The silica-based cell walls of diatoms are prime examples of genetically controlled, species-specific mineral architectures. The physical principles underlying morphogenesis of their hierarchically structured silica patterns are not understood, yet such insight could reveal novel routes towards synthesizing functional inorganic materials. Recent advances in imaging nascent diatom silica allow rationalizing possible mechanisms of their pattern formation. Here, we combine theory and experiments on the model diatom Thalassiosira pseudonana to put forward a minimal model for morphogenesis of branched rib patterns – a widespread feature of diatom cell walls. To this end, we developed an automated image analysis algorithm that enabled quantitative assessment of the morphological discrepancy between the experiments and model predictions. The model proposed here quantitatively recapitulates the time-course of rib pattern formation by accounting for silica biochemistry with autocatalytic formation of diffusible silica precursors followed by conversion into solid silica. We propose that silica deposition releases an inhibitor that slows down up-stream precursor conversion, thereby implementing a self-replicating reaction-diffusion system, recapitulated by a non-classical Turing mechanism. The proposed mechanism highlights the role of geometrical cues for guided self-organization, rationalizing the instructive role for the single initial pattern seed known as primary silicification site present in diatoms. The model features a wide spectrum of possible pattern morphologies depending on the model parameters, suggesting that this model may be applicable in other diatom species. Moreover, due to the generic nature of the proposed model for branching morphogenesis, the mechanism identified here may be relevant also in other biological systems known to exhibit.

This thesis investigates how variations in the oxygen isotopic composition of lake waters in northern Fennoscandia are recorded in lake sediment archives, especially diatoms, and how these variations can be used to infer past changes in climate and atmospheric circulation. Results from analyses of the oxygen isotopic composition of lake water samples (δ18Olakew) collected between 2001 and 2006 show that δ18O of northern Fennoscandian lakes is mainly controlled by the isotopic composition of the precipitation (δ18Op). Changes in local δ18Op depend on variations in ambient air temperature and changes in atmospheric circulation that lead to changes in moisture source, vapour transport efficiency, or winter to summer precipitation distribution. This study demonstrates that the amount of isotopic variation in lake water δ18O is determined by a combination of the original δ18Olakew, the amount and timing of the snowmelt, the amount of seasonally specific precipitation and groundwater, any evaporation effects, and lake water residence time. The fact that the same isotope shifts have been detected in various δ18Olakew proxies, derived from hydrologically different lakes, suggests that these records reflect regional atmospheric circulation changes. The results indicate that diatom biogenic silica isotope (δ18Odiatom) records can provide important information about changes in atmospheric circulation that can help explain temperature and precipitation changes during the Holocene. The reconstructed long-term Holocene decreasing δ18Op trend was likely forced by a shift from strong zonal westerly airflow (relatively high δ18Op) in the early Holocene to a more meridional flow pattern (relatively low δ18Op). The large δ18Olakew depletion recorded in the δ18O records around ca. 500 cal yr BP (AD 1450) may be due to a shift to more intense meridional airflow over northern Fennoscandia resulting in an increasing proportion of winter precipitation from the north or southeast. This climate shift probably marks the onset of the so-called Little Ice Age in this region. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: In press. Paper 2: Submitted. Paper 5: In progress.

The silica-based cell walls of diatoms are outstanding examples of nature’s capability to synthesize complex porous structures with genetically controlled patterns from the nanometer scale to the range of hundreds of micrometers. Formation of the cell wall building blocks (valves and girdle bands) occurs in membrane-bound compartments, termed silica deposition vesicles (SDVs), which are unique organelles in silica-forming protists. Isolation of the SDVs has not yet been achieved, which has severely hampered the efforts to understand the mechanisms of biological silica morphogenesis. The present thesis aimed to address this shortcoming. The foundation was the development of an improved cell cycle synchronization and a fluorescence labeling method for the model diatom Thalassiosira pseudonana that enabled rapid identification of valve SDVs in a cell lysate. Correlative fluorescence and electron microscopy allowed visualizing the development of valve silica with unprecedented spatio-temporal resolution. Elemental analysis and demineralization of immature valves provided the first direct chemical evidence that silica morphogenesis is an interplay of inorganic and organic molecules inside the valve SDVs. Cryo TEM imaging of valve SDVs indicated the formation of organic patterns that precede silica depostion. From these observations, an organic biomolecule dependent, liquid-liquid phase separation based model for pore formation in the diatom T. pseudonana was proposed. The second part of this thesis was focused on the enrichment of valve SDVs from T. pseudonana and the subsequent proteomics based identification of more than 40 potential valve SDV proteins. Among these, three diatom-specific proteins contained conserved protein protein interaction domains (ankyrin-repeats) and were surprisingly predicted to be located in the cytoplasm. The fluorescent tagging of the three proteins (termed dANK1-3) confirmed their association with the valve SDVs. When the respective dank genes were knocked out by CRISPR/Cas9, the valves displayed permanent anomalies in the quantity and the pattern of ~22 nm sized pores. Double knockout mutants lacking both dank1 and dank3 were almost completely devoid of pores. The analysis of valve morphogenesis in the single and double knockout mutants revealed phenotypic changes that were consistent with the liquid-liquid phase separation based model for pore pattern formation in diatom biosilica. The work of this thesis has provided for the first time direct access to valve SDVs, which has opened entirely new possibilities for studying the composition, properties, and working mechanism of an organelle that forms a complex shaped mineral.