Elevated atmospheric concentrations of carbon dioxide (CO₂), partly driven by anthropogenic activity, are decreasing the pH of the oceans. This thesis aimed to assess the biological response of foraminifera to ocean acidification. Foraminifera are single-celled organisms that form the dominant component of many marine communities. A series of laboratory experiments were carried out on benthic intertidal foraminifera from the Eden and Ythan estuaries, NE Scotland, to assess the impacts of ocean acidification. The responses of two dominant intertidal species of foraminifera (Haynesina germanica and Elphidium williamsoni) to ocean acidification were initially investigated in a short-term (6 week) experiment. Multiple species and multiple stressors (seasonal temperature regime and elevated CO₂) were then incorporated in a long-term (18 month) mesocosm study to investigate the physiological consequences (e.g. survival, growth) of ocean acidification. Survival of both Haynesina germanica and Elphidium williamsoni was significantly reduced under low pH conditions. Live specimens of both these calcareous species were however recorded at low pH, in reduced numbers. Following long-term exposure to ocean acidification, foraminiferal populations were still dominated by calcareous forms. Agglutinated foraminifera were recorded throughout the long-term incubations but their numbers were not high enough in the initial sediment collections to allow them to contribute significantly to the populations. Overall, survival of all foraminifera was greatly reduced in elevated CO₂ treatments. Temperature effects were observed on foraminiferal survival and diversity with the largest CO₂ effects recorded under the seasonally varying temperature regime. Foraminiferal test damage for all live species was also highest under elevated CO₂ conditions. Test dissolution was particularly evident in Haynesina germanica with important morphological features, such as functional ornamentation, becoming reduced or completely absent under elevated CO₂ conditions. A reduction in functionally important ornamentation could lead to a reduction in feeding efficiency with consequent impacts on this organism's survival and fitness. In addition, changes in the relative abundance and activities of these important species could affect biological interactions (e.g. food web function) and habitat quality.

As climate change intensifies, the capacity of organisms to adapt to changing environments becomes increasingly relevant. Heat-induced coral bleaching –the breakdown of the symbiotic association between coral hosts and photosynthetic algae of the family Symbiodiniaceae– is rapidly degrading reefs worldwide. Hence, there is a growing interest to study symbioses that can persist in extreme conditions. The Red Sea is such a place, known as one of the hottest seas where healthy coral reef systems thrive. Here (Chapter 1), we tested the potential of symbiont manipulation as means to improve the thermal resilience of the cnidarian holobiont, particularly using heat tolerant symbiont species from the Red Sea. We used clonal lineages of the model system Aiptasia (host and symbiont), originating from different thermal environments to assess how interchanging either partner affected their short- and long-term performance under heat stress. Our findings revealed that symbioses are not only intra-specific but have also adapted to native, local environments, thus potentially limiting the acclimation capacity of symbiotic cnidarians to climate change. As such, infection with more heat resistant species, even if native, might not necessarily improve thermotolerance of the holobiont. We further investigated (Chapter 2) how environment-dependent specificity, in this case elevated temperature, affects the establishment of novel symbioses. That is, if Aiptasia hosts are, despite exhibiting a high degree of partner fidelity, capable of acquiring more thermotolerant symbionts under stress conditions. Thus, we examined the infection dynamics of multi-species symbioses under different thermal environments and assessed their performance to subsequent heat stress. We showed that temperature, more than host identity, plays a critical role in symbiont uptake and overall performance when heatchallenged. Additionally, we found that pre-exposure to high temperature plays a fundamental role in improving the response to thermal stress, yet, this can be heavily influenced by other factors like feeding. Like climate change, ocean acidification is a serious threat to corals. Yet, most research has focused on the host and little is known for the algal partner. Thus, here we studied (Chapter 3) the global transcriptomic response of an endosymbiotic dinoflagellate to long-term seawater acidification stress. Our results revealed that despite observing an enrichment of processes related to photosynthesis and carbon fixation, which might seem beneficial to the symbiont, low pH has a detrimental effect on its photo-physiology. Taken together, this dissertation provides valuable insights into the responses of symbiotic cnidarians to future climate and ocean changes.

Ocean acidification is predicted to lead to global oceanic decreases in pH of up to 0.3 units within the next 100 years. However, those levels are already being reached currently in coastal regions due to natural CO2 variability. Squid are a vital component of the pelagic ecosystem, holding a unique niche as a highly active predatory invertebrate and major prey stock for upper trophic levels. This study examined the effects of a range of ocean acidification regimes on the early life history of a coastal squid species, the Atlantic longfin squid, Doryteuthis pealeii. Eggs were raised in a flow-through ocean acidification system at CO2 levels ranging from ambient (400ppm) to 2200ppm. Time to hatching, hatching efficiency, and hatchling mantle lengths, yolk sac sizes, and statoliths were all examined to elucidate stress effects. Delays in hatching time of at least a day were seen at exposures above 1300ppm in all trials under controlled conditions. Mantle lengths were significantly reduced at exposures above 1300 ppm. Yolk sac sizes varied between CO2 treatments, but no distinct pattern emerged. Statoliths were increasingly porous and malformed as CO2 exposures increased, and were significantly reduced in surface area at exposures above 1300ppm. Doryteuthis pealeii appears to be able to withstand acidosis stress without major effects up to 1300ppm, but is strongly impacted past that threshold. Since yolk consumption did not vary among treatments, it appears that during its early life stages, D. pealeii reallocates its available energy budget away from somatic growth and system development in order to mitigate the stress of acidosis.

The uptake of CO2 by the ocean is causing major changes in its chemistry. These changes are likely to have detrimental effects on many organisms with a severe impact on calcifying species. With future OA, marine organisms will be submitted to hypercapnia (increased pCO2) and acidosis (decreased pH). Skeleton production and maintenance could be impacted due to the increased energetic cost to calcify in less favourable conditions and direct corrosive effect of undersaturated seawater resulting in dissolution of calcium-carbonate unprotected structures. Postmetamorphic echinoderms (juveniles and adults) endoskeleton is made of high magnesium-calcite, one of the most soluble form of CaCO3. Because of their low metabolism and their heavily calcified skeleton, echinoderms were designated as species particularly at risk under OA. However, the effects of OA on calcification and on skeleton maintenance vary among closely related taxa. Hypotheses explaining these contrasted tolerance to OA were stated: (1) regulation of the acid-base balance, which occurs in some echinoderms taxa and not others, plays a major role; (2) populations living in highly fluctuating habitats are adapted or selected, which may confer them a better resistance to acidified conditions. The goal of this thesis was to evaluate these hypotheses using a comparative approach in asteroids (two species) and regular euechinoids (five species). The chosen species differ by their ability to regulate their acid-base physiology and by the amplitude of fluctuations in their habitats. The impacts of OA on corrosion and mechanical properties of their skeletal elements as well as, in selected species, the expression of biomineralization-related genes were investigated. All samples were obtained from individuals exposed to acidified conditions during long-term aquarium experiments or in situ exposures (CO2 vents).Bending and compression mechanical tests analysed by Weibull statistics and expression of biomineralization-related genes appeared particularly unitive endpoints. On the contrary, occurrence of corrosion, i.e. observation in scanning electron microscopy, did not match with mechanical effects, and nanoindentation never revealed differences according to treatment. The results showed that species which were not able to regulate their acid-base physiology also presented the most affected skeleton integrity when submitted to OA. This was particularly true for the temperate sea star Asterias rubens and the Mediterranean sea urchin Arbacia lixula whose skeleton was significantly impacted. In the latter, this went together with a down-regulation of biomineralization-related genes. Temperate and tropical sea urchins that regulated their acid-base physiology (Paracentrotus lividus, Echinometra sp. B and sp. C) presented no or very limited impact of OA on their skeleton and biomineralization-related gene expression (P. lividus). The Antarctic species (the sea star Odontaster validus and the sea urchin Sterechinus neumayeri) showed no sign of acid-base physiology regulation but also no impact of acidified conditions on their skeleton. This could be linked to their particularly low metabolism or to food availability. Living in fluctuating habitats did not appear to confer a particular resistance of the skeleton in front of OA. In particular, the sea star A. rubens from Kiel Fjord, living in highly fluctuating sea water conditions, was impacted by acidified conditions they transiently encounter every year. The same was true for the temperate sea urchin A. lixula. So, it appears that sea stars and sea urchins living in fluctuating habitats might already be at the limit of their tolerance window if they do not regulate their acid-base physiology. In conclusion, it appears that the acid-base regulation may be the key biological trait to address the impact of OA on the skeleton of adult echinoderms. Studies coupling mechanical testing and analysing biomineralization-related gene expression should be extended to more taxa (within and outside echinoderms) to ascertain the relationship between OA sensitivity and absence of acid-base regulation. / Depuis la Révolution Industrielle, la concentration en dioxyde de carbone (CO2) atmosphérique augmente continuellement. Les océans absorbent en partie ce CO2, ce qui induit une diminution de la concentration en ions carbonate ainsi qu’une augmentation de la concentration en protons, processus connus sous le nom d’acidification des océans (AO). Ces changements sont susceptibles d'avoir des effets néfastes sur une variété d'organismes marins qui seront soumis à l’hypercapnie (augmentation de la pCO2) et à l’acidose (diminution du pH). De plus, la calcification fait l’objet d’une attention particulière étant donné la remontée des horizons de saturation en carbonate de calcium dans les océans. La production ainsi que le maintien du squelette pourraient être limités en raison de l'augmentation du coût énergétique de la calcification dans des conditions moins favorables. Cependant, les effets de l’AO sur la calcification et sur le maintien du squelette varient selon les taxons voire au sein d’un même taxon. Des hypothèses ont donc été émises quant aux mécanismes sous-tendant ces différences. Une meilleure résistance face à l’AO pourrait aller de pair avec (1) une capacité à réguler le pH des fluides extracellulaires, (2) une préadaptation due à l’occupation d’habitats fortement fluctuants.Les échinodermes post-métamorphiques (juvéniles et adultes), espèces marines clés, possèdent une biologie générale assez semblable et sont constitués d’un endosquelette composé de calcite hautement magnésienne, une des formes les plus solubles de carbonate de calcium. En raison de leur faible métabolisme et de leur squelette fortement calcifié, les échinodermes ont été désignés comme des espèces particulièrement vulnérables sous l’effet de l’AO. Toutefois, de récentes études montrent que le squelette de certaines espèces d’échinodermes au stade adulte n’est pas affecté lorsque les organismes sont soumis à de bas pH d’eau de mer. L'objectif principal de la présente thèse était d’évaluer les différentes hypothèses par une approche comparative chez les astéroïdes (deux espèces) et les euéchinoïdes réguliers (cinq espèces). Les espèces choisies se différencient par leur capacité à réguler leur physiologie acide-base et par l’amplitude des fluctuations de leur habitat. Les effets de l’AO sur la corrosion et les propriétés mécaniques de leurs éléments squelettiques, ainsi que, chez certaines espèces, l’expression de gènes liés à la biominéralisation ont été étudiés. Tous les échantillons ont été obtenus à partir d’individus exposés à des conditions acidifiées lors d’expériences à long terme ou d’expositions in situ (évents à CO2).Les résultats ont montré que les espèces qui n'étaient pas en mesure de réguler leur physiologie acide-base (l’étoile de mer Asterias rubens et l’oursin Arbacia lixula) présentaient également des squelettes plus affectés lorsqu'elles étaient soumises à l'AO. Les oursins tempérés et tropicaux qui régulent leur physiologie acide-base (Parancetrotus lividus, Echinometra spp.) n’ont présenté aucun impact ou un impact très limité de l’AO sur leur squelette et l’expression des gènes liés à la biominéralisation (P. lividus). Les espèces antarctiques (l’oursin Sterechinus neumayeri et l'étoile de mer Odontaster validus) n’ont montré aucun signe de régulation de la physiologie acide-base mais également aucun impact sur leur squelette dû à une diminution du pH de l'eau de mer. Cela pourrait être lié à leur métabolisme bas ou à la disponibilité de nourriture dans leur environnement. Vivre dans des habitats fluctuants ne semble pas conférer une résistance particulière du squelette face à l’AO. En particulier, l’étoile de mer A. rubens du Fjord de Kiel, qui vit dans des conditions très fluctuantes, a été affectée par des conditions d’acidification qu’elles rencontrent de manière transitoire chaque année. Il en va de même pour l’oursin tempéré A. lixula. Il semble donc que les étoiles de mer et les oursins vivant dans des habitats fluctuants pourraient déjà être à la limite de leur fenêtre de tolérance lorsqu’ils ne régulent pas leur physiologie acide-base. En conclusion, la régulation de la physiologie acide-base est une caractéristiques biologique clé pour adresser les effets de l’AO sur le squelette des échinodermes adultes. Les études couplant les tests mécaniques à l’analyse de l’expression de gènes liés à la biominéralisation devraient être étendues à plus de taxons (au sein et en dehors de échinodermes) afin de déterminer la relation entre la sensibilité de la calcification face à l’AO et l’absence de régulation acide-base. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Climate change and eutrophication, accelerated by anthropogenic activities, have impacted aquatic ecosystems worldwide. These impacts have stimulated the expansion of cyanobacterial blooms which pose severe threats to ecosystem functioning, environmental health, and the economy. However, the long-term effects of environmental change on bloom-forming cyanobacteria are not well understood as traditional paleolimnological approaches are of limited use in the reconstruction of cyanobacterial dynamics through time. Here, sediment DNA (sedDNA) was used to investigate long-term cyanobacterial trends using sediments from two experimental (fertilized L227 and acidified L223) and two reference (L224 and L442) lakes in the Experimental Lakes Area, Canada. First, to determine whether taxonomic bias might arise from the cyanobacterial sediment record, I performed a 1-year incubation experiment comparing the degradation rates of selected cyanobacterial genes under contrasting environmental conditions. Based on first-order linear decay models, Synechococcus sp. (Synechococcales) decayed the slowest under cold, anoxic conditions, followed by Trichormus (Nostocales), then Microcystis (Chroococcales), suggesting differential preservation of DNA. I then compared the quantitative performance of droplet digital polymerase chain reaction (ddPCR) and high-throughput sequencing (HTS) for the analysis of sedDNA and found that the ddPCR results were more consistent with the known history of the lakes. Furthermore, ddPCR showed that cyanobacterial abundance increased over the past century in all study lakes, but the greatest increase was observed in experimentally fertilized L227. HTS revealed shifts in the cyanobacterial community towards Nostocales dominance and a decrease in alpha diversity in response to phosphorus-only additions. An increase in abundance of the mcyE gene (indicative of microcystin producing taxa) was uniquely observed in L227 when nitrogen additions ceased. Heating degree days were important in explaining variation in the cyanobacterial community composition in all lakes, but nutrients had a greater influence on the L227 community. When sediment data were compared to historical surface water phytoplankton records, moderate to strong correlations between the two archives were found, validating the use of sedDNA. This research demonstrated that sedDNA can elucidate cyanobacterial trends at the community, population, and species level over multidecadal timescales in response to environmental change.

Mississippi River affects the carbon dynamics in the northern Gulf of Mexico (N-GoM) significantly. Hence, total alkalinity (TA) algorithms developed for major ocean basins produce inaccurate estimations for this region. A TA algorithm was developed, which addresses the local effects of coastal processes and complex spatial influences. In-situ data collected during numerous previous research cruises in the N-GoM were compiled and used to calculate the efficiency of an existing TA algorithm that uses Sea-Surface-Temperature (SST) and Sea-Surface-Salinity (SSS) as explanatory variables. To improve this algorithm, statistical analyses were performed to improve the coefficients and functional form of this algorithm. Then, chlorophyll-a (Chla) was included as an additional explanatory variable. Chla worked as a proxy for addressing the organic carbon pump’s pronounced effects on coastal waters. Finally, a Geographically Weighted Regression (GWR) algorithm was developed to address spatial non-stationarity, which apparently could not be addressed in the previously developed global algorithm.

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Coastal ecosystems are faced with increasing pressures from human activities. Perhaps one of the most profound impacts is that of excess nitrogen loading which drives a series of negative consequences. Excess nitrogen fuels primary productivity and the subsequent enhanced microbial decomposition of organic matter, consumes oxygen and releases carbon dioxide, which causes large fluctuations in pH. Changes in organic matter availability, oxygen concentrations, and pH can have significant yet unconstrained implications for sediment recycling and removal of biologically important nutrients such as nitrogen and phosphorus. Such changes can also impact the production and consumption of two powerful greenhouse gases – nitrous oxide and methane. Here I use two temperate estuaries, Long Island Sound (New York, USA) and Waquoit Bay (Massachusetts, USA) to assess the role of human impacts on coastal sediment biogeochemical fluxes. In Chapter 1, I investigate the influence of organic matter loading on sediment nutrient cycling, excess nitrogen filtering, and greenhouse gas emissions in Long Island Sound, a heavily nutrient polluted estuary. To provide a comprehensive analysis of these benthic fluxes and their environmental drivers, I incubated sediment cores from five stations along a west to east transect representing a gradient of high to low nutrient inputs and organic matter deposition. I found sediments across the estuary removed only 9% of land-based nitrogen entering the system and had a nitrogen removal efficiency of 30%. Additionally, sediments were often a source of inorganic nitrogen and phosphorus as well as nitrous oxide and methane. This study provides the first directly measured rates of sediment nitrogen removal and production in Long Island Sound. In Chapters 2 and 3, I investigate the effect of coastal acidification on benthic fluxes of greenhouse gases and nutrients across the sediment-water interface in Waquoit Bay. I collected sediment cores from two sites experiencing different rates of nutrient loading and experimentally altered the overlying water pH through a series of incubations representing moderate (pH 7.3) and extreme (pH 6.3) pH conditions. My results show low pH conditions have a strong effect on greenhouse gas and nutrient fluxes and responses vary by site. Specifically, in the high nutrient impacted site, nitrous oxide flux increased and methane flux decreased under acidification. In the low nutrient impacted site acidification drove reduced nitrous oxide flux, while methane flux decreased in the moderate treatment and increased in the extreme treatment. Acidification also affected benthic nutrient fluxes and drove the high nutrient impacted site to become phosphorus limited. Furthermore, the relationships and drivers between nutrient availability and nutrient fluxes shifted under acidification. This dissertation provides additional insight into how coastal ecosystems respond to human impacts. In Chapter 1, I present a critical missing piece of the nitrogen budget of a heavily impacted estuary. In Chapters 2 and 3, I begin to elucidate how low pH conditions can impact sediment biogeochemistry in estuarine ecosystems. Efforts to improve our understanding of human impacts on sediment biogeochemical fluxes will create better informed coastal management practices for these dynamic systems under a changing climate. / 2025-10-23T00:00:00Z

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