A conversão de áreas de florestas da Amazônia em áreas agrícolas e pastoris desregula processos relacionados ao estoque de carbono, sendo considerada depois da queima de combustíveis fósseis a atividade que mais contribui com a emissão de gases do efeito estufa, dentre os quais se encontra o metano. A produção de metano é intermediada pelas arquéias metanogênicas, que atuam na decomposição anaeróbia da matéria orgânica. Portanto, para compreender as alterações do fluxo desse gás no ecossistema amazônico, é necessário que as comunidades microbianas envolvidas nesse processo sejam estudadas. Dessa forma, o presente estudo teve por objetivo monitorar e caracterizar comunidades de arquéias metanogênicas, por análises de enriquecimento destas comunidades, em amostras de solo provenientes de floresta primária, floresta secundária e pastagem da região amazônica. As amostras de solo foram colocadas em meio enriquecido com a adição de acetato, metanol ou H2:CO2, separadamente, para estimular os metabolismos aceticlástico, metilotrófico e hidrogenotrófico. O monitoramento desses cultivos foi realizado por análises de emissão de metano por cromatografia gasosa, quantificação do gene mcrA pela técnica de PCR quantitativo (qPCR) e caracterização da comunidade metanogênica por meio de microscopia e sequenciamento da região V4-V5 do gene 16S rRNA. Analisando a emissão de metano entre os três tipos de fontes de carbono para as três amostras de solo, os enriquecimentos com metanol apresentaram uma produção maior de metano em relação as amostras com o acetato e muito superior aos cultivos com atmosfera de H2:CO2. A maior média de produção de metano ocorreu nos enriquecimentos com metanol, indicando que a via metilotrófica embora considerada alternativa, pode ser importante na produção de metano no solo amazônico. Por meio da técnica de qPCR foi possível quantificar o gene mcrA das amostras de pastagens logo no tempo inicial da incubação, o que não foi possível para as amostras florestais. No tempo final, o número de cópias desse gene foi similar para os três perfis de solo. Foi possível observar pela caracterização fenotípica dos enriquecimentos agregados de células característicos do gênero Methanosarcina, gênero que foi identificado posteriormente pelo sequenciamento do gene 16S rRNA, além de células em formatos de bastonetes e cocos. Os resultados do sequenciamento permitiram identificar 7 grupos distintos de arqueias metanogênicas, afiliados aos filos Euryarchaeota e Bathyarchaeota. Nas amostras iniciais de pastagens foram identificadas sequências que se afiliaram a todos esses grupos, enquanto as amostras florestais apresentaram sequencias afiliadas apenas ao gênero Methanosarcina. A composição final da comunidade das amostras de pastagens foi similar a inicial, porém mais abundante. Os enriquecimentos de amostras de solo de floresta primária e secundária apresentaram uma composição distinta, devido ao enriquecimento de grupos que não foram identificados no início da incubação. Os resultados obtidos mostraram que embora as arqueias metanogênicas estejam em baixa abundância nos solos florestais, podem ser enriquecidos quando submetidos a condições favoráveis, atingindo produção de metano e alcançando composição similar as amostras de pastagens. / Amazonian forest conversion into agricultural and livestock areas disrupts processes related to carbon stock, being considered, after the fossil fuels burning, the activity contributes most to greenhouse gases emission, of which is methane. Methane production is mediated by methanogenic archaea, acting in organic matter anaerobic decomposition. Therefore, to understand the changes in the flow of this gas in the Amazonian ecosystem, it is necessary to study microbial communities involved in this process. This study aims to monitor and characterize methanogenic archaeal communities by population enrichment from soil samples collected in primary, secondary and pasture of the Amazon region. Soil samples were placed into an enriched medium and received separately acetate, methanol, and H2:CO2 to stimulate the three metabolism types: acetoclastic, methylotrophic and hydrogenotrophic. Monitoring was performed by methane emission analysis by gas chromatography, mcrA quantification by the quantitative PCR and the community characterization was performed by microscopy and sequencing of the V4-V5 region of the 16S rRNA gene. Analyzing the methane emission by the three types of carbon sources in the three soil samples, methanol enrichments presented a higher methane yield than the acetate samples and much larger than cultures with H2:CO2. These results indicate that methylotrophic pathway, although considered as an alternative, may be important in methane production in the Amazonian soil. Was possible to quantify the mcrA gene by qPCR from pasture samples at the initial incubation time, which was not possible for forest samples. In incubation final time, copies number of this gene was similar for the three soil profiles. The phenotypic characterization of enrichments revealed aggregated cells, characteristic of the genus Methanosarcina, later identified by 16S rRNA sequencing. The cells in rod-shaped and cocci formats were also observed. Was identify by sequencing 7 different methanogenic archaeas groups affiliated with Euryarchaeota and Bathyarchaeota phylum. In the initial pasture samples, were identified sequences affiliated with all these groups, while forest samples presented sequences affiliated with only a Methanosarcina genus. Pasture samples showed a final community composition similar to initial, however more abundant. Soil samples enrichment from primary and secondary forest presented a distinct composition due to groups enrichment that was not identified at incubation beginning. These results showed that although methanogenic archaeas are in low abundance in forest soils, they can be enriched when submitted to favorable conditions, archive methane production and reaching similar composition pasture samples.

A conversão de áreas de florestas da Amazônia em áreas agrícolas e pastoris desregula processos relacionados ao estoque de carbono, sendo considerada depois da queima de combustíveis fósseis a atividade que mais contribui com a emissão de gases do efeito estufa, dentre os quais se encontra o metano. A produção de metano é intermediada pelas arquéias metanogênicas, que atuam na decomposição anaeróbia da matéria orgânica. Portanto, para compreender as alterações do fluxo desse gás no ecossistema amazônico, é necessário que as comunidades microbianas envolvidas nesse processo sejam estudadas. Dessa forma, o presente estudo teve por objetivo monitorar e caracterizar comunidades de arquéias metanogênicas, por análises de enriquecimento destas comunidades, em amostras de solo provenientes de floresta primária, floresta secundária e pastagem da região amazônica. As amostras de solo foram colocadas em meio enriquecido com a adição de acetato, metanol ou H2:CO2, separadamente, para estimular os metabolismos aceticlástico, metilotrófico e hidrogenotrófico. O monitoramento desses cultivos foi realizado por análises de emissão de metano por cromatografia gasosa, quantificação do gene mcrA pela técnica de PCR quantitativo (qPCR) e caracterização da comunidade metanogênica por meio de microscopia e sequenciamento da região V4-V5 do gene 16S rRNA. Analisando a emissão de metano entre os três tipos de fontes de carbono para as três amostras de solo, os enriquecimentos com metanol apresentaram uma produção maior de metano em relação as amostras com o acetato e muito superior aos cultivos com atmosfera de H2:CO2. A maior média de produção de metano ocorreu nos enriquecimentos com metanol, indicando que a via metilotrófica embora considerada alternativa, pode ser importante na produção de metano no solo amazônico. Por meio da técnica de qPCR foi possível quantificar o gene mcrA das amostras de pastagens logo no tempo inicial da incubação, o que não foi possível para as amostras florestais. No tempo final, o número de cópias desse gene foi similar para os três perfis de solo. Foi possível observar pela caracterização fenotípica dos enriquecimentos agregados de células característicos do gênero Methanosarcina, gênero que foi identificado posteriormente pelo sequenciamento do gene 16S rRNA, além de células em formatos de bastonetes e cocos. Os resultados do sequenciamento permitiram identificar 7 grupos distintos de arqueias metanogênicas, afiliados aos filos Euryarchaeota e Bathyarchaeota. Nas amostras iniciais de pastagens foram identificadas sequências que se afiliaram a todos esses grupos, enquanto as amostras florestais apresentaram sequencias afiliadas apenas ao gênero Methanosarcina. A composição final da comunidade das amostras de pastagens foi similar a inicial, porém mais abundante. Os enriquecimentos de amostras de solo de floresta primária e secundária apresentaram uma composição distinta, devido ao enriquecimento de grupos que não foram identificados no início da incubação. Os resultados obtidos mostraram que embora as arqueias metanogênicas estejam em baixa abundância nos solos florestais, podem ser enriquecidos quando submetidos a condições favoráveis, atingindo produção de metano e alcançando composição similar as amostras de pastagens. / Amazonian forest conversion into agricultural and livestock areas disrupts processes related to carbon stock, being considered, after the fossil fuels burning, the activity contributes most to greenhouse gases emission, of which is methane. Methane production is mediated by methanogenic archaea, acting in organic matter anaerobic decomposition. Therefore, to understand the changes in the flow of this gas in the Amazonian ecosystem, it is necessary to study microbial communities involved in this process. This study aims to monitor and characterize methanogenic archaeal communities by population enrichment from soil samples collected in primary, secondary and pasture of the Amazon region. Soil samples were placed into an enriched medium and received separately acetate, methanol, and H2:CO2 to stimulate the three metabolism types: acetoclastic, methylotrophic and hydrogenotrophic. Monitoring was performed by methane emission analysis by gas chromatography, mcrA quantification by the quantitative PCR and the community characterization was performed by microscopy and sequencing of the V4-V5 region of the 16S rRNA gene. Analyzing the methane emission by the three types of carbon sources in the three soil samples, methanol enrichments presented a higher methane yield than the acetate samples and much larger than cultures with H2:CO2. These results indicate that methylotrophic pathway, although considered as an alternative, may be important in methane production in the Amazonian soil. Was possible to quantify the mcrA gene by qPCR from pasture samples at the initial incubation time, which was not possible for forest samples. In incubation final time, copies number of this gene was similar for the three soil profiles. The phenotypic characterization of enrichments revealed aggregated cells, characteristic of the genus Methanosarcina, later identified by 16S rRNA sequencing. The cells in rod-shaped and cocci formats were also observed. Was identify by sequencing 7 different methanogenic archaeas groups affiliated with Euryarchaeota and Bathyarchaeota phylum. In the initial pasture samples, were identified sequences affiliated with all these groups, while forest samples presented sequences affiliated with only a Methanosarcina genus. Pasture samples showed a final community composition similar to initial, however more abundant. Soil samples enrichment from primary and secondary forest presented a distinct composition due to groups enrichment that was not identified at incubation beginning. These results showed that although methanogenic archaeas are in low abundance in forest soils, they can be enriched when submitted to favorable conditions, archive methane production and reaching similar composition pasture samples.

Tidal freshwater wetlands (TFW) are at significant risk of loss or alteration due to global climate change, and saltwater intrusion from sea level rise is of particular concern for these habitats due to their proximity to coastal areas. A space-for-time model was used to investigate the effects of saltwater intrusion on soil methanogen communities along naturally occurring salinity gradients on the Waccamaw, James, and Hudson Rivers. Amplification of the methyl coenzyme-M reductase (mcrA) functional gene was used in qPCR, reverse transcription qPCR, and T-RFLP to measure the abundance, activity, and community composition of soil methanogens. Both the abundance and activity of methanogens decreased with increasing salinity, and the both total and active methanogen community composition shifted in response to changes in salinity. This research demonstrates that saltwater intrusion will alter carbon cycling in TFWs, potentially altering their ability to sequester carbon and keep pace with rising sea level.

A field survey was conducted following the Deepwater Horizon blowout and it was noted that resulting coastal petroleum deposits possessed distinct geometries, ranging from small tar balls to expansive horizontal oil sheets. A laboratory study evaluated the effect of oil deposit geometry on localized gradients of electron acceptors and microbial community composition, factors that are critical to accurately estimating biodegradation rates. One-dimensional top-flow sand columns with 12-hour simulated tidal cycles compared two contrasting geometries (isolated tar "balls" versus horizontal "sheets") relative to an oil-free control. Significant differences in the effluent dissolved oxygen and sulfate concentrations were noted among the columns, indicating presence of anaerobic zones in the oiled columns, particularly in the sheet condition. Furthermore, quantification of genetic markers of electron acceptor and catabolic conditions via quantitative polymerase chain reaction of dsrA (sulfate-reduction), mcrA (methanogenesis), and cat23 (oxygenation of aromatics) genes in column cores suggested more extensive anaerobic conditions induced by the sheet relative to the ball geometry. Denaturing gradient gel electrophoresis similarly revealed that distinct gradients of bacterial communities established in response to the different geometries. Thus, petroleum deposit geometry impacts local redox and microbial characteristics and may be a key factor for advancing attenuation models and prioritizing cleanup. / Master of Science

If communicating via a teleconference phone the desired transmitted signal (speech) needs to be crystal clear so that all participants experience a good communication ability. However, there are many environmental conditions that contaminates the signal with background noise, i.e sounds not of interest for communication purposes, which impedes the ability to communicate due to interfering sounds. Noise can be removed from the signal if it is known and so this work has evaluated different ways of estimating the characteristics of the background noise. Focus was put on using speech detection to define the noise, i.e. the non-speech part of the signal, but other methods not solely reliant on speech detection but rather on characteristics of the noisy speech signal were included. The implemented techniques were compared and evaluated to the current solution utilized by the teleconference phone in two ways, firstly for their speech detection ability and secondly for their ability to correctly estimate the noise characteristics. The evaluation process was based on simulations of the methods' performance in various noise conditions, ranging from harsh to mild environments. It was shown that the proposed method showed improvement over the existing solution, as implemented in this study, in terms of speech detection ability and for the noise estimate it showed improvement in certain conditions. It was also concluded that using the proposed method would enable two sources of noise estimation compared to the current single estimation source and it was suggested to investigate how utilizing two noise estimators could affect the performance.