Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第15315号 / 工博第3194号 / 新制||工||1481(附属図書館) / 27793 / 京都大学大学院工学研究科都市環境工学専攻 / (主査)教授 角 哲也, 准教授 竹門 康弘, 准教授 武藤 裕則 / 学位規則第4条第1項該当

Les diatomées sont des micro-algues unicellulaires, qui jouent un rôle primordial dans l’eco-système marin. En effet, elles sont responsables de 20% de l’activité photosynthétique sur Terre, et sont à la base de la chaîne alimentaire marine, toujours plus menacée par le changement climatique. Les diatomées établissent diverses interactions microbiennes avec des organismes issus de l’ensemble de l’arbre du vivant, à travers des méchanismes complexes tels que la symbiose, le parasitisme ou la compétition. L’objectif de ma thèse a été de comprendre comment ces interactions structurent la communauté du plancton, à grande échelle spatiale. Pour ce faire, j’ai développé de nouvelles approches basées sur le jeu de données inédit de Tara Océans, une expédition mondiale qui a exploré la diversité et les fonctions des microbes marins, en récoltant plus de 40.000 échantillons à travers 210 sites autour du monde. Grâce à l’analyse de réseaux de co-occurrence microbiens, je montre d’une part que les diatomées agissent comme des « ségrégateurs répulsifs » à l’échelle globale, en particulier envers les organismes potentiellement dangeureux tels que les prédateurs et les parasites, et d’autre part que la co-occurrence des espèces ne s’explique qu’en minorité par les facteurs environnementaux. Grâce à la richesse des données Tara Océans, j’ai par ailleurs permis la charactérisation d’une interaction biotique impliquant une diatomée et un cilié hétérotrophe à l’échelle de l’eco-système, illustrant de surcroît le succès des approches dirigées par les données. Dans l’ensemble, ma thèse contribue à notre compréhension des interactions biotiques impliquant les diatomées, de l’échelle globale à la cellule unique. / Diatoms are unicellular photosynthetic microeukaryotes that play a critical role in the functioning of marine ecosystems. They are responsible for 20% of global photosynthesis on Earth and lie at the base of marine food webs, ever more threatened by climate change.Diatoms establish microbial interactions with numerous organisms across the whole tree of life, through complex mechanisms including symbiosis, parasitism and competition. The goal of my thesis was to understand how those biotic interactions structure the planktonic community at large spatial scales, by using new approaches based on the unprecedented Tara Oceans dataset, a unique and worldwide circumnavigation that collected over 40.000 samples across 210 sites to explore the diversity and functions of marine microbes. Through the analysis of microbial association networks, I show that diatoms act as repulsive segregators in the ocean, in particular towards potentially harmful organisms such as predators as well as parasites, and that species co-occurrence is driven by environmental factors in a minority of cases. By leveraging the singularity of the Tara Oceans data, I provide a comprehensive characterization of a prevalent biotic interaction between a diatom and heterotrophic ciliates at large spatial scale, illustrating the success of data-driven research. Overall, my thesis contributes to our understanding of diatom biotic interactions, from the global patterns to the single cell.

Simultaneous size fractionation of plankton populations associated with NaH^14CO_3 and ^3H-glucose uptake was employed in eutrophic Lake Texoma (Texas and Oklahoma) and oligotrophic Flathead Lake (Montana). Autoradiography was utilized to determine the role of specific microorganisms in community metabolism. Ultraplankton (0.45-10 μm) dominated plankton numbers and metabolic activity in both aquatic systems. Many of the most abundant species were not the most productive, in terms of inorganic C fixation. Rates of heterotrophic uptake of ^3H-glucose were small in comparison to photolithotrophic uptake in both lakes, Photoheterotrophy was more extensive in Flathead Lake, Autoradiographs indicated that bacteria were responsible for observed photoheterotrophy. Oscillatoria sp. exhibited. mixotrophy in Lake Texoma,

Wetland wastewater treatment offers low-cost, energy efficient alternatives to conventional wastewater technologies. In this study, an artificial wetland was constructed at the City of Denton, Texas Pecan Creek Water Reclamation Plant to facilitate diazinon removal from treated effluent.

In light of increasing harmful algal blooms and the need to protect human health and aquatic resources, proactive management approaches merit further study. For this purpose I conducted field samplings to characterize plankton community composition and laboratory experiments to test some approaches to new management schemes in the lower Rincon Delta. On site measurements and microscopic analysis showed that environmental parameters and plankton community composition varied considerably among sampling stations and sampling dates. A recent modeling study suggested that manipulation of freshwater inflow to estuaries might prevent phytoplankton blooms and enhance secondary productivity. To test this theory I conducted three semi-continuous design and flow-through incubation design experiments using natural plankton assemblages. I investigated the effect of two different pulsing regimes of inflow and nutrient loading on zooplankton densities, and phytoplankton biomass and diversity. Despite differences in zooplankton structure and phytoplankton community composition between the two experiment designs, the results confirmed that pulsed inflows might alter plankton dynamics. My findings showed that 3-day pulse treatments consistently supported greater zooplankton densities and higher phytoplankton species diversity when compared to 1-day pulse treatments. In addition, accumulation of phytoplankton biovolume remained low during 3-day pulse treatments. Differences in zooplankton performance between 3-day pulse and 1-day pulse inflow treatments were likely due to the ability of phytoplankton to uptake and store greater amounts of nutrients under conditions of 3-day pulse inflow. This resulted in food of higher quality for zooplankton, and might have supported greater zooplankton population growth rates. Additionally, in an attempt to understand the mechanisms leading to high biodiversity in aquatic ecosystems, I built a resource-storage model and studied the effects of resource-storage on competition of multiple phytoplankton species on multiple abiotic resources. I compared this model with a well-established multi-species competition model. My results showed that for certain species combinations a resource-storage-based model can generate dissimilar outcomes when compared to a model without resource-storage.

In light of increasing harmful algal blooms and the need to protect human health and aquatic resources, proactive management approaches merit further study. For this purpose I conducted field samplings to characterize plankton community composition and laboratory experiments to test some approaches to new management schemes in the lower Rincon Delta. On site measurements and microscopic analysis showed that environmental parameters and plankton community composition varied considerably among sampling stations and sampling dates. A recent modeling study suggested that manipulation of freshwater inflow to estuaries might prevent phytoplankton blooms and enhance secondary productivity. To test this theory I conducted three semi-continuous design and flow-through incubation design experiments using natural plankton assemblages. I investigated the effect of two different pulsing regimes of inflow and nutrient loading on zooplankton densities, and phytoplankton biomass and diversity. Despite differences in zooplankton structure and phytoplankton community composition between the two experiment designs, the results confirmed that pulsed inflows might alter plankton dynamics. My findings showed that 3-day pulse treatments consistently supported greater zooplankton densities and higher phytoplankton species diversity when compared to 1-day pulse treatments. In addition, accumulation of phytoplankton biovolume remained low during 3-day pulse treatments. Differences in zooplankton performance between 3-day pulse and 1-day pulse inflow treatments were likely due to the ability of phytoplankton to uptake and store greater amounts of nutrients under conditions of 3-day pulse inflow. This resulted in food of higher quality for zooplankton, and might have supported greater zooplankton population growth rates. Additionally, in an attempt to understand the mechanisms leading to high biodiversity in aquatic ecosystems, I built a resource-storage model and studied the effects of resource-storage on competition of multiple phytoplankton species on multiple abiotic resources. I compared this model with a well-established multi-species competition model. My results showed that for certain species combinations a resource-storage-based model can generate dissimilar outcomes when compared to a model without resource-storage.

<p align="justify">The Southern Ocean (ca. 20% of the world ocean surface) is a key place for the regulation of Earth climate thanks to its capacity to absorb atmospheric carbon dioxide (CO2) by physico-chemical and biological mechanisms. The biological carbon pump is a major pathway of absorption of CO2 through which the CO2 incorporated into autotrophic microorganisms in surface waters is transferred to deep waters. This process is influenced by the extent of the primary production and by the intensity of the remineralization of organic matter along the water column. So, the annual cycle of sea ice, through its in situ production and remineralization processes but also, through the release of microorganisms, organic and inorganic nutrients (in particular iron)into the ocean has an impact on the carbon cycle of the Southern Ocean, notably by promoting the initiation of phytoplanktonic blooms at time of ice melting.</p><p><p align="justify">The present work focussed on the distribution of organic matter (OM) and its interactions with the microbial network (algae, bacteria and protozoa) in sea ice and ocean, with a special attention to the factors which regulate the biological carbon pump of the Southern Ocean. This thesis gathers data collected from a) late winter to summer in the Western Pacific sector, Western Weddell Sea and Bellingshausen Sea during three sea ice cruises ARISE, ISPOL-drifting station and SIMBA-drifting station and b) summer in the Sub-Antarctic and Polar Front Zone during the oceanographic cruise SAZ-Sense.</p><p><p align="justify">The sea ice covers were typical of first-year pack ice with thickness ranging between 0.3 and 1.2 m, and composed of granular and columnar ice. Sea ice temperature ranging between -8.9°C and -0.4°C, brines volume ranging between 2.9 to 28.2% and brines salinity from 10 to >100 were observed. These extreme physicochemical factors experienced by the microorganisms trapped into the semi-solid sea ice matrix therefore constitute an extreme change as compared to the open ocean. Sea ice algae were mainly composed of diatoms but autotrophic flagellates (such as dinoflagellates or Phaeocystis sp.) were also typically found in surface ice layers. Maximal algal biomass was usually observed in the bottom ice layers except during SIMBA where the maxima was localised in the top ice layers likely because of the snow and ice thickness which limit the light available in the ice cover. During early spring, the algal growth was controlled by the space availability (i.e. brine volume) while in spring/summer (ISPOL, SIMBA) the major nutrients availability inside sea ice may have controlled algal growth. At all seasons, high concentrations of dissolved and particulate organic matter were measured in sea ice as compared to the water column. Dissolved monomers (saccharides and amino acids) were accumulated in sea ice, in particular in winter. During spring and summer, polysaccharides constitute the main fraction of the dissolved saccharides pool. High concentrations of transparent exopolymeric particles (TEP), mainly constituted with saccharides, were present and their gel properties greatly influence the internal habitat of sea ice, by retaining the nutrients and by preventing the protozoa grazing pressure, inducing therefore an algal accumulation. The composition as well as the vertical distribution of OM in sea ice was linked to sea ice algae.</p><p><p align="justify">Besides, the distribution of microorganisms and organic compounds in the sea ice was also greatly influenced by the thermodynamics of the sea ice cover, as evidenced during a melting period for ISPOL and during a floodfreeze cycle for SIMBA. The bacteria distribution in the sea ice was not correlated with those of algae and organic matter. Indeed, the utilization of the accumulated organic matter by bacteria seemed to be limited by an external factor such as temperature, salinity or toxins rather than by the nature of the organic substrates, which are partly composed of labile monomeric saccharides. Thus the disconnection of the microbial loop leading to the OM accumulation was highlighted in sea ice.</p><p><p align="justify">In addition the biofilm formed by TEP was also involved in the retention of cells and other compounds(DOM, POM, and inorganic nutrients such as phosphate and iron) to the brine channels walls and thus in the timing of release of ice constituents when ice melts. The sequence of release in marginal ice zone, as studied in a microcosm experiments realized in controlled and trace-metal clean conditions, was likely favourable to the development of blooms in the marginal ice zone. Moreover microorganisms derived from sea ice (mainly <10 µm) seems able to thrive and grow in the water column as also the supply of organic nutrients and Fe seems to benefit to the pelagic microbial community.</p><p><p align="justify">Finally, the influence of the remineralization of organic matter by heterotrophic bacterioplankton on carbon export and biological carbon pump efficiency was investigated in the epipelagic (0-100 m) and mesopelagic(100-700 m) zones during the summer in the sub-Antarctic and Polar Front zones (SAZ and PFZ) of the Australian sector (Southern Ocean). Opposite to sea ice, bacterial biomass and activities followed Chl a and organic matter distributions. Bacterial abundance, biomass and activities drastically decreased below depths of 100-200 m. Nevertheless, depth-integrated rates through the thickness of the different water masses showed that the mesopelagic contribution of bacteria represents a non-negligible fraction, in particular in a diatom-dominated system./</p><p><br><p><p align="justify">L’océan Antarctique (± 20% de la surface totale des océans) est un endroit essentiel pour la régulation du climat de notre planète grâce à sa capacité d’absorber le dioxyde de carbone (CO2) atmosphérique par des mécanismes physico-chimique et biologique. La pompe biologique à carbone est un processus majeur de fixation de CO2 par les organismes autotrophes à la surface de l’océan et de transfert de carbone organique vers le fond de l’océan. Ce processus est influencé par l’importance de la production primaire ainsi que par l’intensité de la reminéralisation de la matière organique dans la colonne d’eau. Ainsi, le cycle annuel de la glace via sa production/reminéralisation in situ mais aussi via l’ensemencement de l’océan avec des microorganismes et des nutriments organiques et inorganiques (en particulier le fer) a un impact sur le cycle du carbone dans l’Océan Antarctique, notamment en favorisant l’initiation d’efflorescences phytoplanctoniques dans la zone marginale de glace.</p><p><p align="justify">Plus précisément, nous avons étudié les interactions entre le réseau microbien (algues, bactéries et protozoaires) et la matière organique dans le but d’évaluer leurs impacts potentiels sur la pompe biologique de carbone dans l’Océan Austral. Deux écosystèmes différents ont été étudiés :la glace de mer et le milieu océanique grâce à des échantillons prélevés lors des campagnes de glace ARISE, ISPOL et SIMBA et lors de la campagne océanographique SAZ-Sense, couvrant une période allant de la fin de l’hiver à l’été.</p><p><p align="justify">La glace de mer est un environnement très particulier dans lequel les microorganismes planctoniques se trouvent piégés lors de la formation de la banquise et dans lesquels ils subissent des conditions extrêmes de température et de salinité, notamment. Les banquises en océan ouvert étudiées (0,3 à 1,2 m d’épaisseur, températures de -8.9°C à -0.4°C, volumes relatifs de saumure de 2.9 à 28.2% et salinités de saumures entre 10 et jusque >100) étaient composées de glace columnaire et granulaire. Les algues de glace étaient principalement des diatomées mais des flagellés autotrophes (tels que des dinoflagellés ou Phaeocystis sp.) ont été typiquement observés dans les couches de glace de surface. Les biomasses algales maximales se trouvaient généralement dans la couche de glace de fond sauf à SIMBA où les maxima se trouvaient en surface, probablement en raison de l’épaisseur des couches de neige et de glace, limitant la lumière disponible dans la colonne de glace. Au début du printemps, la croissance algale était contrôlée par l’espace disponible (càd le volume des saumures) tandis qu’au printemps/été, la disponibilité en nutriments majeurs a pu la contrôler. A toutes les saisons, des concentrations élevées en matière organique (MO) dissoute et particulaire on été mesurées dans la glace de mer par rapport à l’océan. Des monomères dissous (sucres et acides aminés) étaient accumulés dans la glace, surtout en hiver. Au printemps et été, les polysaccharides dissous dominaient le réservoir de sucres. La MO était présente sous forme de TEP qui par leurs propriétés de gel modifie l’habitat interne de la glace. Ce biofilm retient les nutriments et gêne le mouvement des microorganismes. La composition et la distribution de la MO dans la glace étaient en partie reliées aux algues de glace. De plus, la thermodynamique de la couverture de glace peut contrôler la distribution des microorganismes et de la MO, comme observé lors de la fonte de la glace à ISPOL et lors du refroidissement de la banquise à SIMBA. La distribution des bactéries n’est pas corrélée avec celle des algues et de la MO dans la glace. En effet, la consommation de la MO par les bactéries semble être limitée non pas par la nature chimique des substrats mais par un facteur extérieur affectant le métabolisme bactérien tel que la température, la salinité ou une toxine. Le dysfonctionnement de la boucle microbienne menant à l’accumulation de la MO dans la glace a donc été mis en évidence dans nos échantillons.</p><p><p align="justify">De plus, le biofilm formé par les TEP est aussi impliquée dans l’attachement des cellules et autres composés aux parois des canaux de saumure et donc dans la séquence de largage lors de la fonte. Cette séquence semble propice au développement d’efflorescences phytoplanctoniques dans la zone marginale de glace. Les microorganismes originaires de la glace (surtout ceux de taille < 10 μm) semblent capables de croître dans la colonne d’eau et l’apport en nutriments organiques et inorganiques apparaît favorable à la croissance des microorganismes pélagiques.</p><p><p align="justify">Enfin, l’influence des activités hétérotrophes sur l’export de carbone et l’efficacité de la pompe biologique à carbone a été évaluée dans la couche de surface (0-100 m) et mésopélagique (100-700 m) de l’océan. Au contraire de la glace, les biomasses et activités bactériennes suivaient les distributions de la chlorophyll a et de la MO. Elles diminuent fortement en dessous de 100-200 m, néanmoins les valeurs intégrées sur la hauteur de la colonne d’eau indiquent que la reminéralisation de la MO par les bactéries dans la zone mésopélagique est loin d’être négligeable, spécialement dans une région dominée par les diatomées.</p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution.