This thesis examines playas as integrated ecosystems, through investigation of long- and short-term processes associated with playa geomorphology, hydrology and diatom ecology, in playas of the Yarra Yarra drainage system of Western Australia. This landscape approach was conducted at a range of scales and consequently revealed a level of heterogeneity not previously described in Australian playas. The key result and common thread linking the three facets of the playas investigated is the importance of hydroperiod in defining the playa environment. The morphology and distribution of playas are described and the results presented of an examination of potential mechanisms determining intra-system variability. Measurements of the physical attributes of the playas, including length, area, shape, density and orientation, were made through Geographic Information System analysis and detailed interpretation of aerial photography. Two main morphological groups are distinguished: small (<10 ha), elliptical to circular playas with a NNW-SSE orientation; and large (>30 ha), elongated playas. Regional patterns in geomorphic attributes are markedly different between the west and east sides of the system. The boundary between the two regions coincides approximately with rainfall distribution. In this respect, climate is an overarching driver of geomorphological variation but sub-catchment characteristics are also critical determinants. Littoral drift and segmentation processes that are common to coastal lagoons but not commonly described in playas were identified from visual interpretation of aerial photographs of spits, bars and cuspate shorelines. Six small playas, representing an hydrological continuum from mostly wet to mostly dry, were selected for investigation of their hydrology and diatom ecology, enabling assessment ii of the variability of hydrology, hydrochemistry and of the effects of different hydrological environments on the distribution of taxa. Hydroperiod was highly variable and central to determining playa geomorphology and biology. In the six playas it ranged from 19 to over 211 days, and filling frequency from 1 to 3 cycles between 2002 and 2004, reflecting rainfall and sub-catchment variability. Monitoring a series of nested piezometers revealed that the playas were net discharge points for ground water over the period of survey. However, small local vertical head variations indicate ground water does not discharge at the same rate across the playa surfaces and that playas may have short-lived phases of ground water recharge. Hydrochemically, the playas are typical of salt lakes in Australia. They displayed a wide range of salinity values, neutral to alkaline pH and ionic composition similar to sea water. It is postulated that the geochemical evolution of waters in the playas follows a pathway where low salinity recharge waters with dilute sea water salts progress to Na-Cl dominated brines through evaporative concentration. Surface waters showed an ionic dominance consistent with sea water with minor variations attributed to transitional phases in the geochemical evolution of the waters. Shallow ground waters showed a common and consistent pattern of ionic dominance: Na+ >Mg2+ >K+ >Ca2+ : Cl- >SO4 2- >HCO3 ->CO3 2-.

<p>The objective of the thesis was to explore the potential of diatoms (<i>Bacillariophyceae</i>) as indicators of Holocene climate and environmental change in northern Sweden (Abisko region, 68°21'N, 18°49'E). A modern surface-sediment calibration set including 100 lakes was developed and lake-water pH, sedimentary organic content (assessed by loss-on-ignition) and temperature were identified as most powerful environmental variables explaining the variance within the diatom assemblages. Transfer functions based on unimodal species response models (WA-PLS) were developed for lake-water pH and mean July air temperature (July T), yielding coefficients of determination of 0.77 and 0.70, and prediction errors based on leave-one-out cross-validation of 0.19 pH units and 0.96 °C for lake-water pH and July T, respectively. The transfer functions were validated with monitoring data covering two open-water seasons (lake-water pH) and meteorological records covering the 20th century (July T). The good agreement between diatom-based inferences and measured monitoring data confirmed the prediction ability of the developed transfer functions. </p><p>Analysing a Holocene sediment core from a lake nearby Abisko (Vuoskkujávri), diatoms infer a linearly decreasing July T trend (1.5 °C) since 6,000 cal. BP, which compares well with inferences based on chironomids and pollen from the same sediment core. The lake-water pH inference shows a pattern of moderate natural acidification (c. 0.5 pH units) since the early Holocene, reaching present-day pH values at c. 5,000 cal. BP. By fitting fossil diatom samples to the modern calibration set by means of residual distance assessment within canonical correspondence analysis (CCA), the early Holocene (between 10,600 and 6,000 cal. BP) was identified as a problematic time-period for diatom-based inferences and, consequently, reconstructions during this period are tentative. Pollen-based inferences also show 'poor' fit between 10,600 and 7,500 cal. BP and chironomids probably provide the most reliable July T reconstruction at Vuoskkujávri, with 'poor' fit only during the initial part of the Holocene (between 10,600 and 10,250 cal. BP). </p><p>Possible factors confounding diatom-based July T inferences were investigated. Using detrended CCA (DCCA), Holocene sediment sequences from five lakes indicate that during the early Holocene, mainly physical factors such as high minerogenic erosion rates, high temperature and low light availability may have regulated diatom assemblages, favouring <i>Fragilaria</i> species. In all five lakes, diatom assemblages developed in a directional manner, but timing and scale of development differed substantially between lakes. The differences are attributed primarily to the geological properties of the lake catchments (with strong effects on lake-water pH), but other factors such as climatic change, vegetation, hydrologic setting and in-lake processes appear to regulate diatom communities in each lake differently. The influence of long-term natural acidification on diatom assemblages progressively declined during the Holocene with corresponding increase of the influence of climatic factors.</p>

Les océans couvrent plus de 70% de la surface de la Terre (planète bleue) et la productivité primaire nette (PPN) marine est équivalente à celle terrestre. Alors qu‟il ne représente que 1% de la biomasse totale d‟organismes photosynthétiques de la planète, le phytoplancton est responsable d‟environ 45% de la PPN globale. Le terme phytoplancton décrit un assemblage polyphylétique comprenant des eucaryotes et procaryotes photosynthétiques dérivant avec les courants. Dans les océans contemporains, les diatomées constituent un groupe d‟eucaryotes unicellulaires autotrophes très abondant, responsable de 40% de la PPN marine. Les diatomées appartiennent à la lignée des straménopiles qui sont issus d‟un évènement d‟endosymbiose entre une algue rouge et un hôte hétérotrophe. Elles sont classifiées en deux groupes majeurs : les centriques qui son apparues il y a environ 200 millions d‟années (Ma), et les pennées qui ont évolué il y a environ 90 Ma. Deux génomes de diatomées ont récemment été séquencés : celui de la diatomée centrique Thalassiosira pseudonana (32 Mb), et celui de la diatomée pennée Phaeodactylum tricornutum (27 Mb). Mon sujet de doctorat s‟est focalisé sur l‟étude de différents aspects de la régulation de l‟expression génique ainsi que sur la dynamique et l‟évolution de ces génomes. L‟expression des gènes est régulée à différents niveaux: trancriptionel, post-transcriptionel, et épigénétique. Dans le cadre de mon doctorat, une étude de la régulation transcriptionelle chez les diatomées a été effectuée et comprend l‟identification et l‟analyse in silico des facteurs de transcription (FT). Cela a permis par exemple d‟établir qu‟une classe spécifique de FT, les Heat Shock Factors, sont particulièrement abondants chez les diatomées par rapport aux autres eucaryotes. L‟analyse de la représentation des FT identifiés dans différentes librairies d‟EST élaborées à partir de cultures ayant subi divers stress a permis de détecter certaines spécificités d‟expression. L‟évolution des génomes eucaryotes est largement impactée par les effets directs et secondaires des éléments transposables (ET) qui sont des éléments génétiques mobiles se trouvant dans le génome de la plupart des organismes. Dans le but d‟étudier la dynamique des génomes de diatomées, la recherche de différents types d‟ET a permis d‟établir qu‟une certaine classe, les rétrotransposons de type Copia, est la plus abondante dans ces génomes et constitue un part significativement plus importante du génome de P. tricornutum (5,8%) par rapport à T. pseudonana (1%). D‟autre part, des analyses phylogénitiques ont montré que les rétrotransposons de type copia forment deux classes distinctes et éloignées de la lignée Copia. L‟analyse de leurs niveaux d‟expression a montré que la transcription de deux éléments s‟active en réponse à des stress spécifiques comme la limitation en nitrate dans le milieu de culture. Cette activation est accompagnée par un hypométhylation de l‟ADN et l‟analyse de profils d‟insertions chez différents écotypes de P. tricornutum ainsi que l‟étude d‟autres phénomènes suggèrent que les rétrotransposons de type Copia ont joué un rôle important dans l‟évolution des diatomées. Mon grand intérêt pour les ET m‟a ensuite amené à chercher à les caractériser dans d‟autres génomes récemment séquencés tels celui de l‟algue brune Ectocarpus siliculosus. La recherche in silico de différents gènes codant des protéines capables d‟introduire ou de stabiliser des états épigénétiques telle que la modification des histones et la méthylation de l‟ADN a montré leur présence chez P. tricornutum ainsi que leurs particularités. La présence de certaines modifications d‟histones spécifiques d‟une conformation compacte ou ouverte de la chromatine dans le proteome de P. tricornutum a été montrée. De plus, la mise au point de la technique d‟immunoprécipitation de la chromatine chez P. tricornutum a permis d‟établir que les nucléosomes enrobés d‟éléments transposables étaient marqués par des modifications spécifiques. D‟autres expériences ont permis d‟établir que l‟ADN de différents types d‟éléments transposables est marqué par la méthylation de cytosines chez P. tricornutum. Une expérience permettant l‟analyse du profil de méthylation à l‟échelle de génome en utilisant une puce à ADN a été lancée et permettra de découvrir si certains gènes portent aussi des traces de méthylation. Enfin, les ARN interférents constituent un troisième mode de régulation de l‟expression se situant à l‟interface de la régulation transcriptionelle, post-transcriptionelle et épigénétique. Les mécanismes d‟interférences chez les diatomées ont été étudié par la recherche in silico d‟enzymes clés impliquées dans ce processus ainsi qu‟en établissant expérimentalement un lien direct avec la méthylation de l‟ADN.

<p>Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobenthic biomass. It also contributes to the floristic knowledge of the Baltic Sea. </p><p>Diatom species show large variation in size. The responses of large species (≥1000 μm3) in diatom communities to environmental factors are underestimated if solely measured as relative abundance, as is the common practice. However, relative abundance gives the best gradient resolution, as compared to surface area and biovolume, if species are counted separately in two biovolume classes. Small and large species in the same community may respond differently to the same environmental factors. </p><p>To assess the principal environmental factors structuring diatom communities in the Gulf of Bothnia, 270 quantitative samples were collected from submerged stones. Sampling was carried out in spring in four areas of the Bothnian Bay, characterized by a stable north-south salinity gradient (0.4-3.3 psu), and in three areas of the Bothnian Sea which has a rather uniform salinity of ca. 5 psu. Canonical correspondence analysis (CCA) identified salinity and exposure to wave action as the principal factors structuring the diatom communities of the Bothnian Bay, whereas exposure to wave action was the principal factor in the Bothnian Sea. Measurements of relative ignition loss suggested that the cover of macroalgae, and thereby the higher abundance of epiphytic diatoms in the epilithic samples, was positively correlated with salinity in the Bothnian Bay and with water movement in the Bothnian Sea. </p><p>Two new brackish water species are described, <i>Navicula sjoersii</i> S. Busse & Snoeijs and <i>N. bossvikensis</i> S. Busse & Snoeijs. The new species are compared with <i>N. perminuta</i> Grunow, a common brackish-water species.</p>

<p>This thesis examines the role of dissolved inorganic nutrients in generating changes in phytoplankton community and pigment composition and if such changes can affect the production of the antioxidant astaxanthin in the ecosystem via pelagic copepods. The background of my studies is the possible relationship between eutrophication and a reproductive disturbance in Baltic populations of Atlantic salmon (M74), which is associated with astaxanthin and thiamine deficiencies and oxidative stress. In the southern Baltic Sea, changes in nutrient loads correlate with observed trends of flagellates replacing diatoms in the phytoplankton. Copepods are the main producers of astaxanthin and a major link between phytoplankton and higher trophic levels. In laboratory and field experiments in the Baltic Sea proper and the Norwegian Sea, I show that astaxanthin synthesis in copepods is fast and depends on pigment composition of the phytoplankton diet. Among single-species diets, a diatom and a green algal cyst yielded the highest astaxanthin levels in copepods, and another diatom species, a green alga and a cyanobacterium the lowest. In nutrient-generated phytoplankton blooms in mesocosms, copepods grazing on diverse communities dominated by weakly silicified diatoms produced more astaxanthin compared with copepods grazing on communities dominated by strongly silicified diatoms. This suggests that diatoms invested in defence mechanisms and escaped grazing at surplus Si. A nutrient-starved diatom culture subjected to intraspecific competition exhibited decreased pigment levels, increased thiamine levels and increased oxidative stress. </p><p>My results suggest that diatoms are beneficial for astaxanthin and thiamine production compared to other phytoplankton groups, but not under all circumstances. Copepod growth and development also responded to inorganic nutrient availability and affected total astaxanthin production per volume seawater, with highest production when the copepods grazed on diatoms. From an ecosystem perspective, increased N and P loads seem to promote high astaxanthin production, but not when diatoms disappear completely.</p>

The objective of the thesis was to explore the potential of diatoms (Bacillariophyceae) as indicators of Holocene climate and environmental change in northern Sweden (Abisko region, 68°21'N, 18°49'E). A modern surface-sediment calibration set including 100 lakes was developed and lake-water pH, sedimentary organic content (assessed by loss-on-ignition) and temperature were identified as most powerful environmental variables explaining the variance within the diatom assemblages. Transfer functions based on unimodal species response models (WA-PLS) were developed for lake-water pH and mean July air temperature (July T), yielding coefficients of determination of 0.77 and 0.70, and prediction errors based on leave-one-out cross-validation of 0.19 pH units and 0.96 °C for lake-water pH and July T, respectively. The transfer functions were validated with monitoring data covering two open-water seasons (lake-water pH) and meteorological records covering the 20th century (July T). The good agreement between diatom-based inferences and measured monitoring data confirmed the prediction ability of the developed transfer functions. Analysing a Holocene sediment core from a lake nearby Abisko (Vuoskkujávri), diatoms infer a linearly decreasing July T trend (1.5 °C) since 6,000 cal. BP, which compares well with inferences based on chironomids and pollen from the same sediment core. The lake-water pH inference shows a pattern of moderate natural acidification (c. 0.5 pH units) since the early Holocene, reaching present-day pH values at c. 5,000 cal. BP. By fitting fossil diatom samples to the modern calibration set by means of residual distance assessment within canonical correspondence analysis (CCA), the early Holocene (between 10,600 and 6,000 cal. BP) was identified as a problematic time-period for diatom-based inferences and, consequently, reconstructions during this period are tentative. Pollen-based inferences also show 'poor' fit between 10,600 and 7,500 cal. BP and chironomids probably provide the most reliable July T reconstruction at Vuoskkujávri, with 'poor' fit only during the initial part of the Holocene (between 10,600 and 10,250 cal. BP). Possible factors confounding diatom-based July T inferences were investigated. Using detrended CCA (DCCA), Holocene sediment sequences from five lakes indicate that during the early Holocene, mainly physical factors such as high minerogenic erosion rates, high temperature and low light availability may have regulated diatom assemblages, favouring Fragilaria species. In all five lakes, diatom assemblages developed in a directional manner, but timing and scale of development differed substantially between lakes. The differences are attributed primarily to the geological properties of the lake catchments (with strong effects on lake-water pH), but other factors such as climatic change, vegetation, hydrologic setting and in-lake processes appear to regulate diatom communities in each lake differently. The influence of long-term natural acidification on diatom assemblages progressively declined during the Holocene with corresponding increase of the influence of climatic factors.

This work resulted in the development of multiple distinct and novel methods of cheaply producing large numbers of biologically derived, complex, 3-dimensional microstructures in a multitude of possible compositions. The biologically derived structures employed in this work were diatoms, a type of single celled algae, which grow complex silica shells in species-specific shapes. Due to the wide diversity of naturally occurring diatom shapes (on the order of 105), and the flexibility in tailoring chemical compositions using the methods developed here, real potential exists for cheaply mass-producing industrially relevant quantities of controlled shape and size 3-d particles for the first time. The central theme of this research is the use of diatoms as a transient scaffold onto which a coating is applied. After curing the coating, and in some cases firing the coating to form ceramic, the diatom can be selectively etched away leaving a free standing replica of the original structure with the salient features of the pre-form intact, but now composed of a completely different material. Using this concept, specific methods were developed to suit various precursors. Dip coating techniques were used to create epoxy diatoms, and silicon carbide diatoms. The Sol-Gel method was used to synthesize zirconia diatoms in both the tetragonal and monoclinic phases. A multi step method was developed in which previously synthesized epoxy diatoms were used as a template for deposition of a silicon carbide precursor and then heat treated to produce a silicon carbide/carbon multi-component ceramic. A hydrothermal reaction was also developed to convert Titania diatoms to barium titanate by reaction with barium hydroxide. Finally, the device potential of diatom-derived structures was conclusively demonstrated by constructing a gas sensor from a single Titania diatom. Under suitable conditions, the sensor was found to have the fastest response and recovery time of any sensor of this type reported in the literature. Furthermore, this work has laid the groundwork for the synthesis of many other tailored compositions of diatoms, and provided several compositions for device creation.

BaSIC, which stands for Bioclastic and Shape-preserving Inorganic Conversion, is shape-preserving chemical conversion process of biological (or man-made) silica structures for producing complex 3-D microscale structures. This dissertation reports the BaSIC reaction of halide gases (i.e., TiF4, ZrF4, and ZrCl4) with 3-D silica structures, (i.e., diatom frustules, silicified direct-write assembly scaffolds, and Stöber silica spheres) to produce titania and zirconia replicas of the original 3-D structures. The kinetics of reaction of silica with titanium tetrafluoride gas is analyzed by using a novel HTXRD reaction chamber, nitrogen adsorption, and transmission electron microscope (TEM). The crystal structure and the temperature-induced phase transformation (from the room temperature hexagonal R-3c structure to the higher temperature cubic Pm3m structure) of polycrystalline TiOF2 that was synthesized through metathetic reaction of silica with TiF4(g) is reported. Additionally, potential applications of the converted titania diatom frustules (i.e., as a fast micron-sized ethanol sensor, and as a pesticide hydrolyzing agent) are also demonstrated in this work.

This thesis examines the role of dissolved inorganic nutrients in generating changes in phytoplankton community and pigment composition and if such changes can affect the production of the antioxidant astaxanthin in the ecosystem via pelagic copepods. The background of my studies is the possible relationship between eutrophication and a reproductive disturbance in Baltic populations of Atlantic salmon (M74), which is associated with astaxanthin and thiamine deficiencies and oxidative stress. In the southern Baltic Sea, changes in nutrient loads correlate with observed trends of flagellates replacing diatoms in the phytoplankton. Copepods are the main producers of astaxanthin and a major link between phytoplankton and higher trophic levels. In laboratory and field experiments in the Baltic Sea proper and the Norwegian Sea, I show that astaxanthin synthesis in copepods is fast and depends on pigment composition of the phytoplankton diet. Among single-species diets, a diatom and a green algal cyst yielded the highest astaxanthin levels in copepods, and another diatom species, a green alga and a cyanobacterium the lowest. In nutrient-generated phytoplankton blooms in mesocosms, copepods grazing on diverse communities dominated by weakly silicified diatoms produced more astaxanthin compared with copepods grazing on communities dominated by strongly silicified diatoms. This suggests that diatoms invested in defence mechanisms and escaped grazing at surplus Si. A nutrient-starved diatom culture subjected to intraspecific competition exhibited decreased pigment levels, increased thiamine levels and increased oxidative stress. My results suggest that diatoms are beneficial for astaxanthin and thiamine production compared to other phytoplankton groups, but not under all circumstances. Copepod growth and development also responded to inorganic nutrient availability and affected total astaxanthin production per volume seawater, with highest production when the copepods grazed on diatoms. From an ecosystem perspective, increased N and P loads seem to promote high astaxanthin production, but not when diatoms disappear completely.

Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobenthic biomass. It also contributes to the floristic knowledge of the Baltic Sea. Diatom species show large variation in size. The responses of large species (≥1000 μm3) in diatom communities to environmental factors are underestimated if solely measured as relative abundance, as is the common practice. However, relative abundance gives the best gradient resolution, as compared to surface area and biovolume, if species are counted separately in two biovolume classes. Small and large species in the same community may respond differently to the same environmental factors. To assess the principal environmental factors structuring diatom communities in the Gulf of Bothnia, 270 quantitative samples were collected from submerged stones. Sampling was carried out in spring in four areas of the Bothnian Bay, characterized by a stable north-south salinity gradient (0.4-3.3 psu), and in three areas of the Bothnian Sea which has a rather uniform salinity of ca. 5 psu. Canonical correspondence analysis (CCA) identified salinity and exposure to wave action as the principal factors structuring the diatom communities of the Bothnian Bay, whereas exposure to wave action was the principal factor in the Bothnian Sea. Measurements of relative ignition loss suggested that the cover of macroalgae, and thereby the higher abundance of epiphytic diatoms in the epilithic samples, was positively correlated with salinity in the Bothnian Bay and with water movement in the Bothnian Sea. Two new brackish water species are described, Navicula sjoersii S. Busse &amp; Snoeijs and N. bossvikensis S. Busse &amp; Snoeijs. The new species are compared with N. perminuta Grunow, a common brackish-water species.