The sedimentary sulfur cycle is one of the main components of estuarine biogeochemical systems. It is initiated by the oxidation of organic matter via sulfate reducing bacteria which produce hydrogen sulfide (H2S). The S(II) then reacts via both abiotic and biotic pathways to form sulfur with other oxidation states. The three most widely-studied “operationally”–defined components of the sedimentary sulfur system are total reduced (inorganic) sulfur (TRS), acid volatile sulfide (AVS), and dissolved (=filter-passing) sulfide. This study focused on several parameters that are widely held to be important in determining TRS in sediments and the relative proportions of TRS, AVS and dissolved S(II) forms. The formation of iron sulfide minerals requires metabolizable organic matter and SO4 2- to produce S(II) and “reactive”-Fe as a source for the iron in iron sulfide minerals. One of these components is generally the limiting factor in TRS formation (e.g., Berner 1970). Nine different sites from three locations on the Central Texas coast were studied for a variety of parameters including organic matter, sulfate concentrations, sulfate reduction rate, solid “reactive” and dissolved iron, and grain size, as well as TRS, AVS, and ΣH2S. At each site five sediment cores were taken to a depth of 20 cm whenever possible. The cores were sectioned in 2 cm intervals. The porewater was extracted and both solid and dissolved components were analyzed using a variety of methods, including carbon and sulfur coulometry, acid extraction, chromium extraction, and drying the sediment. The results of he analyses showed that the central Texas coast is a widely diverse system. Some sites were very sandy while others were fine-grained. This variety was especially true for the Nueces Bay and Baffin Bay sites. The East Matagorda Bay sites showed more homogeneity in almost all analysis. While the heterogeneity of locations along the Central Texas coast makes it difficult to make a definitive statement about the controls on TRS in this area, most sites are controlled by the low amounts of iron in the system, which limits the amount of iron sulfide that can form. Low reactive iron concentrations and high degrees of pyritization (DOPs) support this argument. Exceptions exist for low-salinity (sulfate-limited) or very fine-grained (organic matter limited) sites.

Thesis (Ph.D.)--University of Tulsa, 1992. / Bibliography: v.1, leaves 268-296.

Thesis (Ph.D.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Thesis (Ph.D.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

No description available.

Os manguezais compõem um bioma de interface entre o continente e o oceano em regiões intertropicais, ambiente este caracterizado por condições únicas ambientais e uma elevada biodiversidade. Este projeto tem como objetivo estudar, utilizando abordagens de metagenômica e metatranscriptomica, as comunidades microbianas encontradas nos manguezais localizados nos municípios de Bertioga/SP e Cananeia/SP, com enfoque nos genes relacionados ao processo de redução do sulfato. Para tanto, uma biblioteca metagenômica contendo 12.960 clones em vetor fosmídeo foi triada por meio de PCR específico para o gene dsrB, ao mesmo passo que esta foi completamente sequenciada em plataforma Illumina HiSeq2000. Foram obtidos três insertos metagenomicos (23D5, MGV 10001431 e MGV 10016026, com 31, 31 e 34 kb, respectivamente). Estes foram então anotados e analisados mais detalhadamente. A inserção 23D5 foi a única a apresentar genes essenciais para a redução dissimilatória do sulfato (apr, hdr, dsr, sat). A diversidade taxonômica dos grupos relacionados ao ciclo do enxofre demonstrou a predominância dos filos Bacteroidetes e Proteobacteria enquanto a análise filogenética para gene dsrB apresentou diferenças entre os três insertos, afiliando os mesmos a sequências similares a Firmicutes e Deltaproteobacteria e revelando serem diferentes das sequências presentes em base de dados. A análise de metatrascriptomica dos quatro manguezais apresentou um padrão de expressão diferencial para o cluster dsr de acordo com o estado de conservação dos manguezais estudados. Estes resultados compõem o primeiro acesso a fragmentos genômicos e a funcionalidade dos mesmos em microrganismos redutores de sulfato em solos de manguezais. / Mangrove is a biome composed of the interface between the continent and the ocean in tropical areas, characterizing by unique environmental conditions and high biodiversity. Here, we aimed to study, using metagenomic and metatranscriptomic approaches, the microbial communities identified in the mangroves located in the cities of Bertioga/SP and Cananeia/SP, focusing on genes related to the sulfate reduction process. For this purpose, a metagenomic library containing 12.960 clones in fosmid vector was screened by PCR for the specific dsrB gene, and the whole library was also completely sequenced by the Illumina HiSeq2000 platform. Three metagenomic inserts were obtained (23D5, MGV 10016026 and MGV 10001431, with 31, 31 and 34 kb, respectively), which were recorded and detail analyzed. The insertion 23D5 was the only one that presents essential genes for dissimilatory sulfate reduction (apr, hdr, dsr, sat). The taxonomic diversity of groups related to the sulfur cycle demonstrated the predominance of Bacteroidetes and Proteobacteria phyla, while phylogenetic analysis to dsrB gene showed differences between the three inserts, affiliating them to similar sequences of Firmicutes and Deltaproteobacteria, and revealing differ from the sequences present in the data base. The metatranscriptomic analysis of the four mangroves showed a pattern of differential expression for the DSR cluster according to the conservation status of the studied mangroves. These results constitute the first access of genomic fragments and functionality of the sulfate reducing microorganisms in mangrove soils.

Os manguezais compõem um bioma de interface entre o continente e o oceano em regiões intertropicais, ambiente este caracterizado por condições únicas ambientais e uma elevada biodiversidade. Este projeto tem como objetivo estudar, utilizando abordagens de metagenômica e metatranscriptomica, as comunidades microbianas encontradas nos manguezais localizados nos municípios de Bertioga/SP e Cananeia/SP, com enfoque nos genes relacionados ao processo de redução do sulfato. Para tanto, uma biblioteca metagenômica contendo 12.960 clones em vetor fosmídeo foi triada por meio de PCR específico para o gene dsrB, ao mesmo passo que esta foi completamente sequenciada em plataforma Illumina HiSeq2000. Foram obtidos três insertos metagenomicos (23D5, MGV 10001431 e MGV 10016026, com 31, 31 e 34 kb, respectivamente). Estes foram então anotados e analisados mais detalhadamente. A inserção 23D5 foi a única a apresentar genes essenciais para a redução dissimilatória do sulfato (apr, hdr, dsr, sat). A diversidade taxonômica dos grupos relacionados ao ciclo do enxofre demonstrou a predominância dos filos Bacteroidetes e Proteobacteria enquanto a análise filogenética para gene dsrB apresentou diferenças entre os três insertos, afiliando os mesmos a sequências similares a Firmicutes e Deltaproteobacteria e revelando serem diferentes das sequências presentes em base de dados. A análise de metatrascriptomica dos quatro manguezais apresentou um padrão de expressão diferencial para o cluster dsr de acordo com o estado de conservação dos manguezais estudados. Estes resultados compõem o primeiro acesso a fragmentos genômicos e a funcionalidade dos mesmos em microrganismos redutores de sulfato em solos de manguezais. / Mangrove is a biome composed of the interface between the continent and the ocean in tropical areas, characterizing by unique environmental conditions and high biodiversity. Here, we aimed to study, using metagenomic and metatranscriptomic approaches, the microbial communities identified in the mangroves located in the cities of Bertioga/SP and Cananeia/SP, focusing on genes related to the sulfate reduction process. For this purpose, a metagenomic library containing 12.960 clones in fosmid vector was screened by PCR for the specific dsrB gene, and the whole library was also completely sequenced by the Illumina HiSeq2000 platform. Three metagenomic inserts were obtained (23D5, MGV 10016026 and MGV 10001431, with 31, 31 and 34 kb, respectively), which were recorded and detail analyzed. The insertion 23D5 was the only one that presents essential genes for dissimilatory sulfate reduction (apr, hdr, dsr, sat). The taxonomic diversity of groups related to the sulfur cycle demonstrated the predominance of Bacteroidetes and Proteobacteria phyla, while phylogenetic analysis to dsrB gene showed differences between the three inserts, affiliating them to similar sequences of Firmicutes and Deltaproteobacteria, and revealing differ from the sequences present in the data base. The metatranscriptomic analysis of the four mangroves showed a pattern of differential expression for the DSR cluster according to the conservation status of the studied mangroves. These results constitute the first access of genomic fragments and functionality of the sulfate reducing microorganisms in mangrove soils.

The hydrogen economy is a possible component of an energy future based on use of alternative and renewable energy sources, deemed desirable from the general consensus of the worldwide community that we do not want to further exacerbate the climate problems that we have introduced over the last two centuries from burning fossil fuels. The burning of fossil fuels emits toxic pollutants into the air, such as sulfur compounds and oxidized forms of nitrogen (NOx) but also emit copious amounts of the inert carbon dioxide. The latter is widely recognized as the major cause of the global warming phenomenon. For a hydrogen economy to develop, efficient means of hydrogen generation are required. Thermochemical cycles were conceived in the 1960s but only one operating pilot plant and no commercial installations based on the processes have been built. In the present work the use of a membrane reactor to enable the newly conceived Sulfur-Sulfur cycle, based on equations 1 - 3 is modeled. / 4H₂O+4SO₂ -> H₂S + 3H₂SO₄ Eq. 1 / H₂SO₄ -> SO₂ + H₂O + 1/2O₂ Eq. 2 / H₂S + 2H₂O -> SO₂ + 3H₂ Eq. 3 / The rationale for the use of a membrane reactor to enable the cycle is based on enhancing extent of reaction beyond its predicted equilibrium point due to the severely unfavorable thermochemical parameters for the steam reforming of hydrogen sulfide reaction (Eq. 3 above) which has a low equilibrium concentration of products. The membrane reactor will employ a molybdenum sulfide catalyst driving the steam reformation of hydrogen sulfide reaction and simultaneous extraction of hydrogen (one of the products) will allowing for the reaction to occur to higher extent. A computational model of a catalytic membrane reactor was constructed using the well-known finite element model package Comsol v4.1 in which a catalytic microchannel reactor separated from a sweep gas by a thin hydrogen permeable membrane is built and parametric sweeps to evaluate the effect of membrane transport parameters, pressure and gas feed velocities are calculated. Though the steam reforming of hydrogen sulfide reaction has a competing thermal cracking reaction, the present work focuses on modeling one reaction only (the steam reformation reaction) for simplicity. Fully dense metallic membranes with chemselective permeability to hydrogen are modeled with transport parameters derived from reported literature values for similar applications. The results show that employing a membrane reactor does significantly affect the completeness of the reaction by product extraction (if you do run the model with membrane transport set to zero, compare the extent at zero with extent at 3.6x10⁻⁶ mol.s⁻¹.m⁻²). The effect of changing sweep gas velocity is contingent on membrane properties, and membranes with small diffusion coefficients severely limit the ability of extraction of hydrogen from the feed. Therefore, it is more important that membranes with very high hydrogen permeability be employed in designing a reactor to implement this process, allowing for effective hydrogen separation and high conversion of the reactants in the process. Reactor pressure has minimal effect on the extent of reaction and therefore reactors designed to implement the process may be designed to operate at close to ambient pressure. / Graduation date: 2012

Alguns ecossistemas chamam atenção devido à particular combinação de condições ambientais únicas, que resultam na evolução de espécies capazes de colonizar estes ambientes. Os manguezais compõem um bioma composto por espécies de plantas, animais e microrganismos que interagem neste ambiente, que tem como principal característica a interface entre o continente e o oceano em regiões intertropicais. Nosso objetivo foi acessar via sequenciamento massivo de DNA e RNA (via Illumina HiSeq 2000) o perfil taxonômico e funcional da comunidade microbiana de quatro manguezais com distintos níveis de contaminação. As sequências foram analisadas na plataforma MG-RAST, para a análise taxonômica foi utilizado BlastN contra a base de dados RDP ou M5NR, enquanto que a análise funcional foi baseada na comparação por BlastX das sequências obtidas com as disponíveis no banco de dados M5RNA e M5Nr. Na análise funcional, as sequências classificadas foram ainda integradas na classificação hierárquica SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) e COG (Clusters of Orthologous Group). No total, foram obtidas 682 milhões de sequências válidas ( 88,2, 303,1 e 290,9 milhões a partir das análises de DNA, RNA total e RNA purificado, respetivamente). Estas indicaram como grupos taxonômicos mais abundantes as classes Gammaproteobacteria e Deltaproteobacteria (dentro do domínio Bacteria), e Methanomicrobia e Methanobacteria (dentro do domínio Archaea). Além destas observações, alterações na representação de determinados grupos quando as análises de DNA e RNA são comparadas. Em relação a classificação funcional das sequências, foi possível observar uma similaridade no número de funções encontradas nos diferentes manguezais, mas uma maior quantidade de sequências anotadas foi observada, como esperado, na análise de DNA. De maneira mais detalhada, o estudo das funções relacionadas a transformação de nitrogênio e enxofre indicou que há uma correlação entre a abundância de sequências de um referido gene na análise metagenômica, e sua correspondente quantidade dentro dos grupos de dados de metatranscriptômica. Os grupos microbianos mais representados nestes ciclos foram Deltaproteobacteria e Gammaproteobacteria, atuantes principalmente nos processos de fixação de nitrogênio atmosférico (N2), desnitrificação e redução de sulfato, enquanto que para oxidação do enxofre as classes mais frequentes foram Gammaproteobacteria, Betaproteobacteria e Epsilonproteobacteria. De maneira geral, este estudo fornece indícios sobre a atividade microbiana nos manguezais, e indica que as frequentemente correlações observadas entre os resultados da análise metagenômica e metatranscriptômica, porém essas correlações se tornam menos evidentes quando analisamos em nível de ordem ou em níveis mais específicos. / Some ecosystems call particular attention due to unique combination of environmental conditions that result in evolution of species capable of colonizing these environments. Mangroves constitute a biome composed of species of plants, animals and micro-organisms that interact in this environment, whose main characteristic is the interface between the continent and the ocean in tropical areas. Our goal was to access via massive sequencing of DNA and RNA (via Illumina HiSeq 2000) the taxonomic and functional profile of the microbial community four mangroves with different levels of contamination. The sequences were analyzed on MG-RAST platform for taxonomic analysis was performed using BLASTN against the RDP database or M5NR, while the functional analysis was based on comparison of the sequences obtained by BlastX available on M5RNA with the database and M5Nr . In functional analysis, the sequences were classified yet integrated into the hierarchical classification SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (Clusters of Orthologous Group). A total of 682 million valid sequences were obtained (88.2, 303.1 and 290.9 million from DNA analyzes, purified total RNA and RNA, respectively). These indicated as the most abundant taxa Gammaproteproteobacteria and Deltaproteobacteria classes (within the domain Bacteria), and Methanomicrobia and Methanobacteria (within the domain Archaea). In addition to these observations, changes in the representation of particular groups when analyzes of DNA and RNA are compared. Regarding the functional classification of the sequences was observed in the number of a similarity functions found in different mangrove, but a greater amount of annotated sequences was observed, as expected, the analysis of DNA. In more detail, the study of the functions related to transformation of nitrogen and sulfur indicated that there is a correlation between the abundance of sequences of said gene in metagenomic analysis, and its corresponding quantity within the metatranscriptômica data groups. The microbial groups were over-represented in these cycles and Deltaproteobacteria Gammaproteobacteria mainly active in nitrogênioatmosférico fixation processes (N2), the denitrification and sulfate reduction, while for sulfur oxidation were the most frequent class Gammaproteobacteria, and Betaproteobacteria Epsilonproteobacteria. Overall, this study provides evidence of microbial activity in the mangroves, and often indicates that the correlations observed between the results of metagenomics and metatranscriptômica analysis, but these correlations become less evident when we look at order level or other specific levels.

Alguns ecossistemas chamam atenção devido à particular combinação de condições ambientais únicas, que resultam na evolução de espécies capazes de colonizar estes ambientes. Os manguezais compõem um bioma composto por espécies de plantas, animais e microrganismos que interagem neste ambiente, que tem como principal característica a interface entre o continente e o oceano em regiões intertropicais. Nosso objetivo foi acessar via sequenciamento massivo de DNA e RNA (via Illumina HiSeq 2000) o perfil taxonômico e funcional da comunidade microbiana de quatro manguezais com distintos níveis de contaminação. As sequências foram analisadas na plataforma MG-RAST, para a análise taxonômica foi utilizado BlastN contra a base de dados RDP ou M5NR, enquanto que a análise funcional foi baseada na comparação por BlastX das sequências obtidas com as disponíveis no banco de dados M5RNA e M5Nr. Na análise funcional, as sequências classificadas foram ainda integradas na classificação hierárquica SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) e COG (Clusters of Orthologous Group). No total, foram obtidas 682 milhões de sequências válidas ( 88,2, 303,1 e 290,9 milhões a partir das análises de DNA, RNA total e RNA purificado, respetivamente). Estas indicaram como grupos taxonômicos mais abundantes as classes Gammaproteobacteria e Deltaproteobacteria (dentro do domínio Bacteria), e Methanomicrobia e Methanobacteria (dentro do domínio Archaea). Além destas observações, alterações na representação de determinados grupos quando as análises de DNA e RNA são comparadas. Em relação a classificação funcional das sequências, foi possível observar uma similaridade no número de funções encontradas nos diferentes manguezais, mas uma maior quantidade de sequências anotadas foi observada, como esperado, na análise de DNA. De maneira mais detalhada, o estudo das funções relacionadas a transformação de nitrogênio e enxofre indicou que há uma correlação entre a abundância de sequências de um referido gene na análise metagenômica, e sua correspondente quantidade dentro dos grupos de dados de metatranscriptômica. Os grupos microbianos mais representados nestes ciclos foram Deltaproteobacteria e Gammaproteobacteria, atuantes principalmente nos processos de fixação de nitrogênio atmosférico (N2), desnitrificação e redução de sulfato, enquanto que para oxidação do enxofre as classes mais frequentes foram Gammaproteobacteria, Betaproteobacteria e Epsilonproteobacteria. De maneira geral, este estudo fornece indícios sobre a atividade microbiana nos manguezais, e indica que as frequentemente correlações observadas entre os resultados da análise metagenômica e metatranscriptômica, porém essas correlações se tornam menos evidentes quando analisamos em nível de ordem ou em níveis mais específicos. / Some ecosystems call particular attention due to unique combination of environmental conditions that result in evolution of species capable of colonizing these environments. Mangroves constitute a biome composed of species of plants, animals and micro-organisms that interact in this environment, whose main characteristic is the interface between the continent and the ocean in tropical areas. Our goal was to access via massive sequencing of DNA and RNA (via Illumina HiSeq 2000) the taxonomic and functional profile of the microbial community four mangroves with different levels of contamination. The sequences were analyzed on MG-RAST platform for taxonomic analysis was performed using BLASTN against the RDP database or M5NR, while the functional analysis was based on comparison of the sequences obtained by BlastX available on M5RNA with the database and M5Nr . In functional analysis, the sequences were classified yet integrated into the hierarchical classification SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (Clusters of Orthologous Group). A total of 682 million valid sequences were obtained (88.2, 303.1 and 290.9 million from DNA analyzes, purified total RNA and RNA, respectively). These indicated as the most abundant taxa Gammaproteproteobacteria and Deltaproteobacteria classes (within the domain Bacteria), and Methanomicrobia and Methanobacteria (within the domain Archaea). In addition to these observations, changes in the representation of particular groups when analyzes of DNA and RNA are compared. Regarding the functional classification of the sequences was observed in the number of a similarity functions found in different mangrove, but a greater amount of annotated sequences was observed, as expected, the analysis of DNA. In more detail, the study of the functions related to transformation of nitrogen and sulfur indicated that there is a correlation between the abundance of sequences of said gene in metagenomic analysis, and its corresponding quantity within the metatranscriptômica data groups. The microbial groups were over-represented in these cycles and Deltaproteobacteria Gammaproteobacteria mainly active in nitrogênioatmosférico fixation processes (N2), the denitrification and sulfate reduction, while for sulfur oxidation were the most frequent class Gammaproteobacteria, and Betaproteobacteria Epsilonproteobacteria. Overall, this study provides evidence of microbial activity in the mangroves, and often indicates that the correlations observed between the results of metagenomics and metatranscriptômica analysis, but these correlations become less evident when we look at order level or other specific levels.