published_or_final_version / abstract / Biological Sciences / Doctoral / Doctor of Philosophy

We are coming to understand that the ecological importance of diatoms is not limited to primary productivity, as many diatoms produce extracellular polymeric substances (EPS), which are vital components in algal and bacterial “biofilms.” While great effort has been made to chemically identify the types of molecules and polymers used to create and modify diatom EPS there is still much about the process we do not know. Rather than studying this process chemically, we have elected to search for the genes involved in EPS production and secretion. We assembled transcriptomes from three EPS-producing diatoms (Cyclophora tenuis, Lucanicum concatenatum, Thalassionema frauenfeldii) and two diatoms which do not (Astrosyne radiata, Thalassionema sp. ‘BlueH20’). In an attempt to limit the differences to EPS-related transcripts, the taxa were selected in a phylogenetic framework (which is also discussed in this dissertation), where EPS-producing taxa were closely-related to taxa which did not produce EPS (A. radiata, C. tenuis, L. concatenatum as one set, T. frauenfeldii and T. sp. ‘BlueH20’ as the other). The resulting pool of transcripts sorted for contigs which appeared in the EPS-producing taxa but not their closely-related non EPS-producing counterparts, and those contigs were then compared to two annotated diatom genomes and sorted by function, looking specifically for genes related to secretion, polysaccharide assembly or modification and carbohydrate metabolism. In the Thalassionema clade, 41 contigs with the aforementioned annotations were found, while 22 such contigs were found in the Cyclophora/Lucanicum/Astrosyne clade. These putative EPS-related markers are identified in this dissertation for further study on their function and evolution across diatoms. / text

The aim of this study was to analyze water chemical samples and diatoms to determine if there are any differences between the sample points in deformations, tax numbers and metal contents. Furthermore the aim is to investigate whether there is a correlation between metals and deformations, to study the bioavailable content of metals and whether deformations and tax loss are area specific. The data is from the years 2015-2018 and comprises 114 sample points from water streams in northern Sweden. The data includes diatoms, deformations, tax numbers and content measurements from the metals As, Cu, Cd, Ni, Pb, U and Zn. Regression analysis was performed between the bioavailable content of metal (Cu, Ni, Pb, Zn) and dissolved content, and also between the metal contents and the deformations to investigate a possible correlation. Two different regression analyzes where made for the metal contents and the deformations, because there are two test points that have very high deformations (10,5% and 9,5%). The comparison between the different sample points shows that it is not obvious that elevated metal contents have an influence on the diatom community. The first regression analysis (n=114) for metals and deformations indicates that Ni and Zn are significant, both the bioavailable- and the dissolved content. The second regression analysis (n=112) indicates that the bioavailable content of Cu and the dissolved content of U are significant. For both analysis the coefficient of determination is far too low for it to be reliable. More studies need to be done, including more metals and diatom species.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. March 2016 / Coastal waterbodies along the east coast of southern Africa evolved from fluvial origins that were slowly drowned by rising sea levels during the Holocene. The accumulation of sediment in these systems is relatively undisturbed, providing ideal sites from which longer term observations of palaeo-climatic variability over most of the Holocene period can be made. Lake St. Lucia, on the north coast of KwaZulu- Natal, is the largest estuarine lagoon in Africa and is widely regarded as one of the most important shallow water systems globally. Despite the importance of this system, little is currently know about the processes driving the long-term evolution of the lake. This study aimed to reconstruct the hydrological changes associated with the Holocene evolution of Lake St. Lucia using fossil diatoms. Analyses were performed on two sediment cores from the North Lake (15.6 m) and False Bay (15.9 m) basins of Lake St. Lucia. Age models, each based on eight radiocarbon dates, revealed continuous sedimentary records covering ~8300 cal. yr BP. A total of 150 samples were examined resulting in a total of 113 species recorded which were used to infer changes in environmental conditions based on their reported ecological preferences. / GR 2016

Dans le contexte actuel d’accroissement de la population mondiale, il est nécessaire de construire d’avantage d’infrastructures pour répondre à la pression industrielle grandissante. Ces constructions se font principalement sur la mer comme les ports, les îles artificielles ou encore les logements touristiques. Le béton est le matériau majoritairement utilisé en raison de son faible coût de production mais aussi de sa résistance à l’eau de mer. Comme tout matériau immergé en milieu marin, le béton est colonisé par les organismes vivants, devenant ainsi support de leur développement. Cependant, l’eau de mer est un milieu particulièrement agressif vis-à-vis des matériaux cimentaires ; des dégradations physiques, chimiques et biologiques sont observées dans le temps. Les deux premiers types de dégradation sont particulièrement bien documentés par la communauté scientifique. En revanche, les dégradations biologiques sont peu étudiées. L’objectif de cette thèse est donc de tout d’abord mettre en place un dispositif expérimental en laboratoire, permettant la colonisation d’un matériau cimentaire par des microorganismes. Des outils pertinents pour caractériser le biofilm sur le matériau ont été choisis après une étude bibliographique, dans le but de mieux comprendre la cinétique de colonisation. Des analyses chimiques du matériau ainsi que de l’eau de mer artificielle ont été effectuées à échéances régulières pour évaluer les actions du biofilm sur le matériau cimentaire. Différents matériaux ont été formulés pour étudier l’impact de la formulation sur la colonisation. / In the current context of increased world population, it is necessary to built more infrastructures to meet the increasing industrial pressure. These constructions are erected on the sea as harbors, artificial islands or tourist accommodation. Concrete is mainly used because of its low-cost and durability in the marine environment. Like any material immersed in seawater, concrete is colonized by living organisms, becoming an habitat for their development. However, seawater is a very aggressive environment towards cementitious materials; physical, chemical and biological degradations are observed with time. Nowadays, physical and chemical degradations are well understood and reported in the literature but there is a lack of knowledge concerning biological effects. The aim of this thesis is first develop an experimental device in laboratory, allowing the colonization of cementitious material by microorganisms. Relevant tools to characterize the biofilm on the material were chosen to better understand colonisation’s kinetic. Chemical analysis of material and seawater were made to evaluate the actions of the biofilm on cementitious material. Different materials were produced to study the impact of the formulation on the colonization.

My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa. The work described here is grouped into two major topics, 1) endosymbiosis and genome evolution, and 2) harmful algal blooms. I discuss my work related to endosymbiosis and genome evolution in chapters 2-4. Chapters 5-6 cover the work related to harmful algal blooms. In chapter 1, I introduce the state-of-art of what is known about the history of plastids and evolution of photosynthesis in eukaryotes, an overview of marine harmful algae, and the specific aims of my dissertation. In chapter 2, I describe the design and implementation of the phylogenetic sorting tool, PhyloSort and the assembly of a high-throughput phylogenomic pipeline. Together, PhyloSort and the pipeline has become a key tool for multiple subsequent studies. chapter 2 also presents a case study using these tools in which we provide an estimate of the number of cyanobacterial genes that have been transferred to the nuclear genome of Plantae through primary endosymbiotic gene transfer; I use the model unicellular green alga Chlamydomonas reinhardtii for this purpose. In chapter 3, I discuss another case of prokaryotic contribution to the nucleus of photosynthetic eukaryotes. Here, the intriguing relationship of Chlamydiae-like bacteria and plants and algae is examined in a large-scale analysis, in which we scanned all available genomes of the primary photosynthetic organisms for genes of potential Chlamydiae origin. Surprisingly, we identified more than fifty Chlamydiae-derived genes in plants and algae. Here, we propose a model for the role that a Chlamydiae-like symbiont might have played in the establishment of the primary plastid in the common ancestor of Plantae. In chapter 4, I describe a study in which we explored the complete protein models of two diatom organisms as representative for photosynthetic chromalveolates and looked for genes that might have been acquired through endosymbiotic (secondary) or horizontal transfers from red or green algae. In contradiction of the “chromalveolate hypothesis” which states that photosynthesis in chromalveolates originated via the engulfment of a red alga symbiont, our study shows an unexpected green algal contribution that is fourfold greater than that of the canonical red algal symbiont. Our data suggest that the chromalveolate history includes a previously unrecognized green algal endosymbiont that was captured and lost prior to the more recent establishment of the red alga plastid, which is widespread in extant photosynthetic chromalveolates. In chapter 5, I discuss the identification of the phylogenetic origin of the genes involved in the biosynthetic pathway of saxitoxin in cyanobacteria. Here, we used a pyrosequencing approach to sequence de novo genomes of two strains of Anabaena circinalis, one of which is saxitoxin-producing and the other is non-toxic. Using comparative and phylogenetic analyses, I show that, within the saxitoxin gene cluster, genes that encode the key and unique enzymes in the pathway are of foreign origin that originated via horizontal transfer from non-cyanobacterial sources. These genes introduced the ability to produce saxitoxin in the ancestor of the toxic cyanobacterial clade. In chapter 6, I describe a gene expression study in which we used massively parallel signature sequencing (MPSS) to investigate RNA abundance patterns in the toxic dinoflagellate Alexandrium tamarense. This work provides the first clear evidence for the utilization by dinoflagellates of transcriptional to regulation. Moreover, using MPSS, we provide an estimate of the number of the distinct genes in Alexandrium tamarense; i.e., remarkably 40,000 loci. Taken together, our data indicate that dinoflagellates possess a great metabolic flexibility that allows them to efficiently toggle between photoautotrophy and heterotrophy based on the environmental conditions.

Stratigraphic analyses of lacustrine sediments provide powerful tools for reconstructing past environments. The records that result from these analyses are key to understanding present-day climate mechanisms and how the natural environment may respond to anthropogenic climate change in the future. This doctoral dissertation research investigates climate and environmental history at Laguna Saladilla (19° [degrees] 39' N, 71° [degrees] 42' W; ca. 2 masl), a large (220 ha) lake along the north coast of Hispaniola. I reconstructed changes in vegetation and environmental conditions over the mid to late Holocene based on pollen, microscopic charcoal, and diatoms in an 8.51 m sediment core recovered from the lake in 2001. Fieldwork in December 2009 included the use of ground penetrating radar to identify subaqueous deltas that indicate past positions of the Masacre river, which flows into the lake from the Cordillera Central. Laguna Saladilla was deeper and more saline from the base of the sediment profile approximately 8030 cal yr BP to about 3500 cal yr BP. Mangrove (Rhizophora) pollen percentages were highest around 7650 cal yr BP, when mollusk shells in the core suggest marine conditions. The lake became progressively brackish ca. 3500 cal yr BP, followed by a transition ca. 2500 cal yr BP to its current freshwater state. This shift in water chemistry was likely due in part to a change in the position of the Masacre river. Diatoms show that lake levels decreased as evaporation/precipitation ratios increased. Amaranthaceae and other herbs dominated the pollen record under the drier conditions of the last 2500 cal yr BP; pollen of fire-adapted taxa, particularly Pinus, increased in the last 800 years. Patterns of microscopic charcoal influx at Laguna Saladilla over the Holocene are similar to patterns at Lake Miragoane, Haiti and Laguna Tortuguero, Puerto Rico. The changes in fire frequency or extent indicated by these Caribbean charcoal records may be driven by increased winter insolation at ca. 5000 cal yr BP that led to earlier winter drying. Comparing the charcoal record to archeological data and other paleoenvironmental records facilitated the disentangling of changes in climate from anthropogenic impacts.

Thesis (Ph. D.)--University of Chicago, Dept. of Molecular Genetics and Cell Biology, June 1997. / Includes bibliographical references. Also available on the Internet.

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

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