Increasing socio-economic growth and development of South Africa’s freshwater systems require continuous augmentation of water sources to meet the growing water requirements of communities and industries. Anthropogenic disturbances have caused the water quality of many freshwater systems to drastically deteriorate due to constant disposal of domestic, industrial, and agricultural waste into surface waters. Government agencies make use of biomonitoring programmes to effectively manage the countries’ freshwater resources. These programmes use a variety of biological indicators (e.g., macroinvertebrates, fish, diatoms and algal species) and physico-chemical variables to determine the state of the environment. However, attempts to use microbial community structures as bioindicators of anthropogenic perturbations are greatly neglected. This study used molecular techniques (PCR-DGGE and 454-pyrosequencing) and multivariate analysis to develop a robust monitoring technique to determine the impacts of environmental disturbances on bacterial community compositions in river systems in the North West Province. Significant contributions made by this project included the establishment of a bacterial diversity framework for South African freshwater systems that are impacted by a variety of anthropogenic activities (e.g., urban and informal settlements, agriculture and mining). Furthermore, case studies demonstrated the prevalence of specific taxa at polluted sites, as well as positive and negative associations between taxa and environmental variables and pollutants. Finally, biogeochemical cycles could be partially matched to bacterial community structures in river systems. The first part of the project included a pilot study that investigated bacterial structures in a segment of the Vaal River in response to environmental parameters using molecular techniques and multivariate analysis. The most important observations made during this study included the generation of a larger bacterial diversity dataset by pyrosequencing compared to PCR-DGGE. In addition, metagenomic and multivariate analyses provided clues about potential biogeochemical roles of different taxa. The second and third part of the project included two case studies that investigated bacterial communities in the Mooi River and Wonderfonteinspruit in response to environmental activities. Both these systems are impacted by a variety of external sources such as urban and informal settlements, agriculture, and mining. The results demonstrated that perturbations nearby the Mooi River and Wonderfonteinspruit caused the overall water quality to deteriorate which in turn had a profound impact on bacterial community composition. Bacterial community structures at reference/control sites (Muiskraal and Turffontein dolomitic eye) had overall high species diversity (richness and evenness), whereas polluted sites showed lower species diversity and were dominated by the Beta- and Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia. In addition, various potential pathogens (e.g. Eschirichia/Shigella, Legionella, Staphylococcus, Streptococcus etc.) were identified at impacted sites. Multivariate analysis suggested that bacterial communities and certain taxa (Malikia, Algoriphagus, Rhodobacter, Brevundimonas and Sphingopyxis) at polluted sites were mainly impacted by temperature, pH, nutrient levels, and heavy metals. Finally, the proportion of nitrogen and sulphur bacteria corresponded well with the nitrogen and sulphur levels measured in the Wonderfonteinspruit. Based on these results, it was concluded that bacterial community structures might provide a good indicator of anthropogenic disturbances in freshwater systems and may be incorporated into biomonitoring programs. / PhD (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

This dissertation examines the bacterial diversity of hyperarid and arid regions of the Atacama Desert, Chile, as a first step towards understanding the global biogeochemical significance of arid-land microbial communities. The specific objectives were to characterize bacterial diversity and infer the possible metabolic potential of these bacterial communities, and to evaluate the influence of moisture exposure on community structure. In addition, the strengths and limitations of available tools for probing microbial diversity and activity in terrestrial ecosystems were characterized for their application to extreme oligotrophic communities. Preliminary PCR-DGGE analysis of a west-east elevational transect from the Pacific Ocean near Antofagasta to the western slopes of the central Andes indicated that bacterial communities along this transect belonged to two distinct community types: 1) hyperarid (700 - 2000 m) and 2) arid (2500 - 4500 m) communities that included both vegetated and unvegetated regions. Subsequent diversity analysis of these two regions revealed novel but distinct communities in both regions. A greater diversity was observed in the unvegetated arid regions than in the unvegetated hyperarid areas. The unvegetated arid sites were characterized by a bacterial community harboring a combination of radiotolerant and halotolerant heterotrophs as wells as diverse phylotypes closely related to chemolithoautotrophs. These rare phylotypes may be uniquely adapted to arid ecosystems. Molecular tools evaluated for community diversity analysis included PCR-DGGE, Sanger-clone and 454-pyrosequencing analysis of 16S rRNA gene libraries, and the use of reverse transcriptase quantitative PCR (RT-qPCR) for quantifying the impact of environmental variables on the metabolic activity of a specific organism. These techniques were evaluated using the ecosystems of the Atacama Desert as well as model ecosystems designed to address specific questions. Molecular tools are invaluable to the study of microbial ecology because they facilitate the study of fastidious organisms that are difficult or impossible to culture, but the analysis presented in this dissertation demonstrates that each of these methods has limitations and biases which must be acknowledged to avoid inaccurate conclusions from skewed results. The most complete picture of the taxonomic and functional profile of a microbial community is obtained by employing a combination of molecular techniques.

Premise plumbing can contain copper and lead bearing fixtures, and although copper is considered primarily an aesthetic issue, the neurotoxic effects of lead present a significant public health concern. Utilities approach corrosion control in low alkalinity water by increasing the pH (>9) or adding a phosphate inhibitor at neutral pH. Phosphate inhibitors, pH and chlorine are known to affect lead and copper release through their direct action as corrosion inhibitors or oxidizing agents or through an indirect action via microbial growth. Biofilms are often an implied cause of premise plumbing corrosion, although little is known about their community structure or ability to store metals. The central hypothesis of this thesis is that biofilm contributes to lead and copper release in premise plumbing. This thesis addresses a unique gap in corrosion literature by integrating traditional corrosion chemistry methods with microbiological and molecular biology techniques. The experiments used three distinct approaches: (i). electrochemical cell experiments to determine the key factors in decreasing lead and copper corrosion in galvanically coupled systems while maintaining microbial control (ii). galvanic macrocells using premise plumbing components to examine the unintended consequences of adding a phosphate based corrosion inhibitor and (iii). an annular reactor study to examine the impacts of two commonly applied corrosion control strategies. In the electrochemical cell experiments, the pH 9.2 with zinc orthophosphate and chlorine treatment achieved both goals: decreased lead and copper release and limited microbial growth. In galvanic macrocells experiments with premise plumbing components, zinc orthophosphate addition was shown to be positively correlated with increased bulk water bacteria, biofilm growth and biofilm community structure as measured by DGGE. Biofilm was also observed to sorb 3-29% of lead and 3-16% of copper from the bulk water. The comparison of the two corrosion control strategies showed that the majority of lead released was in the particulate form, and the results further alluded to the potentially significant role lead particles play in biofilm formation.

Investigations were carried out to assess biofilm formation within a model warm water distribution system (test rig) under a variety of conditions. Analysis methods included ATP-/ culture-based analysis, SEM and confocal microscopy. Molecular-based community analysis was carried out using PCR/DGGE. High pH (9.53-10.08), induced by the presence of a sacrificial anode within the water heater, had a profound inhibitive effect on the culturability of biofilm bacteria on copper (Cu) pipe within the test rig. Concurrent investigations into the effect of stagnation (varied periods of non-flushing) appeared to contradict the widely held view that stagnation is conducive to biofilm formation, with greater flushing frequencies resulting in increased biofilm. It was concluded that a higher frequency of nutrient-delivering events were largely responsible for this and that in systems where lengthier stagnation periods were employed, factors such as low oxygen and reduced nutrient levels inhibited biofilm formation on previously uncontaminated Cu pipe. Thermal purging (TP) over a 28 day period of 30 second, 12 hourly flushing at 41 °C and three-daily one minute purging with 70 °C water resulted in a 99% reduction in the culturability of biofilm bacteria on both Cu and LLDPE. However, confocal microscopical analysis of bacterial numbers indicated that 25.06% (Cu) and 21.55% (LLDPE) of the initial bacterial population remained viable. A large proportion of non-viable biofilm bacteria were also observed. Further work is therefore required in order to optimize TP within the test rig. Biofilm formation on a range of different materials; Cu, stainless steel, PEX, and EPDM, showed significantly greater biofilm development on EPDM in comparison to the other materials. Preliminary investigations of LLDPE and tap outlet fittings showed that laminar flow outlet fittings may act as reservoirs for the development and subsequent dissemination of biofilm. Molecular bacterial community structural studies of test rig biofilms clearly showed that biofilm community composition was significantly affected by both temporal and environmental factors, and varied at points within the same system. Sequencing did not provide a great insight into the composition of the bacterial communities within the test rig, and further work is required to gain a more complete picture of bacterial community diversity within the test rig. These studies show that biofilm formation within the test rig is greatly influenced by a wide variety of factors. The test rig’s unique design necessitates a cautionary approach when making comparisons with, for example, larger water distribution systems

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Muitos fatores, como variações sazonais, tipos de tecido vegetal, cultivares e espécies de hospedeiro, tipo de solo, interação com microrganismos benéficos ou patógenos entre outros, afetam a estrutura e a composição da comunidade bacteriana das plantas. A introdução de plantas geneticamente modificadas (PGM) foi somada ao conjunto desses fatores, podendo acarretar efeitos diretos e indiretos sobre a comunidade bacteriana. Cana-de-açúcar é uma cultura de grande importância no Brasil; a área de cultivo está em expansão devido aos incentivos para a produção de álcool. Uma bactéria potencialmente importante para a cultura de cana-de-açúcar é a Methylobacterium, um importante endófito de diversas culturas de interesse econômico e que, em cana-de-açúcar, pode melhorar a germinação de sementes, promover um aumento do peso da planta e da área foliar, além do número de internódios. Dessa forma, o trabalho teve como objetivos: i) avaliar os efeitos da canade- açúcar transgênica resistente a insetos e a herbicida sobre a comunidade bacteriana associada; ii) avaliar se o suposto efeito causado pela cana-de-açúcar transgênica resistente a herbicida deriva diretamente do transgene ou dos tratos culturais diferenciados aos quais a planta transgênica é submetida; iii) avaliar a interação entre Methylobacterium spp. e cana-de-açúcar. Analisando a densidade bacteriana das plantas de cana-de-açúcar convencionais e transgênicas não foi possível constatar diferenças relacionadas à introdução dessas plantas. Analisando somente quanto ao manejo de ambos os experimentos, foi possível observar que diferenças em trato cultural ou manejo de plantas, decorrentes ou não da transgenia, podem influenciar a comunidade bacteriana. Por meio de ARDRA, foi possível observar distribuição diferenciada dos ribotipos com a introdução das PGMs. No experimento realizado somente com plantas transgênicas para resistência a Imazapyr, foi possível notar que, em 17 meses, a presença da planta transgênica e a aplicação do herbicida Imazapyr podem ter resultado na redução da densidade bacteriana associada à rizosfera de cana-de-açúcar. Por meio de DGGE, foi visto que o estado fisiológico da planta foi a maior fonte de variação. Novamente por meio de ARDRA, foram observados ribotipos cuja presença foi afetada pelo cultivo da planta transgênica. Esses ribotipos diferentemente distribuídos poderiam resultar em alterações na atividade bacteriana dessas plantas, uma vez que esses ribotipos podem representar grupos funcionais importantes. A colonização de Methylobacterium spp. em cana-de-açúcar foi analisada por meio de microscopia eletrônica de varredura, reisolamento e microscopia óptica de fluorescência. Foi visto que as linhagens utilizadas colonizam cana-de-açúcar, sendo que os pontos de maior colonização são os flanges cuticulares e as regiões pilosas da raiz. Outros estudos são necessários para o melhor aproveitamento dessa bactéria na cultura de cana-de-açúcar. / Many factors, such as seasonal variations, kinds of vegetal tissue, cultivares and host species, kind of soil, interaction with beneficial or pathogen microorganisms, among others, affect the structure and composition of plants bacterial community. The introduction of genetically modified plants (GMP) was added to the set of these factors, making it possible to cause direct and indirect effects on the bacterial community. Sugarcane is a very important crop in Brazil; the cultivation area is expanding due to incentives to alcohol production. A potentially important bacterium for sugar cane cultivation is the Methylobacterium, which is an important endophyte for several cultures of economic interest and which can improve seed germination in sugar cane, promote an increase of plant weight and foliar area, and also the internodes. Thus, the work had as objectives: i) to assess the effects of transgenic sugarcane resistant to insects and herbicide on the associated bacterial community; ii) to assess if the presumed effect caused by transgenic sugarcane resistant to herbicides derives directly from the transgene or differentiated cultural handlings to which the genetically modified plant is undertaken; iii) to assess the interaction between Methylobacterium ssp. and sugarcane. Analyzing the bacterial density of conventional and transgenic sugarcane plants it was not possible to see differences related to the introduction of these plants. Analyzing only in relation to the handling of both experiments, it was possible to see that differences in cultural wielding or handling of plants derived or not from transgenia can influence the bacterial community. By means of ARDRA, it was possible to see a differentiated distribution of ribotypes with the introduction of GMPs. In the experiment made only with transgenic plants for Imazapyr resistance, it was possible to see that in 17 months, the presence of the transgenic plant and the application of Imazapyr herbicide can bring result regarding the bacterial density reduction associated to sugarcane rizosphere. By means of DGGE, it was seen that the physiological status of the plant was the greatest variation source. Again, by means of ARDRA, ribotypes whose presence was affected by transgenic plant cultivation were observed. If distributed differently, these ribotypes can represent important functional groups. The Methylobacterium ssp. Colonization in sugarcane was analyzed and by means of scanning electronic microscopy, re-isolation, and fluorescence optical microscopy. It was observed that the utilized lineages colonize sugarcane being cuticle flange and perilous regions of root the highest colonization points. Other studies are needed to a better good use of this bacterium in sugarcane culture.

Os micro-organismos desempenham importante papel na reciclagem dos elementos em ecossistemas de manguezais, uma vez que como produtores primários podem controlar reações químicas. O grupo particular das cianobactérias atua promovendo a entrada de carbono e nitrogênio por meio da sua capacidade de realizar fotossíntese oxigênica e fixação de nitrogênio atmosférico. No Brasil, as florestas de manguezais ocupam uma área de aproximadamente 25.000 km2 e no Estado de São Paulo, 240 km2 da área total está coberta por este ecossistema. O objetivo deste trabalho foi avaliar a diversidade de cianobactérias que colonizam as folhas de Avicennia schaueriana, Rhizophora mangle e Laguncularia racemosa do manguezal da Ilha do Cardoso, um ambiente pristino, bem como acessar e comparar a população de cianobactérias dos solos dos manguezais da Ilha do Cardoso e de Bertioga, este último contaminado com óleo bruto. Para este propósito, as técnicas de DGGE e biblioteca de clone do gene RNAr 16S, ARISA e TRFLP do gene nifH foram utilizadas. Os resultados da filosfera evidenciaram uma sutil influência do gênero de árvore na colonização das cianobactérias, entretanto, um forte efeito da localização destas dentro do manguezal foi observado. As folhas das árvores do meio da área de manguezal apresentaram uma maior diversidade de gêneros de cianobactérias. No geral, foram identificados 19 gêneros e várias sequências de cianobactérias não cultiváveis. Uma predominância de sequências com alta similaridade com representantes das ordens Nostocales e Oscillatoriales foi observada. Sequências com identidade com o gênero Symphyonemopsis (ordem Stigonematales) foram recuperadas em maiores quantidade. Com relação à diversidade no solo, os resultados de DGGE e ARISA demonstraram que a população de cianobactérias é distinta entre os manguezais estudados, porém os perfis eletroforéticos das amostras coletadas próximo ao mar se agruparam, sugerindo que a colonização é influenciada pelas condições de inundação. O perfil mais diferente foi obtido no ponto próximo à floresta no manguezal de Bertioga, local mais afetado pela contaminação de óleo. As bibliotecas de clones claramente indicaram diferenças das sequências do gene RNAr 16S entre os pontos amostrados. Um total de 99 UTOs foi obtido, com 61 "singletons". Na localidade próxima ao mar os gêneros Procholorococcus e Synechococcus foram dominantes em ambos os manguezais. A maioria das sequências de RNAr 16S encontradas nos outros pontos foram relacionadas com cianobactérias não cultiváveis. A diversidade alfa sugeriu que o local com menor diversidade foi o meio do manguezal de Bertioga, e o maior foi em Bertioga próximo à floresta, os demais pontos tiveram valores similares. Os maiores índices de riqueza foram encontrados nos pontos próximos à floresta, enquanto menores valores foram observados nos pontos próximos ao mar. A maioria das sequências de RNAr 16S obtidas em Bertioga no meio do manguezal e próximo à floresta tiveram identidades menores do que 90% com as disponíveis no GenBank. Estas sequências podem representar novos táxons ou cianobactérias conhecidas, porém ainda não sequenciadas. O TRFLP do gene nifH indicou que os locais próximos ao mar e meio do manguezal na Ilha do Cardoso abrigaram populações de diazotróficos semelhantes, enquanto que em Bertioga estes pontos apresentaram diferenças nos perfis de TRFLP. As maiores diferenças estavam nos locais próximos à floresta em ambos os manguezais. / Microorganisms play important role in the recycling of elements in mangrove ecosystems, since as primary producers they can control chemical reactions. The particular cyanobacteria group act promoting the input of carbon and nitrogen through their ability to realize oxygenic photosynthesis and fixing atmospheric nitrogen. In Brazil, the mangrove forests occupy an area of approximately 25.000 km2, and in the total area of São Paulo State, 240 km2 are covered by this ecosystem. The aim of this work was to evaluate the cyanobacterial diversity that colonize Avicennia schaueriana, Rhizophora mangle and Laguncularia racemosa leaves from Cardoso Island mangrove, a pristine site, as well as to assess and compare the soil cyanobacterial population from both Cardoso Island and Bertioga mangroves, this last one contaminated with crude oil. For this purpose, the techniques of DGGE and clone library of 16S rRNA gene, ARISA, and TRFLP of nifH gene were used. The phyllosphere results evidenced a subtle difference of the genus of tree on the colonization of cyanobacteria, however a strong effect from tree’s location within the mangrove was observed. The tree leaves from the middle of mangrove area showed a greater diversity of cyanobacterial genera. In geral, 19 genera and several uncultivated cyanobacteria were identified. A predominance of sequences with high similarities to representatives of the order Nostocales and Oscillatoriales were observed. Sequences with similarities to the genus Symphyonemopsis (order Stigonematales) were recovered in higher quantity. Regarding to the soil diversity, DGGE and ARISA results showed that the cyanobacterial population is distinct among both mangroves studied, however the electrophoretic profiles from samples collected near to the sea grouped together, suggesting that colonization is influenced by flood conditions. The most different profile was obtained in the site near to the forest in Bertioga mangrove, location more affected by the oil contamination. Clone libraries clearly showed 16S rRNA sequences differences among sites sampled. A total of 99 OTUs were obtained, with 61 singletons. In the site near to the sea the Procholorococcus and Synechococcus genera were dominant in both mangroves. The majority of 16S rRNA sequences found in the other sites were related to uncultured cyanobacteria. Alpha diversity suggested that the site with lowest diversity was middle of the Bertioga mangrove, and the highest was Bertioga near to the forest, the remainder sites had similar values. The highest richness indices were found in the sites near to the forest, while lower values were observed in the sites near to the sea. The majority of the 16S rRNA sequences obtained from the middle of the mangrove and near to the forest in Bertioga showed identities lower than 90% with that available in the GenBank. These sequences may represent novel cyanobacterial taxa or known cyanobacteria not yet sequenced. The TRFLP of nifH gene indicated that the sites near to the sea and middle of the Cardoso Island mangrove harbored similar diazotrophic populations, while in Bertioga these sites presented differences in TRFLP profiles. The greatest differences were in the sites near to the forest in both mangroves.

Dentre os contaminantes de água subterrânea de maior importância está o tetracloroeteno (PCE), o qual é altamente tóxico e potencialmente carcinógeno. As comunidades bacterianas de águas subterrâneas contaminadas com PCE e a diversidade de bactérias capazes de degradar esses organoclorados são pouco conhecidas. O objetivo deste trabalho é comparar a estrutura das comunidades de bactérias de amostras de água subterrânea em uma área contaminada com PCE e selecionar um consórcio microbiano capaz de degradar eficientemente o PCE em reator horizontal de leito fixo (RHLF). Amostras de água subterrânea de oito poços de monitoramento, instalados em uma área contaminada com PCE foram coletadas e analisadas para determinação de oxigênio dissolvido, potencial redox, condutividade elétrica, pH e concentração de tetracloroeteno, tricloroeteno, cis-dicloroeteno e cloreto de vinila (COVs). As amostras foram analisadas também para a determinação da estrutura das comunidades de bactéria por PCRDGGE e seqüenciamento de clones do gene rRNA 16S. Os parâmetros físico-químicos oscilaram consideravelmente ao longo do tempo em todos os poços de monitoramento (PM). Tetracloroeteno e tricloroeteno foram detectados apenas no PM6. As estruturas das comunidades bacterianas dos PMs analisados mostraram tanto variação temporal quanto espacial. As análises das comunidades bacterianas nos PM6 e PM8, contaminado e não-contaminado com PCE, revelaram resultados semelhantes aos obtidos por DGGE. Uma maior riqueza estimada de espécies bacterianas foi observada nas amostras do PM8, pelo menos em duas épocas de amostragem, sugerindo que a contaminação com PCE está associada com a redução da diversidade bacteriana em água subterrânea. Cultivos de enriquecimento e ensaios de degradação do PCE foram realizados utilizando-se um RHLF, o qual foi preenchido com sedimento do PM6 imobilizado em espuma de poliuretano e enriquecido com meio mineral básico suplementado com PCE. A análise das alterações nas comunidades de bactérias nos reatores foi feita por PCRDGGE e seqüenciamento parcial do gene rRNA 16S. No ensaio de degradação do PCE no RHLF foi utilizado meio com PCE suplementado ou não com lactato e acetato. Tanto pelo DGGE quanto pelo seqüenciamento, foi observada a seleção de bactérias específicas no reator. A partir das análises de seqüenciamento, essas bactérias foram identificadas como Alphaproteobacteria e Sphingobacteria. No ensaio de degradação do PCE, os parâmetros físico-químicos do meio não mostraram variações ao longo do comprimento dos reatores. As análises de COVs mostraram uma grande eficiência na degradação do PCE (98%), com um tempo de retenção de 12 horas, não havendo diferença significativa na percentagem de degradação em meio com lactato ou acetato, com relação ao controle sem fonte de carbono. No processo de degradação nenhum dos produtos da via de degradação do PCE foi detectado, o que sugere uma via alternativa de degradação do PCE, a qual ocorre em aerobiose. / Tetrachloroethene (PCE) is one of the most important contaminants of groundwater, since it is highly toxic and potentially carcinogenic. The bacterial communities of PCE contaminated groundwater and the diversity of bacteria capable of degrading this contaminant are barely known. The objective of this work is to compare the structure of bacterial communities from groundwater samples from a PCE contaminated site and select a microbial consortium capable to degrading efficiently PCE in a horizontal fixed bed reactor (HFBR). Groundwater samples from eight monitoring wells, installed in a PCE contaminated site were collected and analyzed for determination of dissolved oxygen, redox potential, electrical conductivity, pH, and concentrations of tetrachloroethene, trichloroethene (TCE), cis- and trans-dichloroethene, vinyl chloride (VOCs). The structure of the bacterial communities was determined by PCR-DGGE and 16S rRNA gene clone sequencing. The physical-chemical parameters oscillated considerately throughout time in all the monitoring wells (MW). PCE and TCE were detected only in MW6. The bacterial community structures in the groundwater from the MWs analyzed showed temporal and spatial variation. The analysis of the bacterial communities in MW6 and MW8, contaminated and non-contaminated with PCE, respectively, based on sequencing of 16S rRNA gene clones revealed results to the ones observed by DGGE. Estimated richness of bacterial species was higher in samples from MW8, at least in two sampling times, suggesting that the contamination with PCE is associated with reduction of bacterial diversity in groundwater. Enrichment cultures and PCE biodegradation assays were performed in a HFBR, which was filled with sediment from MW6 immobilized onto polyurethane foam and enriched with basic mineral medium supplemented with PCE. Shifts in bacterial community structure were analyzed using PCRDGGE and partial sequencing of 16S rRNA gene clones. In the PCE biodegradation assays in the HFBR, were performed in medium containing lactate or acetate. DGGE and 16S rRNA gene clone sequencing data suggest selection of specific bacteria in the reactor. Sequencing data showed that these bacteria belong to Alphaproteobacteria and Sphingobacteria. In the PCE biodegradation assays, media physical-chemical parameters did not show variation along the reactor length. VOC analyses showed a great efficiency in the degradation of PCE (98%) with a residence time of 12 hours in the reactor, and no significant differences were observed in the presence of lactate or acetate, as compared to the medium without a carbon source. During the biodegradation process, none of the products from the anaerobic pathway of PCE reductive dechlorination was detected, suggesting that an alternative PCE biodegradation pathway is occurring in aerobiosis.

Os micro-organismos desempenham importante papel na reciclagem dos elementos em ecossistemas de manguezais, uma vez que como produtores primários podem controlar reações químicas. O grupo particular das cianobactérias atua promovendo a entrada de carbono e nitrogênio por meio da sua capacidade de realizar fotossíntese oxigênica e fixação de nitrogênio atmosférico. No Brasil, as florestas de manguezais ocupam uma área de aproximadamente 25.000 km2 e no Estado de São Paulo, 240 km2 da área total está coberta por este ecossistema. O objetivo deste trabalho foi avaliar a diversidade de cianobactérias que colonizam as folhas de Avicennia schaueriana, Rhizophora mangle e Laguncularia racemosa do manguezal da Ilha do Cardoso, um ambiente pristino, bem como acessar e comparar a população de cianobactérias dos solos dos manguezais da Ilha do Cardoso e de Bertioga, este último contaminado com óleo bruto. Para este propósito, as técnicas de DGGE e biblioteca de clone do gene RNAr 16S, ARISA e TRFLP do gene nifH foram utilizadas. Os resultados da filosfera evidenciaram uma sutil influência do gênero de árvore na colonização das cianobactérias, entretanto, um forte efeito da localização destas dentro do manguezal foi observado. As folhas das árvores do meio da área de manguezal apresentaram uma maior diversidade de gêneros de cianobactérias. No geral, foram identificados 19 gêneros e várias sequências de cianobactérias não cultiváveis. Uma predominância de sequências com alta similaridade com representantes das ordens Nostocales e Oscillatoriales foi observada. Sequências com identidade com o gênero Symphyonemopsis (ordem Stigonematales) foram recuperadas em maiores quantidade. Com relação à diversidade no solo, os resultados de DGGE e ARISA demonstraram que a população de cianobactérias é distinta entre os manguezais estudados, porém os perfis eletroforéticos das amostras coletadas próximo ao mar se agruparam, sugerindo que a colonização é influenciada pelas condições de inundação. O perfil mais diferente foi obtido no ponto próximo à floresta no manguezal de Bertioga, local mais afetado pela contaminação de óleo. As bibliotecas de clones claramente indicaram diferenças das sequências do gene RNAr 16S entre os pontos amostrados. Um total de 99 UTOs foi obtido, com 61 “singletons”. Na localidade próxima ao mar os gêneros Procholorococcus e Synechococcus foram dominantes em ambos os manguezais. A maioria das sequências de RNAr 16S encontradas nos outros pontos foram relacionadas com cianobactérias não cultiváveis. A diversidade alfa sugeriu que o local com menor diversidade foi o meio do manguezal de Bertioga, e o maior foi em Bertioga próximo à floresta, os demais pontos tiveram valores similares. Os maiores índices de riqueza foram encontrados nos pontos próximos à floresta, enquanto menores valores foram observados nos pontos próximos ao mar. A maioria das sequências de RNAr 16S obtidas em Bertioga no meio do manguezal e próximo à floresta tiveram identidades menores do que 90% com as disponíveis no GenBank. Estas sequências podem representar novos táxons ou cianobactérias conhecidas, porém ainda não sequenciadas. O TRFLP do gene nifH indicou que os locais próximos ao mar e meio do manguezal na Ilha do Cardoso abrigaram populações de diazotróficos semelhantes, enquanto que em Bertioga estes pontos apresentaram diferenças nos perfis de TRFLP. As maiores diferenças estavam nos locais próximos à floresta em ambos os manguezais. / Microorganisms play important role in the recycling of elements in mangrove ecosystems, since as primary producers they can control chemical reactions. The particular cyanobacteria group act promoting the input of carbon and nitrogen through their ability to realize oxygenic photosynthesis and fixing atmospheric nitrogen. In Brazil, the mangrove forests occupy an area of approximately 25.000 km2, and in the total area of São Paulo State, 240 km2 are covered by this ecosystem. The aim of this work was to evaluate the cyanobacterial diversity that colonize Avicennia schaueriana, Rhizophora mangle and Laguncularia racemosa leaves from Cardoso Island mangrove, a pristine site, as well as to assess and compare the soil cyanobacterial population from both Cardoso Island and Bertioga mangroves, this last one contaminated with crude oil. For this purpose, the techniques of DGGE and clone library of 16S rRNA gene, ARISA, and TRFLP of nifH gene were used. The phyllosphere results evidenced a subtle difference of the genus of tree on the colonization of cyanobacteria, however a strong effect from tree’s location within the mangrove was observed. The tree leaves from the middle of mangrove area showed a greater diversity of cyanobacterial genera. In geral, 19 genera and several uncultivated cyanobacteria were identified. A predominance of sequences with high similarities to representatives of the order Nostocales and Oscillatoriales were observed. Sequences with similarities to the genus Symphyonemopsis (order Stigonematales) were recovered in higher quantity. Regarding to the soil diversity, DGGE and ARISA results showed that the cyanobacterial population is distinct among both mangroves studied, however the electrophoretic profiles from samples collected near to the sea grouped together, suggesting that colonization is influenced by flood conditions. The most different profile was obtained in the site near to the forest in Bertioga mangrove, location more affected by the oil contamination. Clone libraries clearly showed 16S rRNA sequences differences among sites sampled. A total of 99 OTUs were obtained, with 61 singletons. In the site near to the sea the Procholorococcus and Synechococcus genera were dominant in both mangroves. The majority of 16S rRNA sequences found in the other sites were related to uncultured cyanobacteria. Alpha diversity suggested that the site with lowest diversity was middle of the Bertioga mangrove, and the highest was Bertioga near to the forest, the remainder sites had similar values. The highest richness indices were found in the sites near to the forest, while lower values were observed in the sites near to the sea. The majority of the 16S rRNA sequences obtained from the middle of the mangrove and near to the forest in Bertioga showed identities lower than 90% with that available in the GenBank. These sequences may represent novel cyanobacterial taxa or known cyanobacteria not yet sequenced. The TRFLP of nifH gene indicated that the sites near to the sea and middle of the Cardoso Island mangrove harbored similar diazotrophic populations, while in Bertioga these sites presented differences in TRFLP profiles. The greatest differences were in the sites near to the forest in both mangroves.

Entre as principais oleaginosas eleitas para a produção de biodiesel, encontra-se a mamona (Ricinus communis L.), por possuir elevado teor de óleo, conhecido como óleo de rícino, extraído pela prensagem das sementes, contendo 90% de ácido graxo ricinoléico, o qual confere ao óleo suas características singulares, possibilitando ampla gama de utilização industrial. A produção brasileira de mamona concentra-se na caatinga baiana. A agricultura desta região, embora seja feita sem o uso de insumos agrícolas mantém uma produtividade regular. Com isso, tornou-se importante avaliar o efeito ambiental desta cultura sobre os estoques de C (carbono) e N (nitrogênio) no solo e os mecanismos de sua manutenção. Este trabalho foi realizado em solos de uma fazenda na região de Irecê-BA, tendo como objetivos calcular os estoques de C e N no solo; calcular o fluxo de gases do efeito estufa dos resíduos de mamona; calcular os valores C e N da biomassa microbiana no solo (BMS) e analisar o perfil da comunidade de bactérias fixadoras de N2 no solo por PCR-DGGE. Os resultados indicaram a ausência de variações nos estoques de C entre os tratamentos de mamona com 10, 20 e 50 anos de cultivo (48 Mg ha-1) sendo superados pelos valores encontrados na caatinga (90 Mg ha-1); mesma condição para o estoque de N (5,3 Mg ha-1 nos tratamentos de mamona e 8 Mg ha-1 na caatinga). Já os valores de C-microbiano foram superiores na caatinga, mas não apresentaram diferenças entre os cultivos de mamona; para o N-microbiano, os valores não sofreram diferenças entre as camadas, porém foram inferiores no tratamento de mamona com 10 e 50 anos de cultivo. O fluxo de gases de N-N2O e C-CO2 foram maiores para o tratamento com aplicação de resíduos orgânicos de mamona chegando a 160 mg m-2 h-1 de C-CO2 e 600 mg m-2 h-1 de N-N2O. O teste de redução de acetileno (ARA) e a análise de DGGE indicaram que o perfil da comunidade de bactérias diazotróficas do solo nos diferentes tratamentos sofreu alteração e permitiu a estocagem de N no solo durante os 50 anos de cultivo viabilizando, ambientalmente, a produção de mamona nesta região. / Among the main oils elected for biodiesel production is the castor bean (Ricinus communis L.) for its high oil content, known as castor oil extracted by pressing the seeds containing 90% ricinoleic acid, which gives the oil its unique features, allowing a wide range of industrial use. Brazilian production of castor oil is concentrated in the tropical dry forest of Bahia. Farming in this region, although it is made without the use of agricultural inputs remains a regular productivity. With this, it became important to assess the \"environmental effect\" of this culture on the stocks of C (carbon) and N (nitrogen) in soil and the mechanisms for its maintenance. This work was carried out in soils of a farm in Irecê-BA, aimed to calculate the stocks of C and N in soil, calculated the flows of greenhouse gases from oil waste; to figure out the values of carbon (C) and nitrogen (N) of microbial biomass in soil (BMS and to analyze the profile of the community of N2-fixing bacteria in soil through denaturing gradient gel electrophoresis (DGGE). Results indicated the absence of changes in C stocks between treatments of castor oil with 10, 20 and 50 years of cultivation (about 48 Mg ha-1) being outweighed by values found in the tropical dry forest (90 Mg ha-1); same condition verified for the stock of N (5.3 Mg ha-1 treatments of castor and 8 Mg ha-1 in tropical dry forest). As for values of microbial-C, they were higher in the tropical dry forest and did not present differences between the cultures of castor oil; regarding microbial-N values, there have not been differences between the layers, but they were lower for castor oil with 10 and 50 years of cultivation. The gases flow accumulated N-N2O was significantly higher than that of CCO2 and higher for the treatment of soil with organic fertilizer castor reaching 160 mg m- 2 h-1 of C-CO2 and 600 mg m-2 h-1 of N-N2O. ARA analysis and DGGE indicated that the profile of the diazotrophic community of soil in different treatments had change, allowing the storage of N in soil during the 50 years of cultivation enabling, in environmental terms, the production of castor oil in this region.