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Thesis (Ph. D.)--University of Washington, 1996. / Vita. Includes bibliographical references (leaves [122]-141).

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: This thesis investigates questions surrounding the role that iron-rich colloids (nominally sized between 0.02 μm and 0.2 μm) and particulates (>0.2-0.45 μm) play in the context of the greater iron biogeochemical cycle. To this end, this study complements a review of reported size-fractionated iron (Fe) measurements with chemical and mineralogical data derived from synchrotron-based xray measurements. From an extensive literature review, the global surface ocean colloidal iron (cFe) pool is found to be highly dynamic, frequently exhibiting seasonal trends and nutrient-like behaviour. Spatial variability in surface ocean colloidal iron concentration is primarily a function of total iron supply, although the concentration and strength of iron-binding ligands, and inorganic thermodynamic constraints are additional influential factors. The size-fractionated study of colloidal Fe has rendered considerable evidence pointing towards direct or indirect biological utilization of this cFe pool; however, a more complete understanding of cFe-biological interaction necessarily requires better knowledge of cFe chemistry and mineralogy. To address these issues, this thesis documents the development of a novel x-ray microscopy and spectroscopy technique for determining the Fe speciation of individual Fe-rich particles under environmental conditions. Variations in the peak splitting in iron L3-edge XANES (X-ray Absorption Near-Edge Structure) spectra reflect changes in the local coordination environment surrounding the metal centre. Specifically, the energy splitting ( ΔeV) and intensity ratio of the split peaks at the L3-edge vary as a function of the Fe valence state, the number and chemistry of coordinating ligands and polyhedral distortion effects; and combinations of the two parameters are found to be characteristic of individual Fe minerals. To understand Fe speciation, the Δ eV versus intensity ratio plot was successfully applied to a variety of environmental Fe particles (greater than 20 nm diameter) collected from two ocean basins; the Southern Ocean and the south western Pacific Ocean. Speciation differences in Fe particles collected from the Southern Ocean show distinct compositional trends between the coasts of South Africa and Antarctica, with different Fe pools associated with the different oceanographic frontal zones. Despite the oxygenated nature of the seawater sampled, the presence of significant particle-hosted Fe(II) was observed in both the Southern Ocean at high latitudes, and at sampling sites proximal to the Kermadec Ridge in the Pacific Ocean. Ferrous iron particles at the latter study area were shown to be strongly associated with carbon functional groups, notably alcohol and carboxamine moieties. These findings, relating to particle chemical differences and associations with organic matter, have significant implications for our understanding of particle behaviour, their surface interactions and the role that they play in primary productivity and global elemental cycles. / AFRIKAANSE OPSOMMING: Hierdie tesis ondersoek kwessies met betrekking tot die rol wat ysterryke kolloïede (van nominale groottes tussen 0.02 μm en 0.2 μm) en partikels (>0.2-0.45 μm) in die konteks van die groter ysterbiogeochemiese siklus speel. Vir hierdie doel bou die studie voort op ’n oorsig van aangemelde grootte-gefraksioneerde yster- (Fe-)metings met behulp van chemiese en mineralogiese data wat uit sinchrotrongebaseerde x-straalmetings verkry is. Na aanleiding van ’n uitvoerige literatuurstudie, blyk die globale poel kolloïdale yster (cFe) op die see-oppervlak hoogs dinamies te wees en toon dit dikwels seisoenale tendense en voedingstofagtige gedrag. Ruimtelike veranderlikheid in die cFekonsentrasie op die see-oppervlak is hoofsaaklik ’n funksie van totale ystervoorsiening, hoewel die konsentrasie en sterkte van ysterbindende ligande sowel as anorganiese termodinamiese beperkings ook ’n invloed kan hê. Die grootte-gefraksioneerde studie van kolloïdale Fe het beduidende bewyse opgelewer wat op die direkte of indirekte biologiese benutting van hierdie cFe-poel dui. Tog verg ’n vollediger begrip van cFe- biologiese interaksie noodwendig meer kennis van die chemie en mineralogie van cFe. Om hierdie kwessies te ondersoek, dokumenteer hierdie tesis die ontwikkeling van ’n innoverende X-straalmikroskopie- en X-straalspektroskopietegniek om die Fe-soortvorming van individuele Feryke partikels in omgewingsomstandighede te bepaal. Variasies in die pieksplitsing van yster-L3 rand-XANES- (“X-ray absorption near-edge structure”-)spektra weerspieël veranderlikheid in die lokale koördinasie-omgewing rondom die metaalkern. In die besonder wissel die energiesplitsing ( eV) en intensiteitsverhouding van die splitsingspieke by die L3-rand na gelang van die Fevalensietoestand, die getal en chemie van koördinasie-ligande, en poliëdriese distorsie-effekte, en kombinasies van die twee parameters blyk kenmerkend van individuele Fe-minerale te wees. Om Fe-soortvorming te verstaan, is die stipping van Δ eV versus intensiteitsverhouding suksesvol toegepas op ’n verskeidenheid Fe-omgewingspartikels (groter as 20 nm in deursnee) wat uit twee oseaankomme – die Suidelike Yssee en die suidwestelike Stille Oseaan – bekom is. Soortverskille in Fe-partikels wat uit die Suidelike Yssee bekom is, toon kenmerkende samestellingspatrone tussen die kus van Suid-Afrika en Antarktika, en verskillende Fe-poele word met die verskillende oseanografiese frontsones verbind. Ondanks die suurstofhoudende aard van die seewatermonsters, is beduidende Fe(II) in partikels opgemerk in die Suidelike Yssee by hoë breedteliggings sowel as op studieterreine naby die Kermadec-rif in die Stille Oseaan. Ysterhoudende partikels van laasgenoemde studieterrein het ’n sterk verband met koolstof- funksionele groepe, veral alkohol en karboksamien, getoon. Hierdie bevindinge met betrekking tot die chemiese verskille tussen partikels en die verband met organiese materie het beduidende implikasies vir ons begrip van partikelgedrag, die oppervlak-interaksies van partikels, en die rol wat dit in primêre produktiwiteit en globale elementsiklusse speel.

Orientador: Lucia Maria Carareto Alves / Coorientador: Alessandro de Mello Varani / Banca: Hugo Miguel Preto de Morais Sarmento / Banca: Rodrigo Matheus Pereira / Banca: Everlon Cid Rigobelo / Banca: Silvana Pompéia do Val de Moraes / Resumo: O composto orgânico produzido a partir de carcaças, resíduos animais e vegetais é uma alternativa viável para a substituição total ou parcial dos fertilizantes minerais utilizados na atualidade. No processo de compostagem participam diferentes populações microbianas, e com isso o composto torna-se um sistema rico para utilização como fertilizante no solo, complementando assim as necessidades nutricionais e microbianas do meio ambiente. Entretanto, há poucos trabalhos envolvendo análise da diversidade bacteriana em solos sob uso de composto orgânico feito a partir de carcaças, e também pouco se conhece sobre o impacto ambiental do uso agrícola de composto orgânico na qualidade da água. Existe também a questão se há influência da água utilizada para irrigação na qualidade do solo. O objetivo central desse trabalho foi analisar a diversidade bacteriana e perfil funcional de um solo de horta e da água de um córrego utilizada para irrigação. E como objetivo secundário, através do isolamento de bactérias da água verificar o potencial biotecnológico de produção e uso de exopolissacarídeo como bioemulsificante de óleo e hidrocarbonetos. As amostras de solo e água utilizadas nesse trabalho foram coletadas na área do departamento rural da Fundação Parque Zoológico de São Paulo, em setembro de 2014. Todo material coletado foi transportado até o Laboratório de Bioquímica de Micro-organismos e de Plantas, onde realizou-se a extração de DNA total e sequenciamento através de tecnologia Ion ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The organic compost produced from carcasses, animal and vegetable waste is a viable alternative to full or partial replacement of mineral fertilizers used nowadays. In the composting process there are involved different microbial populations, and the compost becomes a rich system for use as a fertilizer in the soil, thereby supplementing the nutritional and microbial requirements of the medium. However, there are few studies involving the analysis of bacterial diversity in soil under use of organic compost made from carcasses, and also little is known about the environmental impact of agricultural use of organic compost in water quality. Furthermore, there is also the question of whether there is influence of the water used for irrigation on soil quality. Because of these questions, the central objective of this study was to analyze the bacterial diversity and functional profile of a soil from vegetable garden and freshwater used for irrigation from a local stream. As a secondary objective, we aimed to verify the production and biotechnology potential of a bacterial exopolysaccharide as oil and hydrocarbons bioemulsifier. Soil and freshwater samples used in this study were collected at rural department of the Zoo Foundation Park of São Paulo, in September 2014. All material collected was transported to the Laboratório de Bioquímica de Micro-organismos e de Plantas where we proceeded with the total DNA extraction experiments, sequencing through Ion Proton technology (Life Technologies), bacterial isolation, production and application of exopolysaccharide as bioemulsifier. By analyzing the metagenomic DNA it was observed that both freshwater and soil were plenty of bacterial communities normally found in agricultural areas under influence of organic amendments. Through the analysis of genes related to biogeochemical cycles, it was found abundance ... (Complete abstract click electronic access below) / Doutor

Sphingopyxis (formerly Sphingomonas) alaskensis, a numerically abundant species isolated from Alaskan waters and the North Sea represents one of the only pure cultures of a typical oligotrophic ultramicrobacterium isolated from the marine environment. In this study, physiological and molecular characterization of an extinction dilution isolate from the North Pacific indicate that it is a strain of Sphingopyxis alaskenis, extending the known geographical distribution of this strain and affirming its importance as a model marine oligotroph. Given the importance of open ocean systems in climatic processes, it is clearly important to understand the physiology and underlying molecular biology of abundant species, such as S. alaskensis, and to define their role in biogeochemical processes. S. alaskensis is thought to proliferate by growing slowly on limited concentrations of substrates thereby avoiding outright starvation. In order to mimic environmental conditions chemostat culture was used to study the physiology of this model oligotroph in response to slow growth and nutrient limitation. It was found that the extent of nutrient limitation and starvation has fundamentally different consequences for the physiology of oligotrophic ultramicrobacteria compared with well-studied copiotrophic bacteria (Vibrio angustum S14 and Escherichia coli). For example, growth rate played a critical role in hydrogen peroxide resistance of S. alaskensis with slowly growing cells being 10, 000 times more resistant than fast growing cells. In contrast, the responses of V. angustum and E. coli to nutrient availability differed in that starved cells were more resistant than growing cells, regardless of growth rate. In order to examine molecular basis of the response to general nutrient limitation, starvation and oxidative stress in S. alaskensis we used proteomics to define differences in protein profiles of chemostat-grown cultures at various levels of nutrient limitation. High-resolution two-dimensional electrophoresis (2DE) methods were developed and 2DE protein maps were used to define proteins regulated by the level of nutrient limitation. A number of these proteins were identified with the aid of mass spectrometry and cross-species database matching. The identified proteins are involved in fundamental cellular processes including protein synthesis, protein folding, energy generation and electron transport, providing an important step in discovering the molecular basis of oligotrophy in this model organism.

Thalassiosira oceanica, a marine centric diatom, possesses an extracellular reductase that reduces iron (Fe(III)) bound to organic complexes as part of a high-affinity Fe transport mechanism. A number of Fe(III) organic complexes are reduced, including siderophores---effective Fe chelates produced by microorganims in response to Fe stress. Reduction rates are inversely related to the relative stability constants of the oxidized and reduced Fe chelates (log Kox/Kred), and vary by a factor of 2.4 in accordance with theoretical predictions. Under Fe-limiting conditions, reduction rates increase and the ability of T. oceanica to transport Fe from siderophores is enhanced. Iron bound to the siderophore desferrioxamine B (DFB) is reduced 2 times faster than it is taken up, suggesting that the reductase is well coupled to the Fe transporter, and can provide all the inorganic Fe to account for the measured Fe uptake rates in the presence of excess DFB. The efficacy of the reductase in providing inorganic Fe for uptake and growth is ultimately dependent on the relative concentrations of excess ligands in solution and cell surface Fe transporters competing for inorganic Fe. The rates of Fe reduction and uptake are twice as fast in cells grown in NO3- compared to those grown in NH 4+, suggesting a link with cellular N metabolism and with NO3- utilization in particular. Enhanced Fe reductase activity in NO3--grown cells enables them to maintain a 1.6-fold higher cellular Fe concentration under low Fe conditions. / Experiments conducted in the subarctic Pacific, an Fe-limited oceanic region, demonstrated that even indigenous plankton (both prokaryotic and eukaryotic plankton) have the ability to acquire Fe bound to strong organic chelates. Large phytoplankton species (>3 mum) reduce Fe bound to siderophores extracellularly. Because the predominant form of dissolved Fe in the sea is bound to strong organic complexes, a reductive mechanism as described here may be a critical step in Fe acquisition by phytoplankton.

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I examined the distribution of stable isotope ratios of nitrogen $( delta sp{15}$N) and carbon $( delta sp{13}$C) in fish and aquatic invertebrates. Animals are enriched in $ delta sp{15}$N compared to their diet and I hypothesized that among-lake variation in the $ delta sp{15}$N of a top predator should reflect variation in the length of the food chain leading to it. A comparative study of a biomagnifying contaminant, mercury, confirmed that the presence or absence of certain key organisms such as pelagic forage fish and the crustacean Mysis relicta determined among-lake variation in mercury in lake trout, a top predator in the lakes. Mercury levels from the longest food chains where pelagic forage fish and Mysis were present were higher than those from the shortest food chains where these last two components were missing. This biogeographic variation in food chain length was correlated with variation in the $ delta sp{15}$N of trout. The use of $ delta sp{15}$N as a continuous, integrative measure of trophic position was further supported by its correlation to mercury in lake trout. However, such cross-system comparisons in $ delta sp{15}$N can be complicated by differences in $ delta sp{15}$N at the base of the food chain. Using large primary consumers (unionid mussels) as bio-indicators, I showed that $ delta sp{15}$N increases markedly with the human population in the lake watershed, an effect of the high $ delta sp{15}$N of human sewage. Correcting for this baseline variation in $ delta sp{15}$N, I reported that food chains leading up to nearshore fish species varied by about only one trophic level among the 35 lakes studied. A study of the $ delta sp{15}$N of coral reef and intertidal organisms collected along the coast of the the Carribean island of Barbados extended these patterns observed in lakes to coastal systems: baseline variation in $ delta sp{15}$N was related to human density on the adjacent watershed and within-site variation $ delta sp{15}$N

[Truncated abstract] Estimating internal biogeochemical fluxes is essential to the understanding of the dynamic of aquatic ecosystems. Different ecological approaches have been used to gain insight into the internal cycling, but success has been limited. A critical point is the identification of the characteristic scales of patterns and the underlying processes affecting the behaviour of biological and chemical species. Failing to capture these scales leads to misinterpretation of field and numerical data. In this study, key aspects in the design of ecological surveys are identified to ensure that the internal biogeochemical processes are well represented. In the first part of this thesis, a 1D reaction-diffusion-advection equation is used to investigate the formation of patterns and relevant time and spatial scales. This is used to define an approach for the determination of a critical domain size that allows differentiation of the role of local and internal cycling from advective fluxes across the open boundaries in a shallow coastal ecosystem. By using a 3D numerical model, in conjunction with an extensive field data set, it is shown that domain sizes must be larger than this critical value in order to capture the patterns generated within the system. For smaller domains, transport processes control the evolution of the system across the boundaries misleading the interpretation of the internal ecological dynamics. The study of the influence of boundary fluxes on ecological patchiness was motivated by the need to define the size of the domain necessary for the assessment of the impact of a sewage outflow on a coastal regime. The quantification of biogeochemical processes has proven to be difficult to achieve especially under conditions of high spatial and temporal hydrodynamic and biogeochemical variability. In the second part of this thesis, a Lagrangian experimental design is employed to estimate biogeochemical rate coefficients in situ. A set of four drogues and a cross-transect sampling design is used to capture the patchy distribution of phytoplankton and nutrient species, and high transport and mixing rates. ... Total chlorophyll from both models shows similar behavior when the variability in the 3D model, expressed as Chlamax/Chlamin, is low. When Chlamax/Chlamin is high, the difference between the biomass predicted by the two models reaches 30% due to the generation of localised patches. Comparison of the 1D and 3D results highlights the need of using models that are able to resolve the spatial complexity to some extent, as the use of averaged properties may produce misleading results. This is especially important in the presence of patches with differential physiological and biogeochemical characteristics, and nonlinear processes, in which case biomass average is not necessarily linearly related to the averaged environment.

Thesis (Ph. D.)--Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2007. / "September 2007". "Joint Program in Oceanography/Applied Ocean Science and Engineering"--Cover. Title from Web page (viewed on Mar. 24, 2008). Includes bibliographical references (p. 215-225).