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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.

The production of methyl mercury, an acute neurotoxin which readily accumulates in the tissue of organisms, is a biologically mediated process facilitated by sulfate reducing bacteria in aquatic sediments. In-situ capping is a frequently considered risk management strategy for contaminated sediments. Since placement of an in-situ cap will induce anaerobic conditions that are known to be favorable for the growth of sulfate reducing bacteria, there is justifiable concern that capping could increase mercury methylation in underlying sediments. This research builds an understanding of the effects of in-situ capping on underlying biogeochemical processes and elucidates their importance in controlling methyl mercury production. Laboratory experiments and mathematical models were implemented to simulate mercury methylation in redox conditions likely to be induced by capping using sediment from different environments. Mathematical descriptions of processes known to be involved in methylation were incorporated into the model to quantify the effects of these processes. Observations in both well-mixed slurry conditions and intact sediment columns showed that methyl mercury concentrations are strongly dependent upon biogeochemical conditions. Results from experiments with sediment spanning a range of redox conditions and organic contents suggested that sulfate reduction rates, aqueous speciation, and solid phase partitioning are involved in limiting methylation depending on bulk geochemical characteristics. A model with a mechanistic basis that incorporates the effects of these processes provides a useful means of qualitatively and quantitatively considering their cumulative impact in limiting methyl mercury production. High methyl mercury concentrations observed in some lab experiments suggest that there is reason to be concerned about anoxic conditions induced by capping; however, not all anoxic conditions led to equivalent increases in methyl mercury. Experimental and modeling results suggest that in a high organic environment, in-situ capping may produce conditions which accelerate methylation in (formerly) surficial sediment while in a low organic environment, with an overall lower potential for methylation, capping can be expected to have a less dramatic effect. Over time, two processes will temper capinduced increases in methyl mercury. Increases will only last until sulfide builds up to inhibitory levels in underlying sediment or until organic carbon is depleted and overall bacterial activity slows. By providing a more fundamental understanding of the effects of capping on mercury methylation, the results of this research will aid in identifying situations and conditions in which cap-induced increases in methyl mercury have the potential to limit the effectiveness of the management strategy. / text

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.

The potential for life to control its environment was first suggested by Lovelock (1972). Charlson et al (1987) proposed a role for marine planktonic ecosystems in global climate regulation via the production and ventilation to the atmosphere of dimethylsulphide (DMS), a by-product of phytoplankton metabolism. Once in the atmosphere DMS contributes to the formation of cloud condensation nuclei, and increases the amount and brightness of cloud. This affects the albedo of the planet, reflecting more incident sunlight back into space, and cooling the earth. In common with many other 'hypotheses' regarding complex adaptive systems, the hypothesis proposed by Charlson et al (1987) is not experimentally testable. The production and ventilation to the atmosphere of DMS is the result of complex interactions between biological, chemical and physical processes. Consequently, increasing use is being made of mathematical models that simulate these processes to advance understanding of it (Archer et al. 2002). This study examines one of the fundamental mechanisms proposed by the Charlson et al (1987) hypothesis, that increasing global temperatures will lead to increased ventilation of DMS from the ocean to the atmosphere. The study develops one-dimensional biogeochemical models of DMS production by upper ocean ecosystems, based on the model proposed by Gabric et al. (1993b). The models are examined to elucidate their fundamental mathematical properties, and are subjected to sensitivity analysis to identify important processes and parameters. These investigations identify a simpler model that can reproduce the predictions of the Gabric et al. (1993b) model. Predictions derived from model simulations forced by climatologies of measured physical data are compared to a global database of measurements of sea surface DMS concentrations, and to observed depth profiles of DMS in the upper ocean. These comparisons confirm that all models are in good qualitative agreement with measured data. The fifteen global climate prediction models currently in use around the globe all predict substantial warming effects from the ventilation of anthropogenic carbon dioxide to the atmosphere. A simplified DMS model is calibrated to climatologies of Antarctic chlorophyll and DMS data and reproduces the data with great precision. The calibrated model is applied in global warming scenarios to 'test' the efficacy of the mechanism proposed by the Charlson et al (1987) hypothesis. This simulation provides evidence that the response predicted by the hypothesis is indeed feasible, and that substantial increases (up to 45%) in the ventilation of DMS to the atmosphere could be possible in some circumstances. The results of the modelling study provide impetus for further examination of field data. If couplings between marine biota and atmosphere are feasible, then they may be operating contemporarily, and may be detectable. Atmospheric DMS is oxidised to form aerosols (Miller et al. 2002) that influence the aerosol optical depth of the atmosphere. Archives of remote sensed ocean chlorophyll a concentration and aerosol optical depth are examined for evidence of the biologically mediated couplings. A clear coupling between aeolian dust and marine phytoplankton is evident from this analysis, suggesting that the deposition of dust from the atmosphere is a major factor controlling phytoplankton growth in many parts of the ocean. A second coupling between marine phytoplankton and atmospheric aerosols is also detected. This coupling is apparently not related to dust and is symmetrical about the equator, despite the substantial differences in the atmospheres and oceans of each hemisphere. It is speculated that this coupling may reflect the influence of the ventilation of DMS produced by marine phytoplankton on the atmosphere. This thesis provides new evidence supporting the important role of marine ecosystems in global climate regulation by the production of DMS. This evidence is principally obtained from a biogeochemical modelling approach, but is supported by analyses of empirical data. The concordance of results obtained from different approaches suggests that the contribution of marine ecosystems to global climate regulation is real, important and currently active.

Biogeochemistry has been utilized successfully in Australia as a regional or fellow-up geochemical exploration techniques in the arid terranes of Australia. This Master's study is based on the biogeochemistry approach, which relies on the chemical analysis of plant tissues to obtain information on the geology and geochemistry of the underlying rocks. The project involved the systematic sampling and chemical analysis of plant materials and the supporting soils to establish the suitability of using particular tree species for environmental monitoring and their potential as a sample medium in geochemical exploration in the vicinity of the Temora Gold Mine, NSW, Australia. Working on 168 plant tissues (leaves, twigs and bark) in 54 plants species from 8 families at the three sites of background area, mineralized area and tailings area, and 54 supporting soil samples from three strata of 0-5 cm, 20-30 cm, and 30-40 cm, found that there was a good agreement between soil geochemistry and plant geochemistry on the result of a strong geochemical association between Au and As. The As-Au pattern was suggestive of the presence of the Au-As mineralization. Black cypress pine (Callitris endlicheri) LEAVES show a higher ratio of Asminjn/Aumin in the mineralized area than ASbkg/Aubkg in the background area, up to 7 times. The research finding suggests that the LEAVES of Black cypress pine (Callitris endlicheri) have a potential to be a biogeochemical sample medium as better indicators for Au. Golden wattle (Acacia pycnantha) BARK and Yellow box (E. melliodora) BARK appear to be better indicators for Au but more research is required. The most occurrence of anomalies of As, Au, Sb, Cu and Fe were found in Red box (E. polyanthemos) BARK. Red box (E. polyanthemos) BARK may have the potential to be an Au indicator in the area when Red box (E. polyanthemos) is present. Results on test-tolerant plants show that Eucalyptus species: Red box (E. polyanthemos), Coral gum (E. torquata), and Yellow box (E. melliodora) have a higher rate of uptake trace elements from the tailings soils. Therefore, Eucalyptus family generally adapted to metal-rich soils and can be used as cleaning-up indicators and environmental monitors for the tailings area of metal contaminated soils in the Temora Gold Mine.

This research evaluates the decomposition of leaf litter while in litter traps. More specifically this study asks, ‘Does sugar maple (Acer saccharum Marsh.), American basswood (Tilia Americana L.) and American beech (Fagus grandifolia Ehrh.) leaf litter collected bi-weekly from litter traps undergo a loss of dry mass and nutrient content (C, N, P, K, Ca and Mg) in comparison to freshly abscised leaf litter?’The objective of the initial experiment was to determine if sugar maple, basswood and beech leaf litter collecting in litter traps, while exposed to in-situ conditions, experienced decomposition. Results indicated that sugar maple, basswood and beech leaf litter experienced early stages of decomposition and identified precipitation, freezing temperatures and microbial activity as possible mechanisms for the observed decomposition. It was found that the dry weight of sugar maple and basswood differed significantly (p < 0.05 and p < 0.10, respectively) post- 14-day experiment period as compared to the initial dry weight. Consequently, three experiments were completed to examine the aforementioned variables. Conclusions were based on measured changes in the mass and nutrient (C, N, P, K, Ca and Mg) content of freshly abscised sugar maple, basswood and beech leaf litter under ex-situ conditions. It was found that the dry weight sugar maple and basswood leaf litter exposed to 30 mm, 60 mm and 100 mm of precipitation differed significantly (p < 0.05) as compared to freshly abscised leaf litter. In general, this research affirmed that precipitation and freezing temperature contribute to a change in mass and nutrient content of leaf litter collecting in litter traps. Furthermore, through measurable production of CO2 and Community Level Physiological Profiling it was determined that microbes are present and active on the leaf surface and contribute to the decomposition of leaf litter in litter traps.

Chlorine is an essential building block in the environment and can be found in most places. Chlorine participates in a complex biogeochemical cycle and has been discussed for many years and it is well documented that natural chlorination of organic compound takes place in many parts of the ecosystem. Chlorine can be inorganic (Clin) and organically bound (Clorg). Previous studies have shown that the transformation of Clin to Clorg is connected with the amount of organic matter and the microbial activity in the soil. So far, studies have been focused on forest soil and there is a need for analysing the natural chlorination in other soil types. The aim of this study was to provide chlorination rates in agricultural soil which does not weem to have been done previously. Three common agricultural soils experiencing different agricultural practice and different cropping systems were incubated with Na36Cl at 20o C in a 56 days radiotracer experiment. The results show that a chlorination of 36Clin to 36Clorg in agricultural soil occurred and the Clorg levels increased over time. The chlorination rates ranged from 0,040 to 0,063 μg Cl g dry weight soil-1 d1. This was 10-fold lower than rates previously measured in coniferous forest soil. However, when expressed as μg Cl g dry weight organic carbon-1 d-1, rates in the agricultural soil was only slightly (at the most 2-fold) lower than in coniferous forest. This study contributes with new knowledge of natural chlorination rates in agricultural soil and gives further evidence that the natural chlorination can be connected to the amount of organic matter in the soil.