Bacterioplankton are keystone organisms in marine ecosystems. They are important for element cycles, by transforming dissolved organic carbon and other nutrients. Bacterioplankton community composition and productivity rates change in surface waters over spatial and temporal scales. Yet, many underlying biological processes determining when, why and how bacterioplankton react to changes in environmental conditions are poorly understood. Here, I used experiments with model bacteria and natural assemblages as well as field studies to determine molecular, physiological and ecological responses allowing marine bacteria to adapt to their environment. Experiments with the flavobacterium Dokdonia sp. MED134 aimed to determine how the metabolism of bacteria is influenced by light and different organic matter. Under light exposure, Dokdonia sp. MED134 expressed proteorhodopsin and adjusted its metabolism to use resources more efficiently when growing with lower-quality organic matter. Similar expression patterns were found in oceanic datasets, implying a global importance of photoheterotrophic metabolisms for the ecology of bacterioplankton. Further, I investigated how the composition and physiology of bacterial assemblages are affected by elevated CO2 concentrations and inorganic nutrients. In a large-scale experiment, bacterioplankton could keep productivity and community structure unaltered by adapting the gene expression under CO2 stress. To maintain pH homeostasis, bacteria induced higher expression of genes related to respiration, membrane transport and light acquisition under low-nutrient conditions. Under high-nutrient conditions with phytoplankton blooms, such regulatory mechanisms were not necessary. These findings indicate that open ocean systems are more vulnerable to ocean acidification than coastal waters. Lastly, I used field studies to resolve how bacterioplankton is influenced by environmental changes, and how this leads to seasonal succession of marine bacteria. Using high frequency sampling over three years, we uncovered notable variability both between and within years in several biological features that rapidly changed over short time scales. These included potential phytoplankton-bacteria linkages, substrate uptake rates, and shifts in bacterial community structure. Thus, high resolution time series can provide important insights into the mechanisms controlling microbial communities. Overall, this thesis highlights the advantages of combining molecular and traditional oceanographic methodological approaches to study ecosystems at high resolution for improving our understanding of the physiology and ecology of microbial communities and, ultimately, how they influence biogeochemical processes.

A acidificação oceânica, resultante do aumento da concentração de CO2 atmosférico, vem alterando a química dos oceanos resultando na diminuição de seu pH. Diversos estudos avaliaram as consequências dessa diminuição no pH oceânico nas taxas de calcificação, reprodução e desenvolvimento em diversos modelos marinhos, entretanto estudos relacionados a outros processos fisiológicos, como a imunidade, e estudos com indivíduos adultos são escassos. Ouriços-do-mar são espécies aderidas ao substrato, importantes para a ciclagem de nutrientes no ambiente marinho, sendo também animais utilizados como bioindicadores para monitoramento ambiental; assim o estudo da resposta imune inata desses animais frente à acidificação dos oceanos é de extrema importância para prever possíveis alterações fisiológicas desses animais e sua capacidade de adaptação. O presente trabalho teve como objetivo avaliar as alterações provocadas pela acidificação oceânica na resposta imune e no balanço ácido base de duas espécies de ouriço-do-mar tropicais: Lytechinus variegatus e Echinometra lucunter durante as estações de verão e inverno; para isso foram analisados os índices fagocíticos, a capacidade de adesão e espraiamento celular dos amebócitos fagociticos além do balanço acido base do liquido celomático após o período de 24 horas e cinco dias de exposição aos pHs 7,6 e 7,3. Foi também avaliada a capacidade de recuperação dessas espécies com o objetivo de verificar se os parâmetros alterados pela exposição conseguiam ser reestabelecidos. Os resultados mostraram que a redução no pH da água do mar alterou a proporção celular, reduziu a capacidade de fagocitose e espraiamento dos amebócitos fagocíticos assim como também afetou o balanço ácido-base do líquido celomático. Foram encontradas diferenças também entre as estações do ano sendo estas encontradas apenas na espécie Lytechinus variegatus. O teste de recuperação mostrou que os parâmetros alterados pela exposição tendem a retornar aos valores controles, mostrando que em curto prazo essas alterações podem não ser irreversíveis, entretanto, mais estudos são necessários principalmente avaliando períodos de exposição prolongados. Juntos nossos resultados mostram que a acidificação oceânica prejudica parâmetros imunes extremamente importantes para a eliminação de patógenos e consequentemente a sobrevivência desses animais em um futuro oceano acidificado. / Ocean acidification due to increased atmospheric CO2 concentration is altering ocean chemistry resulting in the decrease of its pH. Several studies evaluated the effects of this decrease in ocean pH on calcification rates, reproduction and development in different marine models, however studies related to other physiological processes such as immunity and studies with adult animals are scarce. Sea urchins are species adhered to the substrate, important for nutrient cycling in the marine environment, also being used as bioindicators for environmental monitoring. Thus the study of the innate immune response of these animals due to the acidification of the oceans is extremely important to predict possible physiological changes of these animals and their ability to adapt to this condition. This study aimed to evaluate the changes caused by ocean acidification in the immune response and in the acid-base balance of two sea urchin tropical species: Lytechinus variegatus and Echinometra lucunter during seasons of summer and winter; for this, indexes of phagocytosis, cell adhesion and spreading ability were analyzed in addition to the acid-base balance of the coelomic fluid after 24 hours and five days of exposure to pH 7.6 and 7.3The recover ability of these species were also evaluated in order to verify if the parameters altered by exposition could be reestablished. The results shows that a reduction in the seawater pH changed the cell proportion, reduced the ability of phagocytosis and phagocytic amoebocyte spreading as well as affected the acid-base balance of the coelomic fluid. Differences were also found between seasons, but only in the specie Lytechinus variegatus. The recovery test showed that the parameters altered by exposure tend to return to control values, showing that in the short term these changes may not be irreversible, however, further studies are necessary mainly those related to prolonged periods of exposure. Together our results show that ocean acidification impairs immune parameters extremely important for the elimination of pathogens and consequently the survival of these animals in a future acidified ocean.

The aims of the thesis were to document the history of the Cladocera (Crustacea) community structure in the Starolesnianske Lake (the High Tatra Mountains, Slovakia) with regards to environmental changes (e. g., Medieval Warm Period, Little Ice Age, anthropogenic acidification, recovery from acidification), and to analyze in detail the development of zooplankton (Cladocera, Copepoda, Rotifera) during the peaking acidification and recovery from acidification (1978 - 2015). Based on results of both the approaches, the appropriateness of using historical data on zooplankton in Tatra lakes between 1909 - 1913 (Minkiewicz, 1914) as a reference condition for the evaluating biological recovery from acidification should have been assessed. The methods used were paleolimnological analyses of lake sediment (namely subfossil Cladocera), analysis of recent zooplankton, and analyses of lake water chemistry. It was found that in the historical record, relative abundances of Cladocera species significantly changed cca 150 years ago (at the end of the Little Ice Age and, in the main, in the period of anthropogenic acidification). The lake, though, has had a very stable species composition of Cladocera during the last cca 2,000 years, represented by four species: Alona quadrangularis, Alonella excisa, Ceriodaphnia...

Summary: This thesis is focused on collecting information on the importance of dead wood on biogeochemical cycles of chemical elements in the mountain forest ecosystems of central Europe. The goal of this thesis was to determine the concentration of various elements(C, N, P, Ca, Mg, K, Na, Mn, Al, Fe) in the coarse woody debris of spruce samples of different age, stage of decomposition which were collected in different localities in the national park Šumava. Another goal was to determine the speed of which these elements are released from the dead wood. The information on the quantity of different elements and the speed of their release is currently lacking and could lead to better understanding of various biogeochemical cycles of elements in the mountain forest. During the decomposition the concentration of the elements N, P, Al and Fe increased whereas the Kalium concentration decreased. The other elements' (C, N, Ca, Mg, Mn) concentrations varied. Carbon constituted approximately 50% of weight in all of the samples analyzed. We carried out a laboratory experiment based on decomposition of dead wood samples in various stage of decay during a period of six months. The released concentration of CO2 was measured at two to four weeks intervals. The release of CO2 continually decreased during the experiment.....

Sediments of Bohemian Forest lakes are important natural archives. Their sedimentary record covers postglacial history of the lakes as well as history of natural processes in a wider region. It also documents local settlements and changes in landscape management. The lake sediments have attracted the interest of the scientific community since the end of the 19th century. Despite of the fact that modern paleolimnological and paleoecological investigations were already performed in the second half of the 20th century in the Bohemian Forest Mts., the great potential of the lake sediments was not fully utilized in scientific research so far. The ultimate objective of this thesis is to deepen knowledge of these natural archives and support their utilization in future studies. Several specific objectives have been set to achieve the ultimate objective: i) to compare age of the Bohemian Forest lake sediments with the recent knowledge of local deglaciation at the end of the last ice age, ii) to integrate chronostratigraphic marker horizons as one of the tools of Late Glacial sediment dating, iii) to assess the role of bioerosion in chitinous subfossil freshwater invertebrate remains on the record representativeness, and iv) to prove the presumed dystrophic nature of the lakes during the Holocene using...

The aim of this diploma thesis was to describe species composition and biomass of phytoplankton in the Tatra Mountains lakes (Slovakia, Poland) and environmental factors influencing them. The surface layer of 89 lakes was sampled in September 2004. Flagellates from Chrysophyta, Dinophyta and Cryptophyta most frequently dominated the phytoplankton biomass. Lake in the same valley usually differed in their dominant taxonomic group as a result of different lake morphometry, catchment type and detailed geological structure. Based on the level of phytoplankton biovolume, the majority of lakes were ultraoligotrophic and oligotrophic, however, mesotrophic and even eutrophic conditions were recorded in some forest and meadow lakes. An allometric relationship between phytoplankton biomass and chlorophyll a was revealed. Specific chlorophyll content did not differ among taxonomic groups. Altogether 233 species were determined, the most diverse group were Chlorophyta. Species richness of lake was 3-46 and it was negatively correlated with altitude and positively correlated with lake area. The majority of species were rare both in term of biomass and number of lakes occupied by a particular species. Average local species biomass was positively correlated with regional distribution. The similarity of species...

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Interferons (IFNs) are an essential part of innate immunity and contribute to adaptive immune responses. Here, we employed a loss-of-function analysis with human A549 respiratory epithelial cells with a knockout (KO) of the type I IFN receptor (IFNAR KO), either solely or together with the receptor of type III IFN (IFNAR/IFNLR1 KO). The course of rubella virus (RuV) infection on the IFNAR KO A549 cells was comparable to the control A549. However, on the IFNAR/IFNLR1 KO A549 cells, both genome replication and the synthesis of viral proteins were significantly enhanced. The generation of IFN β during RuV infection was influenced by type III IFN signaling. In contrast to IFNAR KO A549, extracellular IFN β was not detected on IFNAR/IFNLR1 KO A549. The bioenergetic profile of RuV-infected IFNAR/IFNLR1 KO A549 cells generated by extracellular flux analysis revealed a significant increase in glycolysis, whereas mitochondrial respiration was comparable between all three cell types. Moreover, the application of the glucose analogue 2-deoxy-D-glucose (2-DG) significantly increased viral protein synthesis in control A549 cells, while no effect was noted on IFNAR/IFNLR KO A549. In conclusion, we identified a positive signaling circuit of type III IFN signaling on the generation of IFN β during RuV infection and an IFN signaling-dependent contribution of glycolysis to RuV infection. This study on epithelial A549 cells emphasizes the interaction between glycolysis and antiviral IFN signaling and notably, the antiviral activity of type III IFNs against RuV infection, especially in the absence of both type I and III IFN signaling, the RuV replication cycle was enhanced.

La croissance du phytoplancton est limitée par les faibles concentrations de fer (Fe) dans près de 40% de l’océan mondial. Le Pacifique subarctique Nord-Est représente une de ces zones limitées en fer et désignées High Nutrient - Low Chlorophyll (HNLC). Cet écosystème, dominé par des cellules de petite taille telles les prymnésiophytes, est caractérisé par de très faibles concentrations estivales de chlorophylle a et de fortes concentrations de macronutriments. Il a été maintes fois démontré que les ajouts de fer, sous différentes formes chimiques (habituellement FeSO4), dans les zones HNLC, stimulent la croissance et modifient la structure des communautés planctoniques en favorisant la croissance des cellules de grande taille, notamment les diatomées. Ces effets sur la communauté planctonique ont le potentiel d’influencer les grands mécanismes régulateurs du climat, tels la pompe biologique de carbone et la production de diméthylsulfure (DMS). Les poussières provenant des déserts du nord de la Chine sont reconnues depuis longtemps comme une source sporadique importante de fer pour le Pacifique Nord-Est. Malgré leur importance potentielle, l’influence directe exercée par ces poussières sur l’écosystème planctonique de cette zone HNLC n’a jamais été étudiée. Il s’agit d’une lacune importante puisque le fer associé aux poussières est peu soluble dans l’eau de mer, que la proportion biodisponible n’est pas connue et que les poussières peuvent avoir un effet inhibiteur chez le phytoplancton. Cette thèse propose donc, dans un premier temps, de mesurer pour la première fois l’effet de la fertilisation de la communauté planctonique du Pacifique Nord-Est par un gradient de concentrations de poussières désertiques naturelles. Cette première expérimentation a démontré que le fer contenu dans les poussières asiatiques est biodisponible et qu’une déposition équivalente à celles prenant place au printemps dans le Pacifique Nord-Est peut résulter en une stimulation significative de la prise de nutriments et de la croissance du phytoplancton. Mes travaux ont également montré que l’ajout de 0,5 mg L-1 de poussières peut résulter en la production d’autant de biomasse algale que l’ajout de FeSO4, l’espèce chimique utilisée lors des expériences d’enrichissement en fer à grande échelle. Cependant, les ajouts de FeSO4 favorisent davantage les cellules de petite taille que les ajouts de poussières, observation démontrant que le FeSO4 n’est pas un proxy parfait des poussières asiatiques. Dans un deuxième temps, je me suis intéressée à une source alternative de fer atmosphérique, les cendres volcaniques. Mon intérêt pour cette source de fer a été attisé par les observations d’une floraison spectaculaire dans le Pacifique Nord-Est, ma région d’étude, associée à l’éruption de 2008 du volcan Kasatochi dans les îles Aléoutiennes. Forte de mon expérience sur les poussières, j’ai quantifié l’effet direct de ces cendres volcaniques sur la communauté planctonique du Pacifique Nord-Est. Mes résultats ont montré que le fer contenu dans les cendres volcaniques est également biodisponible pour le phytoplancton. Ils ont également montré que cette source de fer peut être aussi importante que les poussières désertiques dans la régulation de la croissance du phytoplancton dans cette partie de l’océan global à l’échelle millénaire. Dans un troisième temps, j’ai estimé comment l’acidification des océans modulera les réponses des communautés planctoniques aux dépositions naturelles de fer mises en évidence lors de mes expériences précédentes. Pour ce faire, j’ai effectué des enrichissements de poussière dans de l’eau de mer au pH actuel de 8.0 et dans l’eau de mer acidifiée à un pH de 7.8. Mes résultats ont montré une diminution du taux de croissance du phytoplancton dans le milieu acidifié mais pas de changement notable dans la structure de la communauté. Les ajouts de poussières et de cendres, de même que les variations de pH, n’ont pas eu d’effet significatif sur la production de DMS et de son précurseur le diméthylsulfoniopropionate (DMSP), probablement en raison de la courte durée (4 jours) des expériences. L’ensemble des résultats de cette thèse montre que le fer contenu dans diverses sources atmosphériques naturelles est biodisponible pour le phytoplancton du Pacifique Nord-Est et que des taux de déposition réalistes peuvent stimuler la croissance de manière notable dans les premiers jours suivant une tempête désertique ou une éruption volcanique. Finalement, les résultats de mes expériences à stresseurs multiples Fer/acidification suggèrent une certaine résistance des communautés phytoplanctoniques à la diminution du pH prédite d’ici la fin du siècle pour les eaux de surface des océans. / Phytoplankton growth is limited by low concentrations of iron (Fe) in about 40% of the world’s oceans. The northeast subarctic Pacific Ocean embodies one of these Fe-limited regions that are termed High Nutrient - Low Chlorophyll (HNLC). Its ecosystem is dominated by small phytoplankton cells, such as Prymnesiophyceae, and is characterized by weak summer concentrations of chlorophyll a and high concentrations of macronutrients. It has repeatedly been shown that Fe additions in HNLC zones, using various artificial forms of Fe (commonly FeSO4), stimulate the growth and modify the structure of planktonic communities by favoring the blooming of large phytoplankton cells such as diatoms. The impacts brought about on the planktonic communities by these Fe additions have the potential of influencing large-scale climate regulating mechanisms, namely the biological carbon pump and the oceanic production of dimethylsulfide (DMS). Dust arising from northern Chinese deserts is well recognized as an important albeit sporadic source of Fe for the northeast Pacific Ocean. Despite their potential importance, the direct influence of these dust deposition events on the planktonic ecosystem of the northeast Pacific has never been studied before. This represents a serious shortcoming considering that, Fe associated with dust is scantily soluble in seawater, the bioavailable proportion of Fe in dust remains unknown, and dust may exert an inhibiting effect on phytoplankton. My thesis thus proposes, firstly, to conduct avant-garde measurements of the fertilization effects of a natural Asian dust gradient on plankton communities of the northeast Pacific. My first experiment shows that the Fe contained in Asian dust is bioavailable and that a deposition event, equivalent to naturally occurring spring depositions in the northeast Pacific, may result in a significant stimulation of nutrient uptake and growth by phytoplankton. My results also demonstrate that the addition of 0,5 mg L-1 of dust may induce as much biomass accumulation as what is observed during large scale fertilizing experiments utilizing FeSO4. However, small-celled phytoplankton assemblages are stimulated by Fe fertilizations, more so through FeSO4 than through dust additions demonstrating the flaws of this proxy in accurately representing Asian dust. In a second step, I focused my attention on an alternative source of atmospheric Fe, specifically volcanic ash. My interest for this subject was instigated by observations of a spectacular bloom occurring in my study region, the northeast Pacific, and associated to the 2008 eruption of the Kasatochi volcano located on one of the Aleutian Islands. I quantified the direct effects of volcanic ash on the plankton community of the northeast Pacific. My results show that the Fe contained in these ashes is also bioavailable for phytoplankton and that this source of Fe may be as important as desert dust in regulating the growth of phytoplankton in this part of the global ocean on a millennial scale. Thirdly, I assessed the manner in which ocean acidification could modulate, on a short timescale, the responses of the plankton communities to natural Fe depositions highlighted in this thesis. In order to do so, I performed dust enrichments in seawater at the contemporary seawater pH of 8.0 and acidified to a pH of 7.8. My results show a reduction in phytoplankton growth rate in the acidified environment with no conspicuous changes to community structure. The additions of dust and ash, as well as the variations in pH, had little significant impacts on the production of DMS or its precursor dimethylsulfoniopropionate (DMSP). This lack of response could likely be attributable to the short timescale (4 days) of investigation carried out. As a whole, the results of this thesis show that Fe contained in various natural atmospheric sources is bioavailable to phytoplankton of the northeast Pacific Ocean. Furthermore, realistic deposition rates may distinctly stimulate phytoplankton growth in the first days following dust storms or volcanic eruptions. Finally, results from the multi-stressor experiments (Fe/acidification) I carried out suggest a demonstrable robustness of surface plankton communities to the pH reduction predicted before the turn of this century.

The mosquito-borne Usutu virus (USUV) is a zoonotic flavivirus and an emerging pathogen. So far therapeutical options or vaccines are not available in human and veterinary medicine. The bioenergetic profile based on extracellular flux analysis revealed an USUV infection-associated significant increase in basal and stressed glycolysis on Vero and with a tendency for basal glycolysis on the avian cell line TME-R derived from Eurasian blackbirds. On both cell lines this was accompanied by a significant drop in the metabolic potential of glycolysis. Moreover, glycolysis contributed to production of virus progeny, as inhibition of glycolysis with 2-deoxy-D-glucose reduced virus yield on Vero by one log10 step. Additionally, the increase in glycolysis observed on Vero cells after USUV infection was lost after the addition of exogenous type I interferon (IFN) b. To further explore the contribution of the IFN response pathway to the impact of USUV on cellular metabolism, USUV infection was characterized on human A549 respiratory cells with a knockout of the type I IFN receptor, either solely or together with the receptor of type III IFN. Notably, only the double knockout of types I and III IFN receptor increased permissiveness to USUV and supported viral replication together with an alteration of the glycolytic activity, namely an increase in basal glycolysis to an extent that a further increase after injection of metabolic stressors during extracellular flux analysis was not noted. This study provides evidence for glycolysis as a possible target for therapeutic intervention of USUV replication. Moreover, presented data highlight type I and type III IFN system as a determinant for human host cell permissiveness and for the infection-associated impact on glycolysis.