Phytoplankton succession and abundance in estuaries is known to be influenced by the relative strengths of various seasonally changing physical and chemical factors. Previous studies of Swan River Estuary phytoplankton biomass and composition have identified salinity, temperature, rainfall and nutrients as the most important controlling factors. These conclusions are generally based on analysis of data from river length transects and depth integrated day-time sampling. They describe influences ,affecting whole system phytoplankton abundance and succession. Many of the typical seasonal bloom that develop are ephemeral and only extend over relatively small areas. The focus of this study is a single site, Ron Courtney Island, considered typical of the upper estuary region. This region of the estuary was chosen as representative of the section of river most influenced by allochthonous nutrient input. It has been the region of most frequent and intense algal blooms over the past decade. The factors, physical, biological or physiological, that have the greatest influence on controlling phytoplankton biomass under various ambient conditions for this system are determined. While previous studies have recognised the importance of nitrogen to phytoplankton growth in the Swan River Estuary, they have focused on NO;, with only anecdotal reference to the importance of the alternative nitrogen source, NH4+. This is the first study to explore the influence of different nitrogen source fluxes on phytoplankton biomass in the upper Swan River Estuary. The roles of physiological adaptation to, and preferences for, 'new' (NO,), recycled (NH4+) and organic (urea) nitrogen sources in relation to ambient nutrient levels are explored. / Specific uptake rates (v), normalised to chlorophyll a, for NO;, NH4+ and urea were 0.2 ± 0.04 - 1831.1 ± 779.19, 0.5 ± 0.26 - 1731.6 ± 346.67 and 3.0 ± 0.60 - 2241.2 ± 252.56 ng N μg Chla-1 respectively. Urea concentration (14.8 - 117.7 μg urea-N 1-1) remained relatively constant over the 12 month study period. Measured ambient specific uptake rates for urea represent between 27.5% and 40.4% of total N uptake over the annual period February 1998 -January 1999. Seasonal nitrate uptake over the same period constituted only 11.3% (±10.77%, n=12) to 24.4% (± 13.02%, n=12) with the highest percentage during winter, when nitrate levels are elevated. It is suggested that urea provides a nutrient intermediary over the spring - summer period during transition from autotrophic to heterotrophic dominated communities. Grazing ,and nitrogen recycling are intricately connected by simultaneously providing top-down biomass control and bottom-up nutrient supply. Zooplankton (> 44 μm) grazing has been shown to reduce up to 40% of phytoplankton standing stock at times. Microheterotrophs (<300 pm) can reduce phytoplankton biomass production by up to 100% (potential production grazed, 11.1% day' - 99.6 % day-1) over an annual cycle. This correlated to mean seasonal day-time grazing loss of 80.47 ± 3.5 ngN μg Chla-1 in surface waters and 20.17 ± 9.7 ngN μg Chla-1 at depth (4.5m). Night time grazing for surface and bottom depths resulted in similar nitrogen loss rates (13.03 ± 4.84 ngN μg Chla-1). / Uptake rates for nitrate (r2 0.501) and urea (r2 0.512), doing with temperature (r2 0.605) were shown to have the greatest influence on phytoplankton distribution over depth and time. This research emphasises the need for more detailed investigations into the physiology of nutrient uptake and the effects of nutrient fluxes on phytoplankton biomass and distribution. Further research into the roles of organic nitrogen and pico and nanoplankton in this system is recommended.

Nahua reservoir is an important water resource for supplying drinking water to the Tainan area and a part of Kaohsiung in Taiwan. In recent years, Nanhua reservoir suffers eutrophication problems as many other reservoirs in Taiwan. In order to study eutrophication problems in reservoirs, a three-dimensional hydrodynamic and water quality model has been constructed using the FVCOM (Finite Volume Coastal Ocean Model) model to simulation the hydrodynamics, the nutrient dynamics and the phytoplankton growth in the Nanhua reservoir. The modeling of 3D hydrodynamics is the basic module dominating the circulation in the reservoir. The 3D eutro-dynamics are also calculated by the water quality module, which includes the dynamic variations of chlorophyll-a (Chl-a), dissolve oxygen (DO), carbon biological oxygen demand (CBOD), ammonia nitrogen (NH3-N), nitrate nitrogen (NO3-N), organic nitrogen (ON), phosphate (PO4) and organic phosphorus (OP). The model was first calibrated with the data measured in 2007 and, then, verified with the 2008 data. The model results are in reasonable agreement with the field measurements, both in the calibration and the verification phases. The water level variations are influenced by daily supply for the drinking water treatment and the inflows from the catchment and from Chiashian aqueduct during the dry season in spring. Nutrients are mainly carried into the reservoir through these routes. The residence time in the reservoir and the phytoplankton response with the nutrient loads are calculated. The model results indicated that phytoplankton growth is limited by low temperature and long residence time during the winter. The chlorophyll levels are getting higher from spring through out summer, which is due to enough sun lights and high nutrient loads carried by the catchment runoff. Surface temperatures are higher then the bottom layers causing stratification that worsen the eutrophication problems. Besides the comparisons by hydrodynamic and water quality parameters, the Carlson Trophic State Index (CTSI) has been calculated to categorize the eutrophication levels in the reservoir, which have shown good agreement with the CTSI calculated from EPA sampling data. Therefore, the model can be used as a tool for water quality management in the Nanhua reservoir.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24454号 / 理博第4953号 / 新制||理||1707(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 中野 伸一, 教授 木庭 啓介, 教授 中務 真人 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

In this thesis I explore the effect of parameter uncertainty in ocean biogeochemical models on the calculation of carbon uptake by the ocean. The ocean currently absorbs around a quarter of the annual anthropogenic CO2 emissions to the atmosphere [Scholes et al., 2009], slowing the increase in radiative forcing associated with the increasing atmospheric CO2 concentration. Ocean biogeochemical models have been developed to study the role of the ocean ecosystem in this process. Such models consist of a greatly simplified representation of the hugely complex ocean ecosystem. This simplification requires extensive parameterisation of the biological processes that convert inorganic carbon to and from organic carbon in the ocean. The HadOCC ocean biogeochemical model is a Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) model that is used to represent the role of the ocean ecosystem in the global carbon cycle in the HadCM3 and FAMOUS GCMs. HadOCC uses twenty parameters to control the processes of biological growth, mortality, grazing and detrital sinking that control the uptake and cycling of carbon in the ocean ecosystem. These parameters represent highly complex and in some cases incompletely understood biological processes, and as a result are uncertain in value. A sensitivity analysis is performed to identify the HadOCC parameters that due to uncertainty in value have the greatest possible effect on the exchange of CO2 between the atmosphere and the ocean—the air-sea CO2 flux. These are found to be the parameters that control phytoplankton growth in the well lit surface ocean, the formation of carbonate by marine organisms and the sinking of biological detritus. The uncertainty in these parameters is found to cause changes to the air-sea CO2 flux calculated by the FAMOUS GCM. The initial effect of these changes is equivalent to the order of the error of current estimates of the net annual carbon uptake by the ocean (2.2 ± 0.3 Pg C y−1 [Gruber et al., 2009], 2.2 ± 0.5 Pg C y−1 [Denman et al., 2007]). This indicates that while the effect of ocean biogeochemical parameter uncertainty is non-negligible, it is within the bounds of the uncertainty of the total (inorganic and organic) ocean carbon system, and is considerably less than the uncertainty in the carbon uptake of the terrestrial biosphere [Houghton, 2007]. However, as the ocean plays a crucial role in the global carbon cycle and the regulation of the Earth’s climate, further understanding and better modelling of the role of the ocean ecosystem in the global carbon cycle and its reaction to anthropogenic climate forcing remains important.

Il est désormais établi que la disponibilité en fer (Fe) contrôle environ 50% de la production primaire des océans du monde. Cependant, les processus régissant l’intensité des puits et des sources du Fe ainsi que la prédominance relative de ces sources au sein des divers bassins océaniques, sont elles-mêmes peu contraintes. Par ailleurs, une fois entrées dans le système océanique, la disponibilité et l’accessibilité des diverses formes de Fe pour les organismes marins restent incertaines. La réactivité du Fe au sein de l’environnement marin dépend de son état d’oxydoréduction et de complexation. Le fer dissous (DFe) est souvent considéré comme la fraction la plus biodisponible pour le phytoplancton et les ligands organiques du Fe augmentent vraisemblablement le temps de résidence du Fe et permettent des concentrations de DFe bien plus élevées que sa solubilité inorganique ne le permet dans l’eau de mer (10 pmol L-1).Dans ce contexte et s’inscrivant dans le programme international GEOTRACES, cette thèse a pour but principal d’implémenter notre savoir du cycle biogéochimique du Fe dans l’océan et ses interactions avec la structure des communautés phytoplanctoniques, en particulier afin de mieux contraindre les formes biodisponibles du Fe. Ainsi, les objectifs de cette thèse reposent sur trois questions scientifiques : 1) Quelles sont les distributions, sources, et puits de Fe ? 2) Quel est le lien entre la structure des communautés phytoplanctoniques et les concentrations en DFe ? 3) Comment la spéciation organique du DFe impacte ses concentrations et sa biodisponibilité ? Ces trois questions ont été explorées sur de deux zones d’études contrastées : l’océan Nord Atlantique (GEOVIDE, GA01 GEOTRACES voyage, PIs G. Sarthou and P. Lherminier) étant occasionnellement et saisonnièrement appauvri en Fe et l’océan Austral (HEOBI, GIpr05 GEOTRACES voyage, PIs A. Bowie, T. Trull, Z. Chase) l’étant de manière permanente. / It is now recognized that iron (Fe) availability dictates the efficiency of the global biological carbon pump such that any perturbation of Fe sources will lead to changes in the carbon cycles with consequences on both other major nutrient cycles and the climate system, controlling about 50% of the worldwide ocean primary production. However, the underlying processes themselves that affect the pathways releasing and trapping Fe, and the relative predominance of Fe sources among the different ocean basins are still poorly constrained. More importantly, the extent to which both the chemical and the physical speciation of Fe are available and accessible for marine organisms, once it enters the ocean, remains uncertain. The reactivity of Fe within the marine environment will depend on its redox and complexation state, with DFe generally considered the most bioavailable form for phytoplankton and Fe-binding organic ligands likely increasing the residence time of Fe that enables enhanced DFe concentrations way above its inorganic solubility in seawater (c.a. 10 pmol L-1).In this context and as part of the international GEOTRACES program, this thesis aims at improving our knowledge on Fe biogeochemical cycle in the ocean and its interactions with the phytoplankton community structure to better constrain the bioavailable forms of Fe. The objectives of this thesis revolve around three scientific questions: 1) What are the distributions, sources, and sinks of dissolved iron? 2) What is the link between the phytoplankton community structure and dissolved iron concentrations? 3) How the organic speciation of dissolved iron affects its concentrations and bioavailability for the phytoplankton community? These three questions were investigated through two contrasted areas: the North Atlantic Ocean (GEOVIDE, GA01 GEOTRACES voyage, PIs G. Sarthou and P. Lherminier) and the Southern Ocean (HEOBI, GIpr05 GEOTRACES voyage, PIs A. Bowie, T. Trull, Z. Chase) the former being occasionally seasonally depleted in Fe, the latter permanently.

Marine microbes are an essential component of global biogeochemical cycles. In oligotrophic marine surface waters, the phytoplankton, phototrophic, single-celled (on occasion, colonial) organisms, is often dominated by the picoplankton (cells <2 micrometers in size), which constitute the base of the marine food chain. The picophytoplankton is composed of three main groups of organisms: two genera of cyanobacteria, Prochlorococcus and Synechococcus, and a third group, the picoeukaryotes. Even though numerically less abundant than cyanobacteria, picoeukaryotes can contribute significantly to biomass and primary production in this size fraction. Furthermore, picoeukaryotes are a diverse group but this diversity is still underexplored and their ecological roles and physiology is poorly understood. Here uncultured protists are investigated using 18S rRNA gene clone libraries, phylogenetic analyses, specific fluorescence in situ hybridization (FISH) probes and other methods in tropical and subtropical waters. Gene sequences comprising a unique eukaryotic lineage, biliphytes, were identified in most samples, whether from high (30 degrees Celsius) or low (5 degrees Celsius) temperature waters. Sequences within this uncultured group have previously been retrieved from mid and high latitudes. Phycobilin-like fluorescence associated with biliphyte-specific FISH probed cells indicated they may be photosynthetic. Furthermore, the data indicated biliphytes are nanoplanktonic in size, averaging between 3.0 and 4.1 micrometers. Using the 18S rRNA gene, sequences belonging to a broadly distributed but uncultivated pico-prymnesiophytes were retrieved. We investigated the ecological importance of these natural pico-prymnesiophyte populations and field experiments showed that they could grow rapidly and contributed measurably to primary production. They also appear to form a large portion of global picophytoplankton biomass, with differing contributions in five biogeographical provinces, from tropical to high latitudes. Finally, the physiology of the picoeukaryote Micromonas was studied under a shift from medium to high light and UV radiation. Results showed that the growth of these photosynthetic cells was synchronized with the light: dark period. Forward angle side scatter and red autofluorescence from chlorophyll increased throughout the light period and decreased during the dark period. This is consistent with cell division occurring at the beginning of the dark period. Additionally, genes proposed to have roles in photoprotection were up-regulated under high light and UV, but not in controls.

Phytoplankton growth is iron limited in at least 20% of the world’s oceans. Iron is an important nutrient required to synthesise enzymes necessary for photosynthesis, respiration, and nitrogen assimilation. Due to its low solubility in seawater, iron limitation of phytoplankton production has been the focus of much recent research. These organisms secrete ligands in order to solubilise the available iron, but not all of the iron dissolved in seawater is biologically available. In this study a molecular based approach was employed to investigate the acclimation of the marine haptophyte Coccolithus pelagicus to iron limitation. Using two dimensional electrophoresis, subtractive cDNA hybridisation, and RT real time PCR, changes in the proteome and in gene expression were examined. Iron limited cells were characterised by slower specific growth rates, lower chlorophyll a concentrations per unit biomass and less extensive calcification relative to iron replete cells. Addition of iron to iron limited cultures resulted in increased specific growth rates and increased chlorophyll a concentration per unit biomass. A subtracted cDNA library revealed seventeen identifiable sequences of which photosystem I protein E (PsaE), a fucoxanthin binding protein transcript, two chlorophyll binding proteins and a predicted membrane protein were shown to be up-regulated in iron-limited cells to varying extents. Two dimensional SDS PAGE revealed 11 differentially expressed proteins in iron limited cells and 1 highly expressed protein exclusive to iron replete cells. The potential utility of each of these as biomarkers of iron-limitation/iron sufficiency for natural populations of coccolithophorids like Coccolithus pelagicus is discussed.

Diatoms constitute a major group of phytoplankton, accounting for ~20% of the world’s primary production. Biological dinitrogen (N2) fixation by diazotrophic cyanobacteria has great biogeochemical implications in nitrogen (N) cycling, being the major source of new N input to the oceans and thereby contributing significantly to carbon (C) export production. It has been shown that iron (Fe) can be the limiting nutrient for phytoplankton growth, in particular, in the HNLC (High Nutrient Low Chlorophyll) regions. Iron plays thus an essential role in governing the marine primary productivity and the efficiency of biological carbon pump. Oceanic systems are undergoing continuous modifications at varying rates and magnitudes as a result of changing climate. The objective of our research is to evaluate the effects of global climate change processes (changing dust deposition, ocean acidification and sea-surface warming) on phytoplankton growth, biological N2 fixation, biogeochemical cycles, and the controlling role of Fe within these impacts. Laboratory culture experiments using a marine diatom Chaetoceros socialis were conducted at two temperatures (13 ℃ and 18 ℃) and two carbon dioxide partial pressures (pCO2, 400 µatm and 800 µatm). The present study clearly highlights the effect of ocean acidification on enhancing the release of Fe upon dust deposition. Our results also confirm that being a potential source of Fe, mineral dust provides in addition a readily utilizable source of macronutrients such as phosphorus (P) and silicon (Si). However, elevated atmospheric CO2 concentrations and ocean acidification may also have an adverse impact on diatom growth, causing a decrease in cell size and possible further changes in phytoplankton composition. Meanwhile, increasing temperature and ocean warming may lead to the reduction of diatom production as well as cell size, inducing poleward shifts in the biogeographic distribution of diatoms. Numerous factors can affect the extent of N2 fixation. A better understanding of the major environmental and nutrient controls governing this process is highly required. Iron and/or phosphorus are thought to be limiting factors in most oceanic regions. Special attention has been given to studying the effects of mineral dust deposition which is believed to promote N2 fixation as it increases the availability of both Fe and P. Three laboratory bioassays (+Fe, +P, +Dust) via incubation experiments were performed on Trichodesmium IMS101, an important contributor to marine N2 fixation. Each addition of Fe, P or desert dust was found to stimulate the growth and the N2 fixation activity of Trichodesmium IMS101. Several adaptive nutrient utilization strategies were observed, such as a Fe luxury uptake mechanism, a P-sparing effect and colony formation. In addition, during a field study in the temperate Northeast Atlantic Ocean using natural phytoplankton assemblages, N2 fixation was remarkably stimulated through the addition of dissolved Fe under low temperature and depleted P conditions, highlighting the critical role of Fe. At the time of this study, no Trichodesmium filaments were found in the region of investigation. The diazotrophic community was dominated by the unicellular cyanobacteria symbiont (prymnesiophyte-UCYN-A1) and heterotrophic diazotrophs, therefore suggesting that Fe could be the ultimate factor limiting N2 fixation of these smaller diazotrophs as well. Recently, the effects of ongoing climate change (ocean warming and acidification) on N2 fixation drew much attention, but various studies led to controversial conclusions. Semi-continuous dilution growth experiments were conducted on Trichodesmium IMS101 under future high pCO2 and warming seawater conditions (800 µatm and 28 °C) and compared to the present-day situations (400 µatm and 24 °C). The results indicate that higher pCO2 and therefore ocean acidification may be beneficial for Trichodesmium growth and N2 fixation. However, the present study suggests that Fe or P limitation in oligotrophic seawaters may offset the stimulation induced on Trichodesmium IMS101 due to ocean acidification. In contrast, ocean warming may not play an important role in Trichodesmium growth and N2 fixation with a 4 °C increase from 24 °C to 28 °C. Nevertheless, ocean warming was previously predicted to cause a shift in the geographical distribution of Trichodesmium toward higher latitudes, extending its niche to subtropical regions and potentially reducing its range in tropical ocean basins.Overall, the biological responses of the marine diatom Chaetoceros socialis and the N2-fixing cyanobacteria Trichodesmium IMS101 to several key climate change processes were presented and discussed in this study. These processes included dust deposition, and ocean acidification and warming, which were shown to have a significant impact on oceanic phytoplankton growth, cell size and primary productivity, biological N2 fixation, phytoplankton distribution and community composition. They would thus affect the C, N, P, Si and Fe biogeochemical cycles in various ways. Iron, as one of the most crucial micronutrients for marine phytoplankton, has in particular strong links to climate change and biogeochemical feedback mechanisms. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished