Fungal spores as palaeoenvironmental indicators of anthropogenic activity

Fungal spores often occur in palynological preparations and have been successfully incorporated in both biostratigraphic and palaeoenvironmental investigations. However, the majority of palynologists choose to ignore such microfossils, primarily because of the difficulties relating to their identification. Where they have been used conventional palynological extraction procedures have been implemented in the preparation of samples. The suitability of such techniques for the recovery of fungal palynomorphs has been assumed in many cases.The objectives of this thesis were to study the effect of different processing techniques on the recovery of fungal palynomorphs, to propose a suitable morphological recording system and to investigate the potential of using fungal palynomorphs as palaeoenvironmental indicators of anthropogenic activity.Following the specification of a suitable extraction procedure for fungal palynomorphs and an appropriate morphological recording system 215 types were described. These types were encountered in samples from modern and archaeological situations and across a variety of different environments. The types fall into 19 morphological categories as defined in the recording system. Many of the types are restricted to either modern or archaeological sample sets although some are common to both. 96 types are comparable to known fungal taxa, 8 are considered algal in origin, 4 are parasite eggs and 1 has been identified as a rhizopod species. The remaining 106 can only be classified morphologically until they can be related to known taxa.Although an objective was to employ the Comparative Approach and use the palynomorph assemblages from known modem environments in the palaeoenvironmental interpretation of the archaeological material, it was not feasible. This is principally because of the limited overlap of taxa between modern and archaeological samples and is most likely a reflection of the restricted range of material considered. However, this approach demonstrates a promising future, subject to more extensive sampling regimes.Palaeoenvironmental interpretation of the archaeological samples was possible using the Indicator Species Approach. The results support and often enhance other forms of palaeoenvironmental analysis and in no instance were contra- indications encounteredThis success testifies to the importance of fungal palynology and the need for continuing research in this area

Microbial Functional Diversity and the Associated Biogeochemical Interactions Across Miami-Dade County, Florida Soils

Decomposition of soil organic matter by microbial processes results in carbon sequestration within soils and/or carbon loss via atmospheric emission of carbon dioxide and methane. Natural as well as anthropogenic factors have been documented to impact soil microbial diversity and the associated biogeochemical functions. The soil microbial communities co-inhabiting Miami-Dade County soils, Florida are under threat because of the ongoing restoration efforts in the adjoining Florida Everglades Parks, predicted climatic changes such as sea-level rise and high rainfall, as well as urbanization. Therefore, an improved understanding of the current microbial functional communities is essential to better assess the impact of soil communities when anthropogenic or climatic disturbances occur. The objectives of the current study were to characterize the biodiversity and distribution of: a) cellulose degrading microbial community, and b) methanogenic guilds responsible for producing the gas methane, across four different Miami-Dade County, Florida soil types using the high throughput technique of GeoChip 5.0 functional microarray. In addition, the influence of vegetation cover, organic content, soil moisture content, pH, and soil texture in shaping the soil functional microbial community was also investigated. The function of cellulose degradation was distributed across wide range of taxonomic lineages with the majority belonging to the bacterial groups of Actinobacteria, Firmicutes, Alphaproteobacteria, and Gammaproteobacteria, whereas Ascomycota and Basidiomycota were the only detected fungal phyla. The cellulolytic bacterial community correlated more with the vegetation cover while fungal groups showed influence of moisture and organic content as well as percent silt. Six out of the seven methanogenic orders, with the greatest numbers found in the Methanomicrobiales, Methanosarcinales, and Methanomassiliicoccales, were identified across all four soil types of Miami-Dade. The abundance of the mcrA gene sequences was significantly greater with respect to soil moisture content. Additionally, the recently classified order Methanomassiliicoccales was identified across all four soils, including soils with lower moisture content not thought to provide ideal redox conditions to support methanogens. The greater number of correlation network interactions amongst the methanogenic guilds in the Florida Everglades wetlands versus the urbanized Miami-Dade County soils depicted the impact of the historical drainage of the Florida Everglades on the methanogenic community. Overall, the current study characterized the biodiversity of cellulolytic and methanogenic organisms across dry and saturated soils of Miami-Dade County and demonstrated that microbial guilds were functionally redundant and were influenced to some extent by the soil abiotic factors. Also, results from network analyses provide a platform to assess the future impacts of disturbances on the microbial community

The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon

<p>Abstract</p> <p>Background</p> <p>The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed.</p> <p>Results</p> <p>We review the evidence that archaea are derived, as well as their biggest differences with bacteria. We argue that using novel data the gap between the superkingdoms is not insurmountable. We consider whether archaea are holophyletic or paraphyletic; essential to understanding their origin. Finally, we review several hypotheses on the origins of archaea and, where possible, evaluate each hypothesis using bioinformatics tools. As a result we argue for a firmicute ancestry for archaea over proposals for an actinobacterial ancestry.</p> <p>Conclusion</p> <p>We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes.</p> <p>Reviewers</p> <p><it>This article was </it>reviewed by Patrick Forterre, Eugene Koonin, and Gáspár Jékely</p

Diversity and Structure of Spider Assemblages in Terai Conservation Area

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Metastable attractors explain the variable timing of stable behavioral action sequences

info:eu-repo/semantics/publishedVersio

Statistical methods for the integrative analysis of single-cell multi-omics data

Single-cell profiling techniques have provided an unprecedented opportunity to study cellular heterogeneity at the molecular level. This represents a remarkable advance over traditional bulk sequencing methods, particularly to study lineage diversification and cell fate commitment events in heterogeneous biological processes. While the large majority of single-cell studies are focused on quantifying RNA expression, transcriptomic readouts provide only a single dimension of cellular heterogeneity. Recently, technological advances have enabled multiple biological layers to be probed in parallel one cell at a time, unveiling a powerful approach for investigating multiple dimensions of cellular heterogeneity. However, the increasing availability of multi-modal data sets needs to be accompanied by the development of suitable integrative strategies to fully exploit the data generated. In this thesis I worked in collaboration with different research groups to introduce innovative experimental and computational strategies for the integrative study of multi-omics at single-cell resolution. The first contribution is the development of scNMT-seq, a protocol for the simultaneous profiling of RNA expression, DNA methylation and chromatin accessibility in single cells. I demonstrate how this assay provides a powerful approach for investigating regulatory relationships between the epigenome and the transcriptome within individual cells. The second contribution is Multi-Omics Factor Analysis (MOFA), a statistical framework for the unsupervised integration of multi-omics data sets. MOFA is a Bayesian latent variable model that can be viewed as a statistically rigorous generalization of Principal Component Analysis to multi-omics data. The method provides a principled approach to retrieve, in an unsupervised manner, the underlying sources of sample heterogeneity while at the same time disentangling which axes of heterogeneity are shared across multiple modalities and which are specific to individual data modalities. The third contribution is the generation of a comprehensive molecular roadmap of mouse gastrulation at single-cell resolution. We employed scNMT-seq to simultaneously profile RNA expression, DNA methylation and chromatin accessibility for hundreds of cells, spanning multiple time points from the exit from pluripotency to primary germ layer specification. Using MOFA, and other tools, I performed an integrative analysis of the multi-modal measurements, revealing novel insights into the role of the epigenome in regulating this key developmental process. The fourth contribution is an extended formulation of the MOFA model tailored to the analysis of large-scale single-cell data with complex experimental designs. I extended the model to incorporate a flexible regularisation that enables the joint analysis of multiple omics as well as multiple sample groups (batches and/or experimental conditions). In addition, I implemented a GPU-accelerated stochastic variational inference framework, thus enabling the scalable analysis of potentially millions of samples

Landscape evolution in Western Amazonia: palynostratigraphy, palaeoenvironments and diversity of the miocence Solimões formation, Brazil

During the Miocene (23.03 to 5.33 Ma), western Amazonia experienced major changes in its geography and biodiversity as a response to Andean uplift. To better understand these changes, the palynology of the Solimões Formation (NW Brazil) is presented with the objective of providing age control, and establishing palaeoenvironments and pollen richness within the framework of geological and climatic events. The ninety-five palynological samples yield 491 palynomorphs, of which 76 pollen and 25 spores are new. Correlation with a nearby calibrated biozonation resulted in ages from 18.7 to 10.7 Ma (late early to earliest-late Miocene). The pollen associations are typical of Amazonian humid forests, with abundant palms, Bombacoideae, trees and grasses, and lack diverse and abundant herbs or dry forest indicators. Spikes in algae and dinoflagellates show phases of lake development and two marine incursions – one between 18.4 and 17.8 Ma, and another between 14.1 and 13.7 Ma. Statistical analyses of the data show inundations had no effect in the vegetation composition. Estimates of diversity using different metrics clearly show a diversity increase and community change at ca. 16 Ma, independent of lithofacies. This change is driven by the Middle Miocene Climatic Optimum and not correlated with any of the marine incursions. Altogether, the results bring more detail to the environmental history of western Amazonia, establishing two inundation events and furthering the climate diversification relationship in Neotropical biomes into the Miocene period

Identification and community profiling of Vaccinium membranaceum root-associated fungi over an elevation gradient in BC's eastern rocky mountains.

Root-associated fungi, including ericoid mycorrhizas, are important to the health of alpine and northern forest ecosystems. These symbiotic root-fungus associations form with shrubs in the family Ericaceae. This is the first report of an attempt to profile the fungal community structure associated with roots of Vaccinium membranaceum (huckleberry) over a biogeoclimatic (BEC) zone elevation gradient in BC's eastern rocky mountains. Four biogeoclimatic zones were targeted on McBride peak: the alpine, ESSF, ICH and SBS. Fungal associates were grown in culture and fungal DNA analyzed directly from the roots. Both techniques generated community profiles that demonstrated differences in root-associated fungal community structure between each of the four zones. The higher elevation alpine and ESSF hosted fungi known to form ericoid mycorrhizas. Lower elevation ICH and SBS tended to host more common fungi. The diversity patterns generated have potential implications in climate change.The original print copy of this thesis may be available here: http://wizard.unbc.ca/record=b160154