Dissertations / Theses on the topic 'Late Archaean'

The greenstone belt of Kenya is an extension of what is commonly referred to as the Tanganyika "Shield". The two supracrustal sequences recognized in Kenya are the Nyanzian and the Kavirondian. The rocks found in these sequences are diverse, with dominant volcanics in the Nyanzian, whereas the Kavirondian is predominantly sedimentary. The Nyanzian lavas represent a diverse range from basalts and basaltic andesites, through andesites and dacites to rhyolites. From geochemical studies the basalts and basaltic andesites are tholeiitic, whereas the andesites, dacites and rhyolites are calc-alkaline. The sedimentary sequence ranges from mudstone, through shales, sandstones and grits to conglomerates. The plutonic rocks range in composition from gabbro to true granites, but tonalite is the dominant rock type. The chemical differences between the tholeiitic basalts and the calc-alkaline andesitic to rhyolitic sequences suggests that these volcanic suites are derived from different sources and/or through different processes. The granitoids have close chemical similarities with the silicic volcanics. From the geochemical and field relationships, the Nyanzian and Kavirondian sequences are considered to have developed on a continental segment which had not yet attained full stability. The model employed for the generation of these volcanics considers the basalts to have been generated in a region undergoing extension, similar to that of a modern back-arc environment, whereas the calc-alkaline sequences, including the granitoids, are broadly comparable with those found in present day continental arc environments.

>Magister Scientiae - MSc
Microorganisms of the class Actinobacteria and domain Archaea are interesting from a biotechnological perspective owing to their metabolic attributes as producers of secondary metabolites and resilience under harsh environmental conditions respectively. Lake Magadi is a soda lake well studied in terms of its geology and limnology. Research attention has also been drawn to the microbial populations which thrive in this unique habitat but currently there are no reports on the assessment of its microflora using molecular methods. This study aimed to assess the actinobacterial and archaeal communities within Lake Magadi, Kenya a hypersaline –highly alkaline habitat using metagenomic methods as a preliminary study to identify potential candidates for exploitative biology Samples from two sites dubbed Lake Magadi station 2 (LM2) and Lake Magadi salt pan 4 (LMS4) within the Lake Magadi were analyzed using the 16S rRNA gene as a phylogenetic marker. Cluster analysis of taxon-specific 16S rDNA PCR-DGGE profiles revealed moderately heterogeneous actinobacterial and archaeal populations across the sample sites under investigation which is probably a reflection of the differences in abiotic conditions at the study sites. This observation was also confirmed from the multi-dimensional scaling (MDS) plot. PCR-based clonal libraries of actinobacterial and archaeal communities of both study sites retrieved a total of thirty-two clones (twenty actinobacterial and twelve archaeal) were sequenced. Analysis of the sequences revealed cultured and uncultured signatures of microorganisms typical of hypersaline and or highly alkaline niches. A few (3) sequences presented novelty (<96%) in identities with any previously identified organism. It was concluded that the species dominance at site LMS4 [situated within the salt flats of Lake Magadi and site for exploration of trona and its mineralized extensions (nacholite and gayllusite)] is likely to be dictated by anthropogenic stress since most of the microbial signals associated with the study site are typical of saline and or alkaline environmental samples exposed to especially mining but also agricultural and waste management practices. Isolation studies also revealed previously identified strains peculiar to hypersaline brines and sediments. The strains retrieved were affiliated to the taxonomically diverse genus Bacillus and Halomonas sp. The true applications and potential opportunities these isolates have for biotechnology have been well documented. Observations made from the culture dependent and culture independent methods suggests strongly that study site LMS4 is subjected to environmental conditions more severe than at site LM2. This study is a guide for future studies as it provides primary information on the haloalkaliphilic representatives of the actinobacteria phylum and domain Archaea within the soda lake environment. It can serve as a pedestal for investigation into the molecular machinery that supports the haloalkaliphilic lifestyles of inhabiting microorganisms and consequently give leads as to how they can be commercially exploited.

From acid seeps and deep-sea thermal vents to glacial ice and hypersaline lakes, extreme environments contain relatively simplified communities consisting of extremophiles that have evolved to survive and thrive under adverse abiotic conditions. In more neutral environments, microorganisms use dormancy as a common life history strategy to weather temporal fluctuations of resources or stresses until more 'optimal' conditions are present. It is unclear if dormancy is an essential survival mechanism for microorganisms in extreme environments; however, recent studies suggest that extreme environments may create stable conditions for extremophiles to the extent that dormancy is of less ecological importance. Using lake salinity levels as measurements of "extreme," we evaluated the dormancy of bacterial and archaeal phyla and lake chemistry in five hypersaline and five freshwater lakes across the western United States. Dormancy was calculated using targeted metagenomics to analyze 16S rDNA and rRNA tag sequences. It was hypothesized that bacteria and archaea in hypersaline lake communities would exhibit lower levels dormancy than bacterial and archaeal communities in geologically similar freshwater lake controls. It was also hypothesized that microbial dormancy would decrease as the dominant extreme environmental variable increased in the lakes. As hypothesized, overall dormancy decreased at least 2-fold in hypersaline compared to freshwater lakes for both bacteria and archaea. Of the predominant phyla and subclasses, Firmicutes, Bacteroidetes, and Gammaproteobacteria each demonstrated at least a seven-fold decrease in dormancy in hypersaline lakes compared to freshwater lakes. Specifically, species within the genus Clostridium were responsible for 85% of the dormancy observed in the phylum Firmicutes. Also as hypothesized, microbial dormancy decreased as salinity increased in the lakes. Lower dormancy in hypersaline lakes correlated with increasing salinity while lower dormancy in freshwater lakes correlated with increasing total phosphorus levels. These results suggest that dormancy is a less common life history strategy for microorganisms in extreme environments; it is proposed that this is due to the relatively stable environment in hypersaline lakes and the reduced number of available microbial niches. These results also suggest that the dominant extreme stress (i.e., salinity) may override other driving factors in an environment to ultimately determine microbial community composition, diversity and richness.

Terrestrial inputs of organic matter contribute greatly to the functioning of aquatic ecosystems, subsidizing between 30-70% of secondary production. This contribution of terrestrial resources is especially important in boreal lakes that are largely nutrient-poor and thus more responsive to these additions. Yet the mechanisms underlying initial processing of terrestrial resources by microbial communities at the base of lake food webs remain poorly understood. With this in mind, this thesis aims to advance our understanding of lake sediment microbial community assembly and functioning along abiotic gradients, primarily reflecting variation in terrestrial organic matter inputs that are predicted to increase with future environmental change. Chapter 1 reviews current knowledge on the terrestrial support of lake food webs and highlights gaps in understanding the factors influencing the microbial processing of terrestrial resources. It also provides an overview of metagenomics methods for microbial community analysis and their development over the course of the thesis. Chapter 2 tests how much of ecosystem functioning is explained by microbial community structure relative to other ecosystem properties such as the present-day and past environment. Theory predicts that ecosystem functioning, here measured as CO2 production, should increase with diversity, but the individual and interactive effects of other ecosystem properties on ecosystem functioning remain unresolved. Chapter 3 further questions the importance of microbial diversity for ecosystem functioning by asking whether more diverse microbial communities stabilize ubiquitous functions like CO2 production and microbial abundances through time. It also aims to identify the biotic and abiotic mechanisms underlying positive diversity-stability relationships. Chapter 4 then explores how microbial communities assemble and colonize sediments with varying types and amounts of terrestrial organic matter in three different lakes over a two-month period. Understanding how microbial communities change in relation to sediment and lake conditions can help predict downstream ecosystem functions. Finally, Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.

Le méthane, un des principaux gaz à effet de serre, est majoritairement produit et consommé par l'activité métabolique de microorganismes affiliés aux domaines des Archaea et des Bacteria. Afin d'appréhender le cycle biogéochimique du méthane, il est essentiel d'identifier l'ensemble des acteurs impliqués dans ce dernier ainsi que les facteurs environnementaux modulant leurs activités. Les lacs d'eau douce constituent une source importante de méthane, car, dans ces écosystèmes, les conditions environnementales favorisent la méthanogenèse au détriment d'autres processus terminaux de la dégradation anaérobie de la matière organique. Au cours de cette thèse, les études sur les communautés impliquées dans le cycle biogéochimique du méthane ont été conduites dans la colonne d'eau et les sédiments anoxiques du Lac Pavin (Auvergne), unique lac méromictique de France. Cet écosystème a été choisi comme site d'étude en raison des fortes concentrations en méthane présentes dans sa couche d'eau profonde qui contrastent avec les faibles émissions de ce gaz vers l'atmosphère. Ces observations géochimiques suggèrent une intense activité de production et de consommation du méthane, offrant un cadre pertinent pour l'étude des communautés ciblées. Les approches moléculaires visant à caractériser la structure spatiale, la composition, les zones d'activité et les facteurs (ascendants et descendants) potentiellement impliqués dans la régulation des communautés de méthanogènes et de méthanotrophes ont été, au cours de ce travail, systématiquement associées à des approches culturales et microcalorimétriques afin d'acquérir des données sur la physiologie des microorganismes impliqués dans le cycle du méthane. Les résultats obtenus mettent en évidence que les communautés de méthanogènes sont distribuées sur l'ensemble de la colonne d'eau anoxique et dans la strate superficielle des sédiments profonds. Ce groupe métabolique, essentiellement représenté par des espèces affiliées aux Methanosaetaceae et aux Methanoregulaceae, est particulièrement actif dans la zone benthique qui constituerait la source principale de méthane dans cet écosystème. Une nouvelle espèce méthanogène, Methanobacterium lacus, a été isolée de ces sédiments et décrite, et vient enrichir le faible nombre d'espèces méthanogènes isolées à ce jour à partir des lacs d'eau douce. L'étude écophysiologique de cette souche suggère que la température pourrait en partie expliquer la faible représentativité des Methanobacteriales dans cet écosystème. Une partie du méthane semble être directement consommée dans la zone anoxique (pélagique et benthique). L'existence de ce processus d'oxydation anaérobie, soutenu par les approches microcalorimétriques, pourrait être, dans les sédiments profonds, sous la dépendance de lignées candidates archéennes dont la physiologie reste encore énigmatique. Le remplacement progressif des méthanogènes par 2 lignées candidates d'archaea (MBG-D et MCG) le long du profil sédimentaire suggère qu'elle se développe dans des niche contrastées. La régulation putative des communautés archéennes par les virus a été analysée. Cette étude est la première à rapporter la présence de particules virales de type "archaeovirus" dans un environnement non-extrême (en termes de température, pH et salinité) ainsi que des particules virales pouvant représentées de nouvelles familles de virus. Une activité virale intense est suggérée dans ces sédiments par le nombre important de cellules infectées, comparativement à d'autres sédiments, et par le changement concomitant de la structure de la communauté virale et procaryotique avec la profondeur. Bien qu'une partie du méthane soit probablement oxydée en anaérobiose, la consommation de ce métabolite est principalement dépendante de l'activité de méthanotrophes aérobies dominées par des espèces affiliées au genre Methylobacter, un des principaux genres de méthanotrophes rencontré en milieu d'eau douce. (...)

L’écologie microbienne concerne l’étude des microorganismes et de leurs interactions biotiques et abiotiques dans un écosystème donné. Ces vingt dernières années, l’avancement des techniques moléculaires pour analyser la diversité microbienne et, notamment, les nouvelles technologies de séquençages (NGS) ont permis de surmonter les limitations associées aux approches traditionnelles basées sur la culture et la microscopie. Ces approches moléculaires ont conduit à une accumulation des données de diversité microbienne et de potentiel métabolique dans des communautés microbiennes des écosystèmes variés.Cependant, ces efforts ont été principalement appliqués sur des environnements facilement accessibles ou liés à l’humain, comme le plancton (marin principalement) et la flore intestinale. Néanmoins, ceci a conduit à une très forte augmentation de données environnementales et au développement de la bioinformatique par le biais de nombreux outils. Parmi les environnements délaissés des études, les environnements faibles en oxygène sont probablement également porteurs de nouveautés phylogénique ou métaboliques.Afin de palier à cela, nous avons choisi d’explorer deux environnements suboxiques relativement peu étudiés : la cave Movile (Roumanie) et les sédiments du lac Baikal (Sibérie, Russie). Notre but étant de montrer les diversités phylogénétiques et fonctionnelles des microbes de ces biotopes.Pour cela, j’ai d'abord développé un pipeline d’analyse de données métabarcoding (petite sous-unités ribosomique). Ensuite, j’ai appliqué cet outil sur des données de métabarcoding de protistes provenant d’échantillons d’eau et de tapis microbiens de la cave de Movile, un écosystème chemosynthétique pratiquement fermé. Nous avons montré que la diversité des protistes de la cave s’étendait à quasiment tous les grands groupes eucaryotes et provenait à la fois d’origine d’eaux douces et marines. De plus, la plupart ont été affiliées à des groupes d’organismes typiquement anaérobies, ce qui est concordant avec les paramètres abiotiques de la cave. Écologiquement, ces protistes sont des prédateurs mais aussi vraisemblablement des partenaires symbiotiques avec des espèces procaryotes de la cave.Dans une deuxième étude, j’ai eu l’opportunité d’appliquer ce pipeline de métabarcoding sur des données procaryotes et eucaryotes provenant des couches superficielles des sédiments du lac d’eau douce Baikal. Comme attendu, les communautés microbiennes dans ces sédiments sont particulièrement diverses et relativement enrichis en archées. Nous avons aussi pu mettre en évidence des lignées que l’on pensait exclusivement marines dans ces sédiments. Ces lignées sont probablement planctoniques mais s’accumulent au fond par sédimentation. Enfin, les échantillons ont été prélevés dans le but de tester les influences de la profondeur, du bassin et de la latitude sur les communautés. Aucune d’elles ne s’est révélée significative.Dans une troisième étude, j'ai utilisé une approche métagénomique afin de révéler les acteurs écologiquement majeurs dans les sédiments, leurs rôles et de reconstruire leurs génomes. Cela nous a permis notamment de mettre en évidence le rôle primordial des Thaumarchaeota dans le cycle de l’azote et la production primaire de molécules de carbone. Les chloroflexi et les protéobacteries ont aussi un rôle important dans la surface des sédiments du lac Baikal. Ce travail de thèse participe à la connaissance globale de la diversité microbienne sur la planète en mettant en lumière des environnements peu étudiés. De plus, l’étude de la surface des sédiments du lac Baikal apporte de nouvelles données sur le sujet de la transition eau douces/eau marines des microbes. Enfin, la métagénomique a permis de révéler le cycle des nutriments et les microorganismes y participant dans ces échantillons de sédiment. En résumé, ce travail vient mettre en lumière l’écologie microbienne d’écosystèmes suboxiques, notamment la surface des sédiments du lac Baikal
Microbial ecology is the science of micro-organisms and their biotic and abiotic interactions in a given ecosystem. As technology has advanced, molecular techniques have been widely used to overcome the limitations of classical approaches such as culturing and microscopy. Indeed, the development of Next Generation Sequencing (NGS) technologies in the past twenty years has largely helped to unravel the phylogenetic diversity and functional potential of microbial communities across ecosystems.Nonetheless, most of the environments studied through these techniques concentrated on relatively easily accessible, tractable and host-related ecosystems such as plankton (especially in marine ecosystems), soils and gut microbiomes. This has contributed to the rapid accumulation of a wealth of environmental diversity and metagenomic data along with advances in bioinformatics leading to the development of myriads of tools. Oxygen-depleted environments and especially their microbial eukaryote components are less studied and may lead to future phylogenetic and metabolic discoveries.In order to address this, we conducted analyses on two poorly studied suboxic ecosystems: Movile Cave (Romania) and lake Baikal sediments (Siberia, Russia). In this task, we aimed at unveiling the taxonomic and functional diversity of microorganims in these environments.To do so, I first evaluated the available bioinformatics tools and implemented a bioinformatics pipeline for 16S/18S rRNA gene-based metabarcoding analysis, making reasoned methodological choices. Then, as a case study, I carried out metabarcoding analyses of the water and floating microbial mats found in Movile Cave in order to investigate its protist diversity. Our study showed that Movile Cave, a sealed off chemosynthetic ecosystem, harbored a substantial protist diversity with species spanning most of the major eukaryotic super groups. The majority if these protists were related to species of freshwater and marine origins. Most of them were putatively anaerobic, in line with the cave environment, and suggesting that in addition to their predatory role, they might participate in prokaryote-protist symbioses.In a second study, I applied my metabarcoding pipeline to explore unique and relatively unexplored environment of Lake Baikal sediments. I first applied a metabarcoding approach using 16S and 18S rRNA genes to describe prokaryotic as well as protist diversity. Overall, the communities within these ecosystems were very diverse and enriched in ammonia-oxidizing Thaumarchaeota. We also identified several typical marine taxa which are likely planktonic but accumulate in sediments. Finally, our sampling plan allowed us to test whether differences across depth, basin or latitude affected microbial community structure. Our results showed that the composition of sediment microbial communities remained relatively stable across the samples regardless of depth or latitude.In a third study, we applied metagenomics to study the metabolic potential of communities associated to Baikal sediments and to reconstruct metagenome-assembled genomes (MAGs) of dominant organisms. This revealed the considerable ecological importance of Thaumarchaeota lineages in lake Baikal sediments, which were found to be the major autotrophic phyla and also very implicated in the nitrogen cycle. Chloroflexi and Proteobacteria-related species also appeared ecologically important.This PhD thesis reveals the taxonomic diversity of poorly studied suboxic ecosystems and therefore contributes to our knowledge of microbial diversity on Earth. Additionally, the analyses of surface sediment samples in lake Baikal adds new light on freshwater-marine transitions. The metagenomic analyses reported here allowed us to postulate a model of nutrient cycle carried out by microorganismsin these sediments. Overall, this work sheds light on the microbial ecology of oxygen-depleted environments, and most notably lake Baikal surface sediments

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Geochemical, whole rock Sm-Nd and detrital zircon U-Pb isotopic data from Archaean metasedimentary successions in the southern Gawler Craton indicate derivation from Late Archaean sources. Detrital zircons from the upper amphibolite-grade Wangary Gneiss have dominant U-Pb age groupings at 2500-2580 Ma and 2600-2720 Ma, with a few analyses ranging up to 2950-3150 Ma. Steep LREE enrichment REE with (La/Yb)N = 46 – 58 and low abundances of compatible trace elements point to a major felsic source component, with REE patterns typical of Na-rich granites. Detrital zircons from the metasedimentary dominated Hall Bay Volcanics (2500-2560 and 2660-2710 Ma) show a similar range of detrital zircon ages to the Wangary Gneiss, suggesting both sequences were derived from a temporally similar Late Archaean source terrain. The Carnot paragneisses and the Hall Bay Volcanics metasedimentary rocks show comparative HREE enrichment ((La/Yb)N = 7.4-12.5 and (La/Yb)N = 10.2-15.7 respectively), suggesting a greater input of mafic or intermediate material relative to the Wangary Gneiss. The correspondence in detrital zircon ages between the Wangary Gneiss and Hall Bay Volcanic metasedimentary rocks suggests both units form part of the same succession. Existing zircon U-Pb data provides no evidence for input of Early Archaean crust into the Wangary Gneiss, Hall Bay Volcanics or Carnot paragneisses, which is further substantiated by Sm-Nd depleted mantle model ages that range from 2900 to 3200 Ma in all metasedimentary rocks. The overlap of detrital zircon and depleted mantle model ages suggests that all three successions in the southern Gawler Craton comprise a single basinal succession. The geochemical compositions of the late Archaean sequences in the southern Gawler Craton are consistent with derivation from a bimodal terrain with variable mixing of three distinct sources: (1) intermediate-felsic volcanics; (2) mafic rocks and (3) highly fractionated Na-rich felsic rocks (tonalites-trondhjemites). These source regions are currently unidentified in the Gawler Craton, however, source terrains for the late Archaean sequences may be preserved in association with the 2500-3000 Ma age crust in rifted off components of the Gawler Craton in Antarctica. Although speculative at this stage, deposition of the Late Archaean sequences in the southern Gawler Craton is likely to have occurred on a rifting margin to a Late Archaean terrain. Sedimentation was terminated during collisional closure of the basin system leading to the 2500-2400 Ma Sleafordian Orogeny.
Thesis (B.Sc.(Hons)) -- University of Adelaide, School of Physical Sciences, 2002

碩士
國立中興大學
生命科學系所
104
Methane is important greenhouse gas, and northern lakes are the significant methane emission sites. And these accumulated methane are mainly contributed by the methanogenic archaea. To investigate the biodiversity of methanogens at northern lakes, sediments samples were collected from two saline meromictic lake Shira and Shunet. After anaerobic enrichment and serial diluted sub-transfer, partially purified cultures and pure isolates were obtained. Based on 16S ribosomal RNA gene sequences analysis, Clostridiales, Acholeplasmatales, Synergistales, Bacteroidales, Methanosarcinales, Methanomicrobiales and Methanobacteriales were detected from methanogenic enrichment cultures or pure isolates from Lake Shira and Shunet. A psychrotolerant, methylotrophic novel Methanolobus species, strain YSF-03, was isolated from sediments of Lake Shira. Cells of strain YSF-03 were non-motile, Gram negative, irregular cocci, 0.8-1.2 μm in diameter. The substrates for methanogenesis used by strain YSF-03 were methanol and trimethylamine. The temperature range of growth for strain YSF-03 was 0oC to 37oC with optimum growth conditions were 30-37oC, pH 7.0-7.4 and 0.17 M NaCl. The DNA G+C content of the genome of strain YSF-03 was 42.0 mol%. Phylogenetic analysis revealed that strain YSF-03 was most closely related to Methanolobus profundi MobMT (98.15% 16S rRNA gene sequence similarity). Genome relatedness between strain YSF-03 and Methanolobus profundi MobMT was computed using both genome-to-genome distance analysis (GGDA) and average nucleotide identity (ANI) with values of 23.5% and 79.3%, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data, it is evident that strain YSF-03 represents a novel species of the genus Methanolobus. It is expected that these methanogens from northern lakes contribute to taxonomy information on psychrophilic methanogenic archaea.