limed in 2003 and the public hill forest of Humont at a lower altitude limed in 1991 and 2008. Results showed that 4 years after liming in mountain forest, the total abundance of macro-invertebrates decreased, while the species richness were similar. However, the community structure strongly differed, and less than 50% of the species were common to limed and control sites. Moreover, 43 species appeared to be indicators of liming. Predator taxa abundance decreased whereas the detritivorous were favoured by lime addition. The in vitro experiments showed a positive effect of liming on soil structuration by earthworm activities (cast production and burrowing activities). In the Humont forest, liming at medium-term (4 years) and long term (20 years) have an important effect on the Aporrectodea velox population, an endemic vosgian species. Related to its high biomass, this increase strongly improved soil physicochemical parameters such as soil structure and humus morphology.

L'objectif principal de ce travail est d'évaluer si l'amendement calco-magnésien de deux bassins versants acidifiés du massif vosgien (un sur grès et un sur granite) engendre des changements de la morphologie des humus, de l'abondance et de la diversité de la mésofaune, de la biomasse fongique, du stockage de carbone dans les horizons organiques 5 et 7 ans après l'amendement. Par ailleurs, nous avons effectué une étude dans des conditions contrôlées de laboratoire en utilisant des microcosmes contenant les horizons organiques du sol provenant de bassins versants acidifiés sur grès et sur granite afin d'évaluer les effets à court terme de l'amendement. Les résultats indiquent que les effets de l'amendement sont beaucoup plus marqués sur le substrat le plus acide. À court terme, sur substrat gréseux, nous observons une diminution de l'abondance de la mésofaune puis une augmentation de celle-ci 5 ans après l'amendement avant de ne montrer plus aucun effet 7 ans après l'épandage. L'effet inverse ou aucun effet n'est par contre observé sur substrat granitique. Le contenu en Ca et Mg de l'horizon OL a augmenté avec l'amendement, mais cet effet n'est également significatif que sur grès. La biomasse fongique du sol n'a pas été affectée par le chaulage, mais est significativement plus élevée sur granite que sur grès. Le chaulage a augmenté l'épaisseur de l'horizon OH sur grès alors qu'il a diminué l'épaisseur de l'horizon OL sur granite, probablement en relation avec les modifications de l'activité biologique (mésofaune ou microorganismes). Enfin, sur substrat gréseux, le stock de carbone de l'humus a augmenté du fait d'un épaississement notable de l'horizon OH avec le chaulage. / The main objective of this work is to assess the consequences of calco-magnesium liming on two acidified forested catchments in Vosges Mountain (sandstone and granite) on humus morphology, abundance and diversity of mesofauna, fungal biomass and carbon storage in organic horizons 5 and 7 years after liming. Moreover, we performed a study to verify under laboratories conditions by using microcosms filled with soil from acidified catchments lying on sandstone and granite in order to study the short-term effect of calco-magnesium liming. During the two field campaigns, we determined calcium and magnesium contents of OL horizon, pH, humus morphology, mesofauna abundance and diversity, fungal biomass, soil carbon storage of organic layers OL, OF and OH.Results indicated that calco-magnesium liming affects studied parameters in different ways according to elapsed time after liming and the geological substrate (sandstone and granite), the more acidic catchment (sandstone) showing the most remarkable reaction. Results of immediate effects of liming showed a decrease of mesofauna abundance and then gradually increasing tendencies in field campaigns after 5 years while no effect after 7 years after liming. The opposite or no effects were observed on granite substrate. Ca and Mg contents in OL horizon increased by liming but this effect were only significant on sandstone substrate. Soil fungal biomass was not affected by liming but was significantly higher on granite substrate than sandstone. Liming increased the OH horizon thickness on sandstone while decreased the OL horizon on granite, under the influence of biological activity (mesofauna vs microorganisms).

L’acidification des océans provoquée par l’absorption du CO2 atmosphérique par l’eau de merest devenue une préoccupation écologique majeure et menace déjà les organismes calcifiants. Suiteà la révolution industrielle, le pH de l’océan de surface a diminué de 0,1 unité-pH. En revanche, celuides eaux profondes reste peu documenté. Les isotopes du bore (11B) dans les carbonatesbiogéniques se sont révélés être un puissant outil géochimique pour la reconstitution du pH, mais n’apas encore été appliqué aux coraux profonds. Un travail analytique sur MC-ICPMS Neptune et uneanalyse géochimique de ces coraux ont été effectués afin de reconstituer et quantifier l’acidificationdes océans. De même, la valeur 11B de l’eau de mer utilisée pour calculer les paléo-pH a étérevisitée et l’homogénéité des océans vérifiée.L’analyse de deux colonies modernes de Lophelia pertusa et Madrepora oculata a permis dequantifier un taux d’acidification pendant la fin du XXème siècle pour les eaux de sub-surface en mer deNorvège et cela après établissement d’une calibration expérimentale à partir de coraux de culture.L’analyse géochimique des coraux profonds a mis en évidence un effet vital lié à la physiologie quidoit être considéré pour quantifier avec précision la variabilité du pH. Celui-ci peut être en partiecorrigé par une analyse statistique des isotopes stables B, C et O. Cette étude a aussi révélél’influence de l’hydrodynamique régionale. Enfin les variations naturelles du pH pendant l’Holocène etle Dernier Maximum Glaciaire sur des coraux profonds fossiles méditerranéens ont été établies etcelles pendant l’aube de l’explosion de la diversité biologique. / Ocean acidification is caused by the absorption of rising atmospheric CO2 by seawater andrepresents a major environmental issue. Since the beginning of the industrial era, seawater pH hasdecreased by 0.1 pH units and is already threatening calcifying organisms. Boron isotopes (11B) haveproved to be a powerful geochemical tool for the reconstruction of pH variations, but has not yet beenapplied to deep-sea corals (DSC). Accurate and precise measurements of boron isotopes in coralsand seawaters were performed in order to measure small pH variations.The technique of pH reconstruction based on boron isotopes (pH-11B) was used on two specimens of the DSC Madrepora oculata and Lophelia pertusa collected alive in the Norwegian Sea and spanning an age of 40 (3) and 67 (3) years, respectively. Acidification rates were calculated by applying a new pH-11B calibration obtained from the geochemical analysis M. oculata and L. pertusa samples cultured under different pCO2 conditions. The contribution of a biological-related vital effect on d11B was observed at macrometer scale, and a correction was finally suggested based on oxygen and carbon isotopes. Overall, the coral δ 11B-based reconstructions show a pH decrease in the Norwegian Sea since the 1940s, which seems to be related to the local hydrodynamics. The pH-11B technique was also applied to fossil DSC fragments from two “on-mound sediment cores” retrieved in the Siculo-Tunisian Strait with the aim to reconstruct the pH during the Last Glacial Maximum and the Holocene periods. Finally, well-preserved limestone samples from the stratigraphic sequence Nama (551-543 Ma) in Namibia were investigated for 11B to study the pH variations at the beginning of the Cambrian evolutive radiation.