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Living systems possess seemingly bottomless complexity. Attempts to parse the details of one cellular process from all other concurrent processes are challenging, if not daunting undertakings. The apparent depth of this problem, as it pertains to biomineralization, is related to the small number of existing studies focused on the development of a mechanism-based understanding of intracellular mineralization processes. Molecular biologists and geneticists have only begun to turn their attention towards identification and characterization of molecules involved in regulating and controlling biomineral formation. With this new knowledge, a number of new and exciting research opportunities are currently awaiting development upon a barren landscape. Silica biomineralization is one of these emerging frontiers. As new information about the chemical and structural nature of the macromolecules involved in biosilicification is revealed, the means these species employ to control the temporal and spatial onset of silica deposition in vivo become available for exploration. The first chapter of this dissertation outlines those aspects of silicate metabolism that are directly relevant to the controlled biomineralization of silica in eukaryotic organisms and identifies pervasive and unanswered questions surrounding biosilica formation. Particular attention is paid to the diatoms, which are the most abundant, and extensively investigated silica-mineralizing organisms in modern seas. The extent, and mechanism through which specific organic moieties work individually or in concert to direct mineral formation at biological interfaces is a central concern of modern biomineralization research. Chapter two addresses this forefront issue for silica mineralizing systems, and reports the results of an experimental investigation designed to measure the effects of individual surface-bound organic functional groups on the rate of surface-directed silica nucleation. Chapter three discusses an additional aspect of this research aimed at investigating the reactivity of nanoparticulate biogenic silica produced by marine phytoplankton and terrestrial plants in natural environments. Density Functional Theory and ab initio molecular orbital calculations are employed to explore potential mechanisms underlying the catalytic activity of divalent metal cations during the hydrolysis of Si – O bonded networks. / Ph. D.

The composition of a community and the environmental conditions in which they exist fundamentally influence productivity and responses of systems to change. In the Northern Gulf of Mexico (NGoM), the relationships between nutrients, salinity, and phytoplankton populations are complex and have been changing over time. This work focuses on describing and analyzing: 1) a case study of diversity and recommendations for change within an academic institution; 2) spatial and temporal trends in surface dissolved inorganic nitrogen (DIN) and phosphorus (DIP) in the NGoM over 35 years; 3) nutrient addition experiments (NAEs) to determine prevailing NGoM surface slope region nutrient limitation; and 4) NGoM surface continental slope phytoplankton community composition and dynamics. Over time, academic institutions have not made progress toward increasing diversity, equity, and inclusion (DEI) in the geosciences. The first chapter of this work serves as a roadmap for other institutions to make progress toward ingraining DEI frameworks into the foundations of our institutional systems. Toward explaining trends in nutrients from 1985 to 2019, I compiled the largest data set of NGoM surface dissolved nutrient concentrations to date and analyzed it to delineate spatiotemporal trends and identify potential drivers of nutrient change. DIP concentrations in both the Mississippi-Atchafalaya River system (MAR) and in the NGoM increased over time, but the increase of NGoM DIP exceeded the DIP loads coming from only the MAR, suggesting additional sources of P to the NGoM. To determine nutrient controls on surface slope NGoM phytoplankton growth and populations, we calculated growth rates and pigment composition using redundancy analyses and a variety of nutrient limitation criteria for each nutrient amendment over 48 hours. Nutrient limitation criteria concluded predominant NP limitation in the NGoM, though single N and P limitation and nutrient replete conditions were also present. In individual NAEs with N and NP amendments, phytoplankton pigment changes were driven by the growth of diatoms and Synechococcus (Syn). Though release from nutrient limitation stimulated responses in some phytoplankton groups, nutrient limitation of phytoplankton growth could not fully be predicted by the criteria and response thresholds evaluated in this study. Additionally, an analysis of environmental variables and phytoplankton pigments was conducted for the surface slope region of the NGoM to determine how phytoplankton community composition varies spatially with the influence of the MAR plume using group-specific chlorophyll a (Chl-a) calculations, bivariate linear regression, multivariate redundancy analysis, and cluster analysis. The largest proportion of Chl-a occurred in the nano/microphytoplankton group, followed by Syn, with both peaking at the high and low ends of the salinity gradient. Redundancy and cluster analyses showed that nutrients and salinity alone cannot predict or subdivide phytoplankton community composition; however, with the addition of pigments, we can characterize specific regions based on shared environmental variables (i.e., low salinity, high biomass) and pigment abundance. In sum, this work produced a straightforward and reproducible guide to leading a DEI task force, the largest NGoM surface nutrient data set to date, and characterizations of NGoM continental slope nutrient limitation and pigment composition and their relation to environmental variables.

The Belgian Coastal Zone (BCZ) in the Southern Bight of the North Sea is a highly dynamic and optically complex area. This is due to high non-algal particles (NAP) and coloured dissolved organic matter (CDOM) content which in spring adds together with undesirable blooms of the haptophyte Phaeocystis globosa. There is a need for improving the algorithms for chlorophyll a (chl a) retrieval in these highly turbid waters and for developing algorithms for species detection in order to attempt to create an early warning bloom system. This information will contribute to the knowledge of the extent and magnitude of the P. globosa bloom in Belgian waters. In this study, pure cultures of the main taxa present in the BCZ, diatoms and P. globosa, were combined with field measurements of light absorption of total particles, phytoplankton and dissolved material, pigment determination and phytoplankton counts to address the main objectives. Sampling was performed during 8 cruises covering winter, spring, summer and late summer, and along nearshore-offshore gradients from 2003 to 2006. The area is characterised by a high spatio-temporal variability of IOPs due to the high dynamics of the area in terms of currents, salinity gradients and biological production. During spring the presence of P. globosa modulates the IOPs across all the area, the particle absorption is significantly higher than summer and there is no significant coast-offshore variability for phytoplankton and CDOM. The design of chl a retrieval algorithms assumes negligible absorption of NAP and CDOM in the near infrared (NIR) and the use of a fixed value of specific phytoplankton absorption. It is shown that neglecting the NAP and CDOM absorption in the NIR will have a significant overestimation impact in retrieval of chl a. On the other hand, the specific phytoplankton absorption was found to be highly variable (0.015 „b 0.011 m2 mg chl a-1). Both results will affect directly the retrieved chl a. The spatial variability of CDOM was significant varying between 0.20-1.31 m-1 in the marine area and between 1.81-4.29 m-1 in the Scheldt estuary. CDOM was found to be related to salinity with conservative mixing within the Scheldt estuary and during some seasons in the BCZ, however deviations from conservative mixing suggest other inputs to the CDOM pool. Analyses of the spectral slope of the CDOM absorption curve revealed two main CDOM pools in the area, an allochthonous one delivered by the Scheldt estuary and an autochthonous one associated with the phytoplankton spring bloom decomposition. Algorithms for CDOM retrieval will be affected if the variability in the relation between CDOM and salinity is not taken into account. The optical characterisation of diatoms and P. globosa from the BCZ in pure cultures revealed that the main differences in the phytoplankton absorption spectra were found at 467 and 500 nm corresponding to the absorption of the pigments chlorophyll c3 (chl c3) characteristic of P. globosa and fucoxanthin, respectively. Accordingly, both the absorption at 467 nm and the ratio 500/467 nm were successfully used to discriminate the two taxa in cultures and field samples. This latter indicator was not preserved in the reflectance signal due to degradation of the signal when passing from absorption to reflectance, and thus could not be used for algorithm development. The spectral feature at 467 nm was later used as the basis for the development of a flag-type algorithm to detect chl c3 using either absorption or water-leaving reflectance data. Also, the correlation between the algorithm¡¦s retrieved chl c3 and P. globosa cell number allowed the quantification of the bloom. The main findings of this thesis highlight the importance of the IOPs characterisation for the improvement and development of ocean colour retrieval algorithms in these highly complex waters.

Present models of Holocene estuary evolution are driven largely by changes in relative sea-level (RSL) with little reference to long-term changes in fluvial regime and regional climate. Recent US studies of estuarine sequences have shown that decadal-centennial scale fluctuations in river discharge and freshwater inflow can be inferred by changes in estuarine palaeosalinity and that the timing of these events reflect changes in regional precipitation. It is therefore becoming apparent that estuarine sequences may hold an archive of mid-late Holocene climate change information, as well as being recorders of RSL change. The principal aim of this study is to produce a palaeosalinity-based climate record for southern England during the late Holocene, based on changes in climate-driven freshwater influx into the estuarine environment. The late Holocene palaeosalinity record of the inner Taw Estuary will be reconstructed using diatom salinity index as a proxy for salinity. Nine periods of below-average or above-average palaeosalinity have been recognised in the Taw Estuary since 300 cal.yr.BC. Four intervals of high river discharge are identified at 520-780, 850-1030, 1215-1315, and 1420-1900 cal.yr.AD. Five intervals of low river discharge are identified at 300-520, 780-850, 1030-1215, 1315-1420, and 1900-2000 cal.yr.AD. This shows that there has been significant climatic variation in southern Britain since c.300 cal.yr.AD, with climatic shifts evident in the estuarine record. In order to validate this record, the fluvial geomorphic history of the lower Taw valley was also investigated. There is a strong correspondence between the dry and wet climatic periods identified in the estuary and the geomorphic fluvial history and flood record of the lower Taw valley. Comparisons with other proxy climate records in the UK and Europe show a high degree of correspondence with the Taw Estuary palaeosalinity-based climate record. As the inner estuary environment will also be influenced by RSL change during the late Holocene, RSL change since c.6600 cal.yr.BP was successfully reconstructed in the Taw Estuary, with eleven new validated SLIPs providing evidence of former MSL. The magnitude and rates of RSL rise in north Devon are compared with other RSL records in southern Britain, suggesting that the isostatic history is similar to other areas bordering the Bristol Channel and with the central south coast of England. Fluctuations in palaeosalinity in the late Holocene are seen to be mainly controlled by centennial-scale changes in climate-driven river discharge, rather than RSL change.

Substrate specificity of epiphytic communities of diatoms (Bacillariophyceae) and desmids (Desmidiales) Bc. Petra Mutinová Master's thesis, Prague, 2015 Abstract It has been always assumed, and frequently reported, that host plants, as biologically active substrates, should have a direct influence on associated epiphyton. However, some studies favoured the neutral substrate hypothesis. Thus the relationship between host plant and epiphytic community remained unresolved. This Master's thesis focused on the basal question that numerous previous studies overlooked. Is there any significant influence of host plant on freshwater algal epiphyton in comparison to the influence of other factors, e.g. site and environmental conditions? In addition, substrate specificity of individual algal taxa was investigated. The research concerned several types of natural plant substrates at several water bodies in the Czech Republic, which provided a more accurate and general insight in the ecology of microphytobenthos. The results have demonstrated that site was the main factor affecting epiphytic community structure, followed by mild, but still noticeable, effect of environmental conditions (pH and conductivity). In contrary, host plant had almost no influence and very few algal species were found to be host specific....

The determination of diatom species is mostly based on morphology of a silicified cell wall. It is complicated by the fact of cell diminution during the vegetative phase of the life cycle, which is conected with shape changes and loss of some taxonomically importat characters. Even though the diminution during the life cycle is generally known phenomeon, there is a lack of studies on this theme. In this masters thesis, four monoclonal populations of model pennate diatom strains were used in order to study shape dynamics during the life cycle. The strains were cultivated for almost three years and parts of the cultures with a different size stages were fixed in permanent preparations. The digital photographs of the cells were used as a material for the geometric morphometrics analyses. The study revealed high contribution of significant allometric changes to an overall shape variability. During the vegetative phase of the life cycle, disparity of the cells increases and complexity of the cells decreases. The contribution of symetric variability to an overall shape variability is more than eighty percent. Phenotypic plasticity in a monoclonal populations is an interesting finding from an evolutionary point of view. It may indicate constraints caused by the silica cell wall. During the size diminution...

A fixação de N2 é uma fonte importante de nitrogênio novo nos ciclos biogeoquímicos, realizado potencialmente por cianobactérias diazotróficas, principalmente em condições de limitação de nitrogênio. O canal de São Sebastião (CSS) é reconhecidamente meso-oligotrófico, porém, eventos episódicos de precipitação podem alterar as concentrações de nutrientes locais interferindo na ocorrência de diazotróficas. Este trabalho investigou o efeito do aumento da pluviosidade na ocorrência e coexistência de diazotróficas no CSS e na baía do Araçá (BA), em 9 cenários distintos. As diazotróficas Trichodesmium spp. e Richelia intracellularis ocorreram após o aumento da pluviosidade nos dois pontos, não co-existindo em dois eventos. R. intracellularis ocorreu somente em endossimbiose com diatomáceas do gênero Hemiaulus, com predomínio em H. membranaceus. Os ventos de SW no CSS indicaram relações diretas na ocorrência das diazotróficas, sugerindo advecção de células provindas de outros locais. A temperatura e o fosfato apresentaram relações significativas com a ocorrência das diazotróficas. As densidades de diazotróficas e da comunidade fitoplanctônica foram maiores na BA em todos os eventos, assim como as concentrações de clorofila-a e nutrientes, ressaltando a importância da interação das águas da BA com o CSS. / The biological nitrogen fixation adds new nitrogen into the biogeochemical cycle. This process is attributed to diazothrophic cyanobacteria, which are known to occur in environments with nitrogen limitation. Although the São Sebastião Channel (CSS) is a meso-oligothrophic environment, local rain can affect nutrients concentrations, hence the occurrence of diazothrophic species. This work addressed how the increase in the precipitation rate alters the occurrence and co-existence of diazothrophic cyanobacteria in nine scenarios in the CSS and Araçá Bay (BA). The diazothrophic species Trichodesmium spp. and Richelia intracellularis occurred after an increase in rainfall, co-occurring in 7 of the 9 scenarios. Richelia intracellularis was always associated symbiotically with Hemiaulus diatoms, specially H. membranaceus. The occurrence of diazothrophic species was highly correlated to intense SW winds, suggesting the allochthonous input of cells in the CSS. The diazothrophic species occurrence was also associated with variations in temperature and phosphate concentration. The abundance of both diazothrophic species and phytoplankton community were higher in the BA in every scenario. The nutrients and chlorophyll-a concentrations were higher in the BA, highlighting the importance of water transport between BA and CSS.

Um estudo interdisciplinar, envolvendo análises de fácies, elementares e isotópicas de carbono e nitrogênio, palinologia e diatomáceas, teve como objetivo reconstruir a dinâmica da vegetação, na Ilha do Marajó, com inferências climáticas. Testemunhos sedimentares foram coletados em dois pontos diferentes na porção leste da Ilha, um no manguezal da Praia do Pesqueiro, outro no Lago São Luís, à ~35Km de distância a oeste e a ~8Km do litoral. Neste local, entre 7521 7433 anos cal AP e ~3.100 anos cal AP, a sedimentação é de argila maciça e laminação plano/paralela, com valores de C/N entre 45 e 15 e \'delta\'15N entre 1,34%o e 5,08%o, que indicam mistura de material orgânico terrestre e fitoplanctônico e a relação C/N e \'delta\'13C material com influência marinha. A concentração de Rhizophora chega a 94,4% do total dos grãos e as diatomáceas marinhas e salobras de Cyclotella striata, Cymatotheca weiisflogii e Paralia sulcata são as mais representativas. Todas essas informações indicam a presença de um manguezal onde atualmente se encontra o Lago São Luis. Entre ~3100 anos cal AP e o presente, as fácies de argila maciça, com os valores de C/N entre 18 e 24 e \'delta\'15N de 1,7 a 6,04%o, que indicam mistura de plantas terrestres com material de algas na matéria orgânica sedimentar, e os valores de \'delta\'13C de -22 a -25%o, que indicam mistura de plantas C3 (espécies arbóreas e herbáceas) e C4 (Poaceae), sugerem significativa mudança ambiental. A palinologia registra uma redução na concentração de Rhizophora e aumento das espécies florestais, como Fabaceae, Melastomataceae/Combretaceae e Myrtaceae e a presença das diatomáceas de água doce, de água doce que suportam condições salobras e de mangue, como Brachysira serians, Frustulia Krammeri, Eunotia sp e Surirella sp. Todas essas informações indicam a formação do lago e a modificação da vegetação no seu entorno, similar a atual. Na Praia do Pesqueiro, entre 1739 1567 e ~614 552 anos cal AP, as fácies de areia com estratificação plano/paralela indicam um ambiente de ante-praia. Valores de \'delta\'13C mais enriquecidos (-25 e -26%o), em relação ao período mais recente (parte superfícial do testemunho), sugerem influência marinha e os bioindicadores estiveram ausentes. De ~614 552 até ~180 160 anos cal AP, fácies de argila maciça indica a presença de uma laguna e valores de C/N de 23,8 e \'delta\'15N de 2,44%o a influência terrestre no material orgânico sedimentar. Palinomorfos de floresta e mangue estão presentes, com concentração de 8,6% e 88,2%, respectivamente, aspectos que sugerem a redução do nível relativo do mar (NRM) e expansão da vegetação de mangue e floresta, que ocupam a área de praia. A preservação de diatomáceas marinhas é registrada pela presença de Coscinodiscus. De ~180 160 anos cal AP até o presente, o manguezal se estabelece, como mostram as fácies de argila laminada e maciça, valores de \'delta\'13C mais empobrecidos (-29,34), C/N entre 18,31 e 24,25 e \'delta\'15N de 0,76 e 2,68%o, que indicam influência terrestre com mistura de matéria orgânica fitoplanctônica. A concentração de Rhizophora chega a 89,8% e as diatomáceas de ambiente salobro, como Cyclotella striata, a 85% do total, onde se infere a contínua redução do NRM / An interdisciplinary study involving facies, elementary and isotopic carbon and nitrogen, pollen and diatom analyses, had the objective to reconstruct the vegetation dynamics at Marajó Island, with climatic inferences. Sedimentary cores of up to 2,5meters were collected in two different points at the eastern part of the island, one in the mangrove at Praia do Pesqueiro, and other at São Luís lake, ~35 km far to the western part and ~8 km from the coast. In this place, between 7521 7433 years cal BP and ~3,100 years cal BP, the deposition of massive and laminated plan/parallel clay, with C/N between 45 and 15 and \'delta\'15N from 1.34 to 5.08%o, indicates a mixture of organic terrestrial material with phytoplankton, and the relation C/N and \'delta\'13C reveals the organic material with marine influence. The Rhizophora concentration is about 94.4% and marine and brackish most representative diatoms were Cyclotella striata, Cymatotheca weissflogii and Paralia sulcata. That batch of information indicates the mangrove presence in the site presently occupied by the Lake São Luís. From ~3100 years cal BP to the present, the massive clay structure and the C/N values between 18 and 24 and \'delta\'15N from 1.7 to 6.04%o that indicates a mixture of terrestrial plants and algae material from sedimentary organic matter and \'delta\'13C values from -22 to 25%o, that indicates a mixture of C3 plants (arboreal and herbs) and C4 (Poaceae), suggest significant environmental changes. The pollen record indicate a reduction of Rhizophora concentration and an increase of forest species, like Fabaceae, Melastomataceae/Combretaceae and Myrtaceae, and the presence of freshwater, freshwater that support brackish conditions and mangrove diatoms, like Brachysira serians, Frustulia Krammeri, Eunotia sp and Surirella sp. This set of information indicates the formation and the vegetation around the lake, similar to modern conditions. At Praia do Pesqueiro, between 1739 1567 and ~ 614 552 years cal BP, the plan/ parallel sand structures indicate a foreshore environment. More enriched \'delta\'13C values (between -25 and -26%o), in relation to the more recent period (shallow part of the core), suggests marine influence, and the bioindicators were absent. From ~614 552 until ~180 160 years cal BP, massive clay facies indicates the lagoon presence, and C/N of 23.8 and \'delta\'15N of 2.44%o values indicates terrestrial influence. Forest and mangrove pollen are present, with concentrations around 8.6 and 88.2%, respectively, suggesting the relative sea level (RSL) falling and the expansion of mangrove and forest vegetation to the beach area. The preserved marine diatom is recorded by the Coscinodiscus presence. From ~180 160 years cal BP to the present, the mangrove vegetation is indicated by the massive and laminated clay structures, more depleted \'delta\'13C values (-29.34 %), C/N around 18.31 and 24.25 and \'delta\'15N of 0.76 and 2.68%o, that indicates the high influence of terrestrial environment, with phytoplankton organic matter mixture. The pollen concentration of Rhizophora is about 89.8% and brackish diatoms, as Cyclotella striata, reaches 85%, which permit the inference of decreased marine influence due to the relative sea level fall

Submitted by Mariana Dornelles Vargas (marianadv) on 2015-03-13T19:36:00Z No. of bitstreams: 1 Diatomaceas_paleogeno.pdf: 3760429 bytes, checksum: 863f541ab0b7856dbc11ac95b17232fd (MD5) / Made available in DSpace on 2015-03-13T19:36:00Z (GMT). No. of bitstreams: 1 Diatomaceas_paleogeno.pdf: 3760429 bytes, checksum: 863f541ab0b7856dbc11ac95b17232fd (MD5) Previous issue date: 2011 / Nenhuma / Diatomáceas são excelentes marcadores bioestratigráficos para as Eras Meso-Cenozóicas e são elementos bastante úteis para estudos paleoecológicos e paleoceanográficos. O presente trabalho consiste no estudo das diatomáceas do intervalo Paleógeno do Poço 356 (DSDP Leg 39), o qual foi perfurado na encosta oeste do Alto de São Paulo (margem sudoeste do Platô de São Paulo). As rochas deste local pertencem à porção distal da Bacia de Santos e as rochas deste intervalo Paleógeno pertencem à Formação Marambaia. A despeito das numerosas e diversas diatomáceas presentes, este intervalo foi zonado por seu conteúdo de foraminíferos plantônicos e nanofósseis calcários, mas não por suas diatomáceas. Este estudo procura proporcionar uma definição bioestratigráfica ao conteúdo diatomítico deste intervalo e discutir brevemente suas implicações geológicas e paleontológicas. Em termos taxonômicos, foram encontrados 92 taxa, sendo 29 gêneros, 68 espécies e 19 espécies previamente classificadas como sp., além de 6 formas ontogenéticas variantes de Asterolampra spp. Em termos bioestratigráficos, quatro biozonas de diatomáceas foram identificadas, abrangendo idades do Mesoeoceno ao Neoligoceno. Quatro hiatos foram identificados, dois externos ao intervalo e dois internos. Os resultados aqui alcançados demandam algumas discussões sobre as correlações previamente feitas entre biozonas de foraminíferos plantônicos, nanofósseis calcários e diatomáceas deste intervalo, bem como sobre os padrões sedimentológicos previamente descritos para este intervalo / Diatoms are excellent biostratigraphic markers to Meso-Cenozoic Eras and are a very useful elements to paleoecologic and paleoceanographic studies. The present work is the study of the diatoms from the Paleogene interval of the 356 Hole (DSDP Leg 39) which was drilled at the southwestern slope of Sao Paulo Ridge (Southeastern margin of Sao Paulo Plateau). The rocks of this site belong to distal portions of Santos Basin, and the rocks of this Paleogene interval to the Marambaia Formation. Despite the numerous and diverse diatoms present, this interval was zoned by their planktonic foraminifers and calcareous nannofossils content but not by their diatoms. This study intent provides a biostratigraphical definition to the diatomite content of this interval and briefly discusses their geologic and paleontologic implications. In taxonomic terms, 92 taxa were found with 29 genera, 68 species, 19 species classified as sp., and 6 ontogenetic variants of Asterolampra spp. In biostratigraphic terms, four diatoms biozonas were identified ranging Mesoeocenic to Neoligocenic ages. Four hiatuses were detected, two external to the interval and two internal. The results achieved here require some discussion about the previously correlations made between planktonic foraminifers, calcareous nannofossils and diatoms biozonas of this interval, as well as about the previously sedimentologic patterns described to this interval.