O sedimento marinho da Península Antártica representa uma área sensível a mudanças ambientais. No entanto, pouco se conhece sobre as comunidades microbianas que habitam esse ecossistema, incluindo a sua diversidade, distribuição e variações temporais. O objetivo foi determinar a estrutura das comunidades microbianas nos sedimentos marinhos da Baía do Almirantado, Ilha Rei George, Península Antártica. Sedimentos da Baía apresentam uma predominância dos Filos Proteobacteria, Firmicutes e Actinobacteria. Análise temporal revelou que comunidades microbianas em sedimentos próximos à estação Ferraz são mais estáveis quando comparadas aos sedimentos em áreas de menor atividade antrópica. No gradiente de profundidade foi observado que a estrutura de comunidade não mudou, indicando tolerância a variações de pressão hidrostática. Organismos heterotróficos dos gêneros Psychrobacter, Psychromonas e Loktanella foram os mais abundantes, sugerindo uma alta concentração de matéria orgânica disponível. O enriquecimento de culturas metanogênicas produziu até 1,70 mmol de CH4 após 120 dias de incubação. Este estudo sugere que as condições dos sedimentos favorecem organismos psicrofílicos de metabolismo heterotrófico. / Marine sediment of the Antarctic Peninsula is a susceptible area to environmental changes. However, little is known about the microbial communities inhabiting this ecosystem, including its diversity, distribution and variations over time. The aim of this study was to determine the structure of microbial communities present in marine sediments of Admiralty Bay, King George Island, on the Antarctic Peninsula. Sediments from Admiralty Bay shown a predominance of the Proteobacteria, Firmicutes, and Actinobacteria phyla. Temporal analysis revealed that microbial communities in sediment, near Ferraz station, are more stable compared to that in the sediments in areas of lower human activity. No variation on the community structure was observed in depth gradient, indicating tolerance to hydrostatic pressure variations. Heterotrophic organisms of the genera Psychrobacter, Psychromonas and Loktanella were the most abundant, suggesting a high concentration of organic matter in the sediment. Enrichment of methanogenic cultures enrichment yielded 1.70 mmol of CH4. This study suggests that conditions in sediments favoring metabolism of heterotrophic and psychrophilic organisms.

Made available in DSpace on 2015-04-20T12:31:44Z (GMT). No. of bitstreams: 1 Tese Ieda.pdf: 2549784 bytes, checksum: a9a4b9fb883e1aa2757719de2c81ea18 (MD5) Previous issue date: 2009-06-24 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Biodiversity is a fundamental element for biotechnology development, especially in Amazon because its incontestable potential. One aspect of high interest is the search for management mechanisms that can promote environmental quality, ensuring the maintenance of natural features of ecosystems. In this context is located an important biotechnology tool that is the bioremediation of environments contaminated with toxic and recalcitrant compounds. Thus the exploration of microrganisms for use in these processes has been a challenge. This work presents a study about sample of bacterial community associated with the aquatic macrophyte Eichornia crassipes, assessing their potential for biodegradation of petroleum hydrocarbons. Selective isolations and preliminary identification of some of the isolates by region of 16S ribosomal DNA sequences to compare with the Gen Bank were done. The potential to produce biossurfactantes was evaluated by the activity of bacteria in emulsification. The growth of strains was assessed by mineral medium with hydrocarbons mixing and mineral medium with crude oil. The rate of toxicity was evaluated in mixture of hydrocarbon extracts with the five strains that showed the best growth. Considering the results of these first tests, it was produced a consortium with bacteria more efficient. It was evaluated the degradation of aliphatic and aromatic hydrocarbons in experiment containing Amazon river water, using the techniques of bioaugmentation and biostimulation. There were isolated 71 bacteria, 42 epiphytic and 29 endophytic. The preliminary identification revealed the predominance of the genera Acinetobacter, Pseudomonas, Bacillus and Stenotrophomonas. There was more bacterial growth in medium with crude oil, especially the strain Stenotrophomonas sp,. reaching around 13.4 x106 UFCs / mL. The methods used in bacterial growth indicated the degradation of petroleum hydrocarbons, whereas they were the sole source of carbon. Highlighted in the production of biossurfactantes the strains Methylobacterium sp and Stenotrophomonas radiotolerans, with better results in the medium with oil. The indices of toxicity showed better results in extracts of bacterial growth compared to control extracts. The strains that showed better results were used for consortium production: Stenotrophomonas sp., Uncultured Klebsiella sp., Enterobacter sp., Methylobacterium radiotolerans and Acinetobacter baumannii. In the experimental design with the consortium, the results showed that the main effect of all parameters studied influenced the degradation of the hydrocarbons studied, however the addition of the consortium was the most important factor in this decline, demonstrating the potential of these strains for use in future processes of bioremediation. / A biodiversidade é elemento fundamental para o desenvolvimento da Biotecnologia, em especial na Amazônia devido sua inconteste potencialidade. Um dos aspectos de elevado interesse é a busca por mecanismos de gestão que possam promover a qualidade ambiental, garantindo a manutenção das características naturais dos ecossistemas. Neste contexto situa-se uma importante ferramenta biotecnológica que é a biorremediação de ambientes contaminados por compostos tóxicos e recalcitrantes. Assim, a prospecção de microrganismos para uso nesses processos tem sido um desafio permanente. No presente trabalho realizou-se estudo de amostra da comunidade bacteriana associada à macrófita aquática Eichornia crassipes, avaliando seu potencial de biodegradação de hidrocarbonetos de petróleo. Foi feito isolamento seletivo e identificação preliminar de parte dos isolados por meio da região do DNA ribossomal 16S com comparação com sequências do Gen Bank. Verificou-se o potencial para a produção de biossurfactantes por meio da avaliação da atividade de emulsificação em cepas bacterianas. O crescimento de cepas foi avaliado em meio mineral com mistura de hidrocarbonetos e em meio mineral com petróleo bruto. O índice de toxicidade foi avaliado nos extratos dos meios com mistura de hidrocarbonetos das cinco cepas que apresentaram melhor crescimento. Considerando os resultados destes primeiros testes, foi produzido um consórcio com as cepas bacterianas mais eficientes. Este consórcio foi avaliado quanto à degradação de hidrocarbonetos alifáticos e aromáticos em experimento contendo água de rio da Amazônia, sendo utilizadas as técnicas de bioaumentação e bioestimulação. Obteve-se no isolamento 71 bactérias, sendo 42 epifíticas e 29 endofíticas. A identificação preliminar revelou a predominância dos gêneros Acinetobacter, Pseudomonas, Bacillus e Stenotrophomonas. Verificou-se melhor crescimento bacteriano no meio com petróleo bruto, destacando-se a cepa Stenotrophomonas sp. que atingiu cerca de 13,4x106 UFCs/mL. O crescimento bacteriano nos meios utilizados indicou a degradação dos hidrocarbonetos de petróleo, considerando que estes eram a única fonte de carbono. Destacaram-se na produção de biossurfactantes as cepas Stenotrophomonas sp e Methylobacterium radiotolerans, com melhores resultados no meio com petróleo. Os índices de toxicidade mostraram melhores resultados nos extratos do crescimento bacteriano em comparação aos extratos controles. As cepas que demonstraram melhores resultados e que foram utilizadas para a produção do consórcio foram Stenotrophomonas sp., Uncultured Klebsiella sp., Enterobacter sp., Methylobacterium radiotolerans e Acinetobacter baumannii. No planejamento experimental com o consórcio, os resultados obtidos demonstraram que o efeito principal de todos os parâmetros analisados influenciaram na degradação dos hidrocarbonetos avaliados, entretanto a adição do consórcio foi o fator mais importante nesta degradação, demonstrando o potencial destas linhagens para uso em futuros processos de biorremediação.

Ehemalige Urangruben tragen durch das anfallende Flutungswasser maßgeblich zur Ausbreitung von Schadstoffen wie Uran und Arsen in teils dicht besiedelte Gebiete bei. Um die Prozesse in den unterirdischen Gruben besser zu verstehen und alternative Strategien zur konventionellen, kostenintensiven Wasserbehandlung entwickeln zu können, war das Ziel der Arbeit, mikrobielle Gemeinschaften aus drei gefluteten Uranerzbergwerken in Sachsen, namens Pöhla, Schlema und Zobes, die unterschiedliche Flutungsstadien repräsentierten, zu charakterisieren und den mikrobiellen Einfluss auf die Mobilität von Uran und Arsen zu untersuchen. Um herauszufinden, welche Mikroorganismen die hydrochemischen Vorgänge im Untergrund der Uranerzbergwerke beeinflussen könnten, wurde die Diversität und Zusammensetzung mikrobieller Gemeinschaften mittels Pyrosequenzierung eines Fragments des 16S rRNA Gens (16S rDNA) und CARD-FISH ermittelt. Wenngleich Clusteranalysen zeigten, dass sich die planktonischen Gemeinschaften hinsichtlich ihrer bakteriellen Zusammensetzung zwischen den drei Uranerzbergwerken unterschieden, wurden alle von chemolithotrophen Schwefeloxidierern der Beta- und Epsilonproteobacteria dominiert, die mit den Gattungen Thiobacillus und Sulfuritalea bzw. Sulfuricurvum und Sulfurimonas vertreten waren. Im Unterschied zu den planktonischen Gemeinschaften bestanden in situ Biofilme, die auf BACTRAPs während einer 3-monatigen Exposition im Flutungswasser anwuchsen, laut Pyrosequenzierung zu einem wesentlichen, mitunter dominanten Anteil aus metall- bzw. sulfatreduzierenden Deltaproteobacteria. In Biofilmgemeinschaften aus Zobes wurden hauptsächlich Geobacter sp. detektiert, die als Fe(III)- und U(VI)-Reduzierer bekannt sind. Obwohl Archaea basierend auf den Ergebnissen der CARD-FISH-Analyse nur einen sehr geringen Anteil der planktonischen Gemeinschaften ausmachten, wurden mittels Pyrosequenzierung planktonische Euryarchaeota der Thermoprotei in allen Gruben detektiert. In planktonischen Gemeinschaften und 3-monatigen Biofilmen aus Pöhla und Zobes wurden zudem methanogene Crenarchaeota, vor allem Methanobacteria und teilweise Methanomicrobia, ermittelt. Die 16S rRNA-Analyse, die ergänzend zum DNA-basierten Ansatz durchgeführt wurde, lieferte Hinweise darauf, dass die detektierten, dominanten Mikroorganismen, Bacteria sowie Archaea, in der planktonischen Gemeinschaft aus Schlema und den Biofilmgemeinschaften stoffwechselaktiv waren. In der planktonischen Gemeinschaft aus Zobes wurden im Vergleich zur DNA-basierten Analyse höhere Abundanzen für Verrucomicrobia, Acidobacteria und Alphaproteobacteria ermittelt, deren Bedeutung offen bleibt. Untersuchungen zum mikrobiellen Stoffwechselpotential planktonischer Gemeinschaften mittels CFU- und MPN-Analysen ergaben, dass Mikroorganismen aus allen Urangruben ein breites Spektrum anaerober Reaktionen (Nitrat-, Eisen-, Mangan-, Arsenat- und Sulfatreduktion und Acetogenese) unter Laborbedingungen abdeckten. In guter Übereinstimmung mit den Sequenzierungsergebnissen konnten methanogene Mikroorganismen nur im Flutungswasser aus Pöhla und Zobes detektiert werden. Die Metaproteomanalyse ergab, dass 61,6% der Peptide in der planktonischen Gemeinschaft aus Schlema von den dominanten Epsilonproteobacteria stammten. Dagegen wurden für Zobes detektierte Peptide mehrheitlich methylotrophen und eisenoxidierenden Betaproteobacteria der Familien Methylophilaceae bzw. Gallionellaceae sowie methylotrophen Gammaproteobacteria der Methylococcaceae zugewiesen. Obwohl die Mehrheit der Proteine an der Translation beteiligt war, konnten insgesamt 49 Proteingruppen ermittelt werden, deren Vertreter für den mikrobiellen Energiestoffwechsel relevant waren. Insbesondere planktonische Gammaproteobacteria aus Zobes konnten so mit dem Kohlenstoff- und Schwefelkreislauf in Zusammenhang gebracht werden. Mithilfe von Labormikrokosmen wurde der potentielle Einfluss mikrobieller Gemeinschaften aus Schlema auf die Mobilität von Arsen und Uran im Flutungswasser mit Acetat als Elektronendonor unter anaeroben Bedingungen über einen Zeitraum von 98 Tagen untersucht. Im Vergleich zu den Kontrollen konnten sowohl die stimulierte, planktonische Gemeinschaft als auch Biofilme natürliches Arsen aus der wässrigen Phase fast vollständig entfernen. Allerdings wies der spätere Anstieg des gelösten Arsens daraufhin, dass der immobilisierte Zustand langfristig nicht stabil blieb. In stimulierten Biofilm-Ansätzen wurde Uran mit bis zu 39 ± 9% (in Anwesenheit von 7 µM natürlichem Uran) bzw. 34 ± 8% (bei Zugabe von 50 µM U(VI)) aus der wässrigen Phase langfristig (98 Tage) immobilisiert. Laserfluoreszenzspektroskopische Untersuchungen zeigten, dass Uran im Biofilm reduziert wurde.

Shallow seagrass ecosystems frequently experience physical disturbance from vessel groundings. Specific restoration methods that modify physical, chemical, and biological aspects of disturbances are used to accelerate recovery. This study evaluated loss and recovery of ecosystem structure in disturbed seagrass meadows through plant and soil properties used as proxies for primary and secondary production, habitat quality, benthic metabolism, remineralization, and nutrient storage and exchange. The efficacy of common seagrass restoration techniques in accelerating recovery was also assessed. Beyond removal of macrophyte biomass, disturbance to seagrass sediments resulted in loss of organic matter and stored nutrients, and altered microbial and infaunal communities. Evidence of the effectiveness of restoration actions was variable. Fill placement prevented additional erosion, but the resulting sediment matrix had different physical properties, low organic matter content and nutrient pools, reduced benthic metabolism, and less primary and secondary production relative to the undisturbed ecosystem. Fertilization was effective in increasing nitrogen and phosphorus availability in the sediments, but concurrent enhancement of seagrass production was not detected. Seagrass herbivores removed substantial seagrass biomass via direct grazing, suggesting that leaf loss to seagrass herbivores is a spatially variable but critically important determinant of seagrass transplanting success. Convergence of plant and sediment response variables with levels in undisturbed seagrass meadows was not detected via natural recovery of disturbed sites, or through filling and fertilizing restoration sites. However, several indicators of ecosystem development related to primary production and nutrient accumulation suggest that early stages of ecosystem development have begun at these sites. This research suggests that vessel grounding disturbances in seagrass ecosystems create more complex and persistent resource losses than previously understood by resource managers. While the mechanics of implementing common seagrass restoration actions have been successfully developed by the restoration community, expectations of consistent or rapid recovery trajectories following restoration remain elusive.

The influence of parent lithology on the development of soil biogeochemical environments and their microbial diversity is explored by characterising soil profiles with respect to their mineral, solution and organic chemistry. Soil profiles were collected from a total of 17 sites, above basalt, granodiorite, shale, sandstone and limestone, across Northern Ireland. The soil system developed above basalt was examined to assess the development of soil bio-physicochemical properties and microbial diversity through the profile. These basalt soils showed two distinct horizons have developed in the previous 15’000 years, where soils from the top 20 cm of the profile were highly influenced by the interactions of soil minerals with soil organic and biological processes. In line with the observed differences in soil properties the microbial community structure varied; in the surface soils the community composition was dominated by root-associated bacteria. However the relative abundance of phyla affiliated with nutrient-limited conditions increased in samples from the base of the profile. Detailed examination of the soil profiles above granodiorite, shale, sandstone and limestone revealed large variations in soil geochemistry between profiles, reflecting the mineral geochemistry of the parent rock. Molecular analysis of SOM revealed compositional changes with depth were comparable between profiles; however TOC concentrations were consistently higher in the soil profiles above basalt suggesting greater stabilisation of SOM in these soils. The chemistry of the soil waters was not reflective of the parent rocks; however variations in soil texture, specifically the abundance of less reactive residual minerals in the sandstone and limestone soils, led to higher concentrations of soluble elements in these soils. Soil pH and DOC were found to have a large control on buffering the release of free Al, Cr and Fe ions into solution. The microbial communities in near-surface soils were similar to each other, regardless of lithology, and were dominated by Proteobacteria, Actinobacteria, and Acidobacteria. However microbial diversity shifted with depth; the abundance of Actinobacteria decreased and Nitrospirae increased, and between rock types where soils next to the basalt, shale and granodiorite bedrock contained sequences affiliated with novel Candidate Phyla AD3 and GAL15. In these soils differences in SOM composition were the main driver of the observed variation with depth, however where labile SOM was depleted, mineral and solution geochemistry may have a larger control on the community composition. To assess the influence of parent lithology on selenium mobility, soils above basalt and granodiorite were amended with sodium selenate. Under anaerobic conditions, the proportion of soluble selenate removed varied (39-77 %) depending on the sample through a combination of abiotic and microbial reduction processes. However, under aerobic conditions, larger concentrations of selenate remained in solution (79-100%).

>Magister Scientiae - MSc / The extreme conditions of Antarctic desert soils render this environment selective towards a diverse range of psychrotrophic microbial communities. Cracks and fissures in translucent quartz rocks permit an adequate amount of penetrating light, sufficient water and nutrients to support cryptic microbial development. Hypolithons colonizing the ventral surface of these quartz rocks have been classified into three types: cyanobacterial dominated (Type I),moss dominated (Type II) and lichenized (Type III) communities. Eukaryotic microbial communities were reported to represent only a minor fraction of Antarctic communities. In this study, culture independent techniques (DGGE, T-RFLP and clone library construction) were employed to determine the profile of the dominant eukaryotes, fungi and microalgae present in the three different hypolithic communities. The 18S rRNA gene (Euk for eukaryotes), internal transcribed spacer (ITS for fungi) and microalgal specific regions of the 18S rRNA gene, were the phylogenetic markers targeted for PCR amplification from hypolith metagenomic DNA. Results suggest that the three hypolith types are characterized by different eukaryotic, fungal and microalgal communities, as implied by nMDS analysis of the DGGE and T-RFLP profiles. Sequence analysis indicates close affiliation to members of Amoebozoa, Alveolata, Rhizaria (general eukaryote), Ascomycota (fungal) and Streptophyta (microalgal). Many of these clones may represent novel species. This study demonstrates that Dry Valley hypolithons harbour higher eukaryote diversity than previously recognised.Each hypolithon is colonized by specialized microbial communities with possible keystone species. The ecological role of the detected microorganisms in the hypolith environment is also theorized, and a trophic hierarchy postulated.

Les tapis microbiens sont des communautés benthiques, calcifiées (i.e. microbialites) ou non, diverses à la fois phylogénétiquement et métaboliquement. Les tapis microbiens fossiles constituent les plus anciennes traces de vie sur Terre et leurs représentants modernes peuvent donc être utilisés pour comprendre le fonctionnement de ces écosystèmes anciens. J'ai étudié les communautés microbiennes (archées, bactéries et eucaryotes) de plusieurs microbialites (lac Alchichica, Mexique) et tapis microbiens (dans une mare du salar de Llamara, Chili) afin de caractériser finement leur structure phylogénétique et d'améliorer notre compréhension de leur fonctionnement. J'ai pour cela utilisé une approche combinant des outils moléculaires (métabarcoding, métagénomique) à des données environnementales (paramètres physico-chimiques de la colonne d'eau ou composition minérale des microbialites). Mon travail de thèse a permis d'affiner le modèle de formation des microbialites d'Alchichica, en montrant notamment que, en plus de la photosynthèse oxygénique cyanobactérienne, le potentiel à précipiter des carbonates de la photosynthèse eucaryote et, surtout, de la photosynthèse anoxygénique est important. Les communautés des tapis de Llamara étaient quant à elles caractérisées par la présence de nombreuses lignées d'archées et de bactéries très divergentes, dont certaines ont été identifiées pour la première fois dans ce travail. Nos analyses ont aussi souligné la diversité des organismes impliqués dans les cycles du soufre et de l'azote au sein de ces systèmes et permis d'identifier de potentielles interactions biotiques entre des lignées procaryotes dont l'écologie est peu connue. Enfin, nous avons mis en évidence que les paramètres environnementaux influencent fortement la composition des communautés associées à ces microbialites et à ces tapis microbiens. L'ensemble de ces résultats permet de mieux comprendre le fonctionnement de ces systèmes ainsi que les facteurs qui influencent leur structure phylogénétique et fonctionnelle. / Microbial mats are phylogenetically and functionally diverse benthic microbial communities, which can be sometimes calcified (i.e. microbialites). Fossil microbial mats constitute the oldest traces of life on Earth and their modern representatives are thus used as analogues of those primordial ecosystems to gain insights into their functioning. I have studied the microbial communities (archaea, bacteria and eukaryotes) of several microbialites (lake Alchichica, Mexico) and microbial mats (in a small pond in the salar de Llamara, Chile). The main objectives of my PhD were to finely characterize their phylogenetic structure and to improve our understanding of the functioning of these complex ecosystems. To do so, I have applied a multi-disciplinary approach combining molecular approaches (metabarcoding, metagenomics) to environmental data (physico-chemical parameters of the water column or mineral composition of the microbialites).The results presented in this thesis allowed refining our model of microbialite formation in Lake Alchichica. We showed that, in addition to cyanobacterial photosynthesis, both eukaryotic and, particularly, anoxygenic photosyntheses were potentially important to promote carbonate precipitation. Llamara mat communities were characterised by the presence of numerous novel archaeal and bacterial lineages, some of which were identified for the first time in this work. Our analyses have also highlighted the diversity of organisms involved in both sulphur and nitrogen cycles in these mats and identified potential biotic interactions between poorly known prokaryotic lineages. Finally, we showed that the composition of the microbial communities associated to these microbialites and microbial mats was strongly influenced by environmental parameters. Overall, these results represent a substantial contribution to our understanding of the ecology of these systems as well as of the factors that influence their phylogenetic and functional structures.

Coal gasification stripped gas liquor (CGSGL) wastewater contains large quantities of complex organic and inorganic pollutants which include phenols, ammonia, hydantoins, furans, indoles, pyridines, phthalates and other monocyclic and polycyclic nitrogen-containing aromatics, as well as oxygen- and sulphur-containing heterocyclic compounds. The performance of most conventional aerobic systems for CGSGL wastewater is inadequate in reducing pollutants contributing to chemical oxygen demand (COD), phenols and ammonia due to the presence of toxic and inhibitory organic compounds. There is an ever-increasing scarcity of freshwater in South Africa, thus reclamation of wastewater for recycling is growing rapidly and the demand for higher effluent quality before being discharged or reused is also increasing. The selection of hybrid fixed-film bioreactor (HFFBR) systems in the detoxification of a complex mixture of compounds such as those found in CGSGL has not been investigated. Thus, the objective of this study was to investigate the detoxification of the CGSGL in a H-FFBR bioaugmented with a mixed-culture inoculum containing Pseudomonas putida, Pseudomonas plecoglossicida, Rhodococcus erythropolis, Rhodococcus qingshengii, Enterobacter cloacae, Enterobacter asburiae strains of bacteria, as well as the seaweed (Silvetia siliquosa) and diatoms. The results indicated a 45% and 79% reduction in COD and phenols, respectively, without bioaugmentation. The reduction in COD increased by 8% with inoculum PA1, 13% with inoculum PA2 and 7% with inoculum PA3. Inoculum PA1 was a blend of Pseudomonas, Enterobacter and Rhodococcus strains, inoculum PA2 was a blend of Pseudomonas putida iistrains and inoculum PA3 was a blend of Pseudomonas putida and Pseudomonas plecoglossicida strains. The results also indicated that a 70% carrier fill formed a dense biofilm, a 50% carrier fill formed a rippling biofilm and a 30% carrier fill formed a porous biofilm. The autotrophic nitrifying bacteria were out-competed by the heterotrophic bacteria of the genera Thauera, Pseudaminobacter, Pseudomonas and Diaphorobacter. Metagenomic sequencing data also indicated significant dissimilarities between the biofilm, suspended biomass, effluent and feed microbial populations. A large population (20% to 30%) of unclassified bacteria were also present, indicating the presence of novel bacteria that may play an important role in the treatment of the CGSGL wastewater. The artificial neural network (ANN) model developed in this study is a novel virtual tool for the prediction of COD and phenol removal from CGSGL wastewater treated in a bioaugmented H-FFBR. Knowledge extraction from the trained ANN model showed that significant nonlinearities exist between the H-FFBR operational parameters and the removal of COD and phenol. The predictive model thus increases knowledge of the process inputs and outputs and thus facilitates process control and optimisation to meet more stringent effluent discharge requirements. / Thesis (PhD)--University of Pretoria, 2017. / Chemical Engineering / PhD / Unrestricted

>Magister Scientiae - MSc / Molecular methods were used to investigate the microbial diversity and community structure of ammonia-oxidizing bacteria (AOB) associated with the roots of the Proteaceae plant family. The identification of ammonia oxidizing bacteria in this ecosystem is of particular interest since Proteaceae are adapted to acidic, low nutrient (e.g. nitrogen) soils. The ammonia monooxygenase operon was used as a molecular marker to identify ammonia-oxidizing bacteria associated with the proteoid roots of the three Proteaceae members and compared to non-plant associated soil. PCR amplification using primer sets targeting the ammonia monooxygenase gene (amoA subunits) were used to construct a clone library. Sequence diversity was determined by RFLP analysis of amoA to identify major groups of AOB of the ~-subclass of Proteobacteria in total community DNA, and DNA sequencing and phylogenetic analysis were also applied. DGGE analysis was performed to determine the community structure and distribution of ammonia-oxidizing bacteria in plant-associated and non-plant associated soils. The AOB genotypic diversity was similar in the plant-associated samples and non-plant associated soil. All AOB phylotypes belonged to Nitrosospira species and clustered with Nitrosospira cluster 3. The abundance of the amoA was quantified to be approximately 4.2 x 107 copies/g of dry soil, using a real-time PCR assay. These data suggest that the Nitrosospira species are the dominant phylotypes in that environment. This investigation provides new insights into the relationships between plants and ammonia-oxidizing bacteria in natural Fynbos ecosystems.

Microbes exert extensive control on redox element cycles. They participate directly orindirectly in the concentration and fractionation of elements by influencing the partitioningbetween soluble and insoluble species. Putative microbially mediated manganese (Mn) oxidesof the birnessite-type, enriched in rare earth elements (REE) + yttrium (Y) were recentlyfound in the Ytterby mine, Sweden. A poorly crystalline birnessite-type phyllomanganate isregarded as the predominant initial phase formed during microbial Mn oxidation. Owing to ahigher specific surface area, this biomineral also enhances the known sorption property of Mnoxides with respect to heavy metals (e.g. REE) and therefore has considerable environmentalimpact.The concentration of REE + Y (2±0.5% of total mass, excluding oxygen, carbon and silicon)in the Ytterby Mn oxide deposit is among the highest ever observed in secondary precipitateswith Mn and/or iron. Sequential extraction provides evidence of a mineral structure where theREE+Y are firmly included, even at pH as low as 1.5. Concentration ratios of Mn oxideprecipitates to fracture water indicate a strong preference for the trivalent REE+Y overdivalent and monovalent metals. A culture independent molecular phylogenetic approach wasadopted as a first step to analyze the processes that microbes mediate in this environment andspecifically how the microbial communities interact with the Mn oxides. Plausible players inthe formation of the investigated birnessite-type Mn oxides are mainly found within theferromanganese genera Hyphomicrobium and Pedomicrobium and a newly identified YtterbyBacteroidetes cluster most closely related to the Terrimonas. Data also indicate that thedetected microorganisms are related to the environmental constraints of the site including lowconstant temperature (8°C), absence of light, high metal content and possibly proximity to theformer storage of petroleum products.