Approximately 6.6 million years ago in the Eastern Equatorial Pacific a large increase in biogenic mass accumulation rates (MAR’s) occurred. This increased level of biogenic mass accumulation persisted until about 4.4 Ma at which time levels returned to those similar to before the transition at 6.6 Ma. The exact nature of the change that facilitated this transition in biogenic MAR’s, however, was not understood. Here we present the results of a study which characterizes the diatom assemblage spanning the depositional transition at 6.6 Ma from sediments taken from ODP Hole 850B. A close inspection of lithology reveals a clear change in lithology from a diatom nannofossil ooze to a nannofossil diatom ooze at 6.6 Ma. This transition is immediately followed by the occurrence of laminated diatom ooze (LDO). Diatom absolute abundance data reveals three levels of productivity associated with pre-transitional, post-transitional, and LDO formational sediments. An increase in the absolute abundance of Thalassionema nitzschioides was the major contributor to the formation of post-transitional, and LDO sediments. The known ecological preferences of this species indicate an overall increase in nutrient availability followed by sporadic changes in nutrient availability. These changes in nutrient availability could be associated with the establishment, or increase in strength, of an upwelling cell and/or the increase in nutrients made available via upwelling due to a shoaling of the thermocline.

Nitrogen-fixation is an essential biochemical reaction involving the reduction of inert, atmospheric dinitrogen (N2) into biochemically accessible ammonia (NH3). Organisms that are capable of this process are collectively called “diazotrophs” and are ubiquitous in marine and terrestrial environments. Despite the wide distribution, little is known about the biological nature of the diverse groups of diazotrophs. This study was designed to address the influence of light and nutrients on nitrogen fixation and growth in several marine diazotrophic symbioses collectively termed “Diatom-Diazotroph Associations (DDAs).” The organisms of interest included the diatoms Hemiaulus haukii Grunow and Hemiaulus membranaceus Cleve, and their diazotrophic endosymbiont Richelia intracellularis Schmidt. The study included acetylene reduction assays, growth rate, and nutrient analysis experiments on both associations in order to better understand the similarities and differences within and between the two DDAs. The results indicate distinct differences in nitrogen fixation rates within and between the species. In the nitrogen addition experiment, the “no added nitrogen” treatment had the highest N2-fixation rate (N2-fixmax = 7.43 x 10-5 nmols N2 heterocyst-1min-1), followed by the added nitrate treatment (N2-fixmax = 6.49 x 10-5 nmols N2 heterocyst-1min-1) and the added ammonium treatment (N2-fixmax = 3.79 x 10-5 nmols N2 heterocyst-1min-1). The maximum growth rate occurred in the “added ammonium” treatment (0.42 divisions day-1), which had a higher percentage of asymbiotic cells than the two other treatments. The maximum recorded rate of N2-fixation for H. haukii was 7.43 x 10-5 nmol N2 heterocyst-1min-1 and the maximum value of N2-fixation for H. membranaceus was 1.88 x 10-4 nmol N2 heterocyst-1min-1. The maximum growth rate for H. haukii was 0.99 divisions day-1, and 1.06 divisions day-1 for H. membranaceus. Growth followed light saturation kinetics in H. haukii with a compensation light intensity (IC) of 10 µmol quanta m-2sec-1 and saturation light intensity (IK) of 100 µmol quanta m-2sec-1. H. haukii and H.membranaceus expressed light saturation kinetics in N2-fixation. N2-fixation was generally limited to the light period, with no evidence of a morning or evening enhancement. The DDAs grew solely on N2-fixation and did not use nitrate. This study contributes to current knowledge of DDAs and their role in global marine nitrogen fixation. / text

The research presented here deals with inferring phylogenetic trees and their use to study the evolution of functional traits in diatoms (Heterokontophyta: Bacillariophyceae). Two chapters are concerned with the phylogeny of a mainly freshwater group, the Cymbellales, with a convoluted taxonomic history and classification. I generated a multi-gene dataset to test the monophyly of the Cymbellales and reconstruct the relationships within the order. The molecular data were equivocal with respect to the monophyly of the Cymbellales, especially when taking into account some problematic taxa like Cocconeis and Rhoicosphenia. Aside from the problem with their monophyly, my work shows that the current genus- and family-level classification of the Cymbellales is unnatural, arguing for the need of nearly wholesale re-classification of the group. The two following chapters make use of phylogenetic trees to model the evolution of functional traits. I explored the evolution of cell size across the salinity gradient finding that the opposing selective forces exerted by marine and fresh waters select for different optimal cell sizes -- larger in the oceans and smaller in lakes and rivers. Thereafter, I modelled the evolutionary histories of habitat preference (planktonic-benthic) and growth form (solitary-colonial) across the diatoms. These traits exhibit markedly different evolutionary histories. Habitat preference evolves slowly, is conserved at the level of large clades, and its evolution is generally uniform across the tree. Growth form, on the other hand, has a more dynamic evolutionary history with frequent transitions between the solitary and colonial growth forms and rates of evolution that vary through time. I hope that these empirical studies represent an incremental advancement to the understanding of the evolution diatom species and functional diversity. / text

Te Waihora – Lake Ellesmere is an expansive, shallow, turbid, brackish, hyper-eutrophic, lowland lake located on the east coast of New Zealand’s South Island. The catchment and lake are in a highly modified state, with much of the catchment used for intensive agriculture and the lake’s level artificially controlled by cutting a channel through the barrier separating the lake from the sea. Although it is known that Waihora is highly modified, it is difficult to determine the factors contributing to the current lake state and what constitutes a natural state for this lake. In order to plan management strategies, it is important to have this information. This study aims to provide insight into these matters using paleoecological techniques, in particular, analysis of sediment characteristics, palynology and diatom analysis, on cores obtained from the lake bed. The results of these analyses show that Waihora has had a diverse history, beginning as a freshwater lake, low in nutrients, not long before c. 7500 years ago, following the fusion of Kaitorete ‘Spit’ with Bank Peninsula. This freshwater state was interrupted by the discharge of a large river into the basin, causing a permanent barrier opening and tidal, brackish conditions to prevail. A second brackish state formed after this, caused either by a shift in the discharge point through the barrier or, more likely, a second avulsion event of the Waimakariri River to a discharge point into Waihora. Upon the avulsion of this river to a discharge point north of Banks Peninsula, a freshwater, nutrient rich lake formed. Subsequently, human influenced lake changes became evident, with a hypereutrophic, shallow, brackish lake forming. This research provides evidence that modern lake management has led to decreased lake levels and increasing salinity within Waihora. Intensive agriculture, particularly since the 1970’s has led to an increase in nutrients within the lake and its current hypereutrophic state. A combination of lake level management and the ‘Wahine Storm’ (1968) has led to the lake’s current turbid, phytoplankton dominated state. Therefore, sediment characteristics, palynological and diatom data suggest that a natural condition for the lake is one with lower nutrient levels, lower salinity with greater depth and area than the current lake, with a large distribution of freshwater riparian vegetation and little halophytic vegetation. If restoration of the lake is a target then (1) the lake should be opened to the sea less frequently, allowing a decrease in lake salinity and conditions conducive to the prevalence of freshwater riparian vegetation to prevail, and (2) a transition from a phytoplankton dominated state to a macrophyte dominated state should be targeted, by maintaining the lake at greater depths, the use of riparian planting practices and decreasing nutrient input. However, the latter will be costly and involve questionable trade-offs between lake values and stakeholders. Regardless of whether or not restoration of Waihora to something resembling a natural state is, or will be, a management aim, a decrease in nutrient input catchment wide and riparian planting in the area surrounding the lake should be a priority and may present a more realistic, short term management objective.

My thesis focuses on copepod-diatom interactions, specifically on the effects of food quality and toxicity on copepod feeding, reproductive success and behavior but as a frame, also includes a quantitative evaluation of copepod carbon requirements compared to other trophic plankton groups. My aim was to evaluate the function of copepods in diatom-dominated spring blooms. I thereby used a series of mesocosm and laboratory experiments. For a realistic extrapolation of the results to natural environments I used different strains of a diatom species, Skeletonema marinoi, which is a common spring blooming species in the Baltic Sea. This species is known to produce polyunsaturated aldehydes (PUA; mainly heptadienal, octadienal and decadienal), which have previously been identified as the potential reasons for the detrimental effects of diatoms on copepod reproduction. All strains varied in size, mineral and biochemical content, and PUA production. I tested the effects on different dominant copepod species from northern temperate waters; Acartia sp. (A. clausi and A. tonsa), Calanus finmarchicus, Pseudocalanus elongatus, and Temora longicornis, as well as the dominant species in the northern Baltic Sea, Eurytemora affinis. The specific contributions of respiratory carbon requiment of mesozooplankton and lower size fractions to carbon cycling during PUA-producing diatom blooms are poorly documented. My results show that nanoplankton and microzooplankton dominated the carbon cycling (> 50% of primary production) whereas the contribution of bacterioplankton varied. Mesozooplankton was always of minor importance with contribution of <6% of primary production.  This illustrates the importance of lower size fractions during a phytoplankton spring bloom. Irrespective of their small contribution to the total community carbon cycling, copepods displayed non-selective and typically high feeding rate on different PUA-producing S. marinoi strains, indicating that there was no feeding deterrence. The effect of feeding on copepod reproductive success, however, varied between different strains, and depending on copepod species. In experiments with monospecific diatom diets reduced egg production rate and hatching success were mainly related to food quality measured as fatty acids and sterols, or algae growth rate, low assimilation efficiency or PUA production / ingestion. On the other hand, copepod reproduction and population development in the diverse diet, including a high concentration of S. marinoi and PUA (both particulate and dissolved), increased with increasing food concentration and was unaffected by the presence of toxic diatoms. I conclude that although a negative correlation between different reproductive variables and PUA production / ingestion may sometimes be observed in laboratory incubations, this is highly dependent on the strain / species used, and the effect of the algal strain can be stronger than the effect of the e.g., growth-stage dependent PUA production. Although copepod grazing might not be very important during a diatom spring bloom, even a highly PUA-producing S. marinoi can be considered an appropriate food source for copepods when occurring among the natural food assemblage, inducing a high reproductive output.

Biosignatures have been extensively studied at hot springs sites, such as Yellowstone, because liquid water is fundamental to the existence of life but also owing to the influx of mineral nutrients in these environments. However, some hot springs have upper temperatures exceeding the boundaries capable of sustaining life in all the spring facies, particularly those nearest the vent. Cold springs provide the same nutrient-rich environment with more ambient temperatures potentially capable of sustaining a diverse consortium of microorganisms across the entirety of the system. Ten Mile Graben Cold Springs, located in Southern Utah, is one such site known for its biota and preservation potential. This study aimed to observe the possible effects of the microorganisms on aragonite and calcite precipitation. Scanning electron microscope imagery observed biogenic fabric such as botryoidal aragonite and aragonite microspheres; however, the δ13C enrichment values of +2.80‰ to +7.30‰ imply the springs were dominantly precipitated through CO2 degassing. This discrepancy in the chemical and morphological data has been observed at other astrobiology analog sites such as Yellowstone; therefore, travertine and tufa seemingly do not preserve isotopic chemical biosignatures.

Magister Scientiae (Biodiversity and Conservation Biology) / Kelp forests are dynamic and productive ecosystems which host large biodiversity of sessile fauna and flora, including diatoms. These microalgae occur at the base of coastal marine food webs and contribute substantially to the productivity of marine ecosystems. Diatoms constitute one of the most common and species-rich groups of both phytoplankton and phytobenthos. Possessing a unique silica cell wall, diatoms play a key role in the global carbon and silicon cycles. As the changes in species composition of diatom communities are a direct reaction to the combination of environmental factors prevailing in their ecosystems, diatom analysis is widely and successfully used in biomonitoring of various environmental conditions and paleoecological reconstructions.

Diatoms are crucially important to the global ecosystem due to their role in regulating the world’s carbon and silicon cycles, and their production of large amounts of organic material in aquatic environments. They are thought to comprise ca. 100,000 species, although some estimates suggest that there could be over a million. Despite their importance and high species diversity, little is known about their phylogeny due to technical issues that hinder the reconstruction of their relationships. However, owing to a new technique that allows for DNA to be amplified from a single isolated cell, it is possible to explore diatom relationships with extensive taxonomic sampling. This thesis aims to demonstrate that the integration of molecular data and morphological characters can provide a new paradigm for future phylogenetic and taxonomic studies of diatoms, especially among closely related and taxonomically complex groups. To achieve this, I examined common species from two naviculoid diatom genera, Frustulia and Navicula using sequence data from three molecular markers (rbcL, atpB, 18S), traditional and fine-scale morphological characters, and frustule shape. The molecular markers rbcL and atpB evolved at a similar rate and performed well at reconstructing species-level phylogenies, whereas 18S was more conserved and best used for resolving relationships at higher taxonomic levels. Hidden diversity was uncovered in what have traditionally been thought as well-circumscribed taxa, and three new species were described. The methods used here show promise for the future of diatom systematics.

Diatom algae, abundantly found in the ocean, has hierarchical micro- and nanopores which inspired lots of metamaterial designs including dielectric metasurfaces. The conventional approach taken in the metamaterial design process is to generate the corresponding optical spectrum by utilizing physics-based simulation software. Although this approach provides high accuracy, the downside is that it is time-consuming and there are also constraints. By setting design parameters and the structure of the material, the optical response could be easily achieved. However, this approach is not able to deal with the inverse problem as simple as in the forward problem. In this study, a deep learning model that is capable of solving both the forward and the inverse problem of a diatom-inspired metamaterial design was developed and it was further verified experimentally. This method serves as an alternative way for the traditional metamaterial design process which greatly saves time and also presents functionality that simulation does not provide. To investigate the feasibility of this method, different input training datasets were examined, and several strategies were taken to improve the model performance. Though with the success in some cases, effort is still needed to employ the technique in a broader aspect. / 2024-01-15T00:00:00Z

The light manipulation performance of plasmonic structures has been widely studied at wavelengths spanning from microwave and terahertz radiation to infrared and visible light. Plasmonic nanostructures with designed sizes and geometries displays strong enhancement and confinement of electromagnetic fields that known for tailoring spectra. By exploiting these properties, color printing at the diffraction limit in the visible light regime has recently been demonstrated. Diatoms, one kind of unicellular microalgae, widely exist in aquatic environments and are well-known for their light-manipulating properties. The abundant biologically evolved micro- and nano-pores enable diatom frustules to be remarkably studied achieving superior optical performances in sensing and solar cell applications. In this work, the diatom-inspired metamaterials for subwavelength plasmonic color printing have been investigated. The nanoporous structures on diatom frustules are examined to develop both Hierarchical Diatom-inspired Nanopattern (HDN) and Misaligned Hierarchical Diatom-inspired Nanopattern (MHDN) with different structural parameters on the metamaterial design. Using finite-element simulations, the practical metal-insulator-metal (MIM) configurations are screened, and electric field distribution is evaluated to uncover the physical mechanisms responsible for color printing. Nanofabrication and optical measurement are conducted as complementary validation for simulation analysis and present the practicality for application. / 2024-01-15T00:00:00Z