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- All Subjects: Geochemistry
- Genre: Doctoral Dissertation
Description
The taxonomic and metabolic profile of the microbial community inhabiting a natural system is largely determined by the physical and geochemical properties of the system. However, the influences of parameters beyond temperature, pH and salinity have been poorly analyzed with few studies incorporating the comprehensive suite of physical and geochemical measurements required to fully investigate the complex interactions known to exist between biology and the environment. Further, the techniques used to classify the taxonomic and functional composition of a microbial community are fragmented and unwieldy, resulting in unnecessarily complex and often non-consilient results.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
ContributorsAlsop, Eric Bennie (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Farmer, Jack (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2014
Description
Amazonia, inhabited and investigated for millennia, continues to astonish scientists with its cultural and natural diversity. Although Amazonia is rapidly changing, its vast and varied landscape still contains a complex natural pharmacopeia. The Amazonian tribes have accrued valuable environmental and geological knowledge that can be studied. This dissertation demonstrates that Indigenous Knowledge considered alongside Western Science can enhance our understanding of the relationship of people to geological materials and hydrological resources, and reveal mineral medicines with practical applications.
I used methods from anthropology and geology to explore the geological knowledge of the Uitoto, a tribe of the Colombian Amazon. The Uitoto use two metaphors to describe Earth systems: 1. the earth is a body, and 2. the Amazon is a tree. I found that they classify surface-water systems according to observable characteristics and use mineral clays to treat various maladies. I argue that Uitoto knowledge about Amazonian mineral resources and surface water is practical, empirically–based and, in many cases, more nuanced than mainstream scientific knowledge.
I studied the mode of action of a natural antibacterial clay from the Colombian Amazon (AMZ) to discover whether the Uitoto’s claims about the clay’s medicinal values was verifiable using the methods of Western Science. Natural antibacterial clays can inhibit the growth of human pathogens. Methods from microbiology and geochemistry were combined to evaluate the mineral-microbe interactions that inhibit growth of model Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The AMZ antibacterial clay contains 45 % kaolinites and 30 % smectites. Its high surface area maintains an acidic environment (pH 4.5) and releases high concentrations of aluminum. Aluminum accumulates in the outer membrane of E. coli by binding to phospholipids. Furthermore, the membrane’s permeability increases due to synergistic effects between aluminum and transition metals released from the AMZ (i.e. Fe, Cu). The changes in the membrane may compromise its function as a barrier. Understanding the antibacterial mechanism of AMZ is key for its safe use as a natural product. These findings can help us harness the capabilities of antibacterial clays more efficiently.
Lastly, I integrated the results of this work in place-based, cross-cultural educational materials tailored for the tribal schools in the Colombian Amazon. The design of the units was informed by principles of curriculum design and successful pedagogic approaches for Native American students. The purpose of these educational materials is to return the results of research, enhance learning and participation of indigenous peoples in geosciences, and respond to the multicultural and plurilingual educational needs in countries such as Colombia.
I used methods from anthropology and geology to explore the geological knowledge of the Uitoto, a tribe of the Colombian Amazon. The Uitoto use two metaphors to describe Earth systems: 1. the earth is a body, and 2. the Amazon is a tree. I found that they classify surface-water systems according to observable characteristics and use mineral clays to treat various maladies. I argue that Uitoto knowledge about Amazonian mineral resources and surface water is practical, empirically–based and, in many cases, more nuanced than mainstream scientific knowledge.
I studied the mode of action of a natural antibacterial clay from the Colombian Amazon (AMZ) to discover whether the Uitoto’s claims about the clay’s medicinal values was verifiable using the methods of Western Science. Natural antibacterial clays can inhibit the growth of human pathogens. Methods from microbiology and geochemistry were combined to evaluate the mineral-microbe interactions that inhibit growth of model Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The AMZ antibacterial clay contains 45 % kaolinites and 30 % smectites. Its high surface area maintains an acidic environment (pH 4.5) and releases high concentrations of aluminum. Aluminum accumulates in the outer membrane of E. coli by binding to phospholipids. Furthermore, the membrane’s permeability increases due to synergistic effects between aluminum and transition metals released from the AMZ (i.e. Fe, Cu). The changes in the membrane may compromise its function as a barrier. Understanding the antibacterial mechanism of AMZ is key for its safe use as a natural product. These findings can help us harness the capabilities of antibacterial clays more efficiently.
Lastly, I integrated the results of this work in place-based, cross-cultural educational materials tailored for the tribal schools in the Colombian Amazon. The design of the units was informed by principles of curriculum design and successful pedagogic approaches for Native American students. The purpose of these educational materials is to return the results of research, enhance learning and participation of indigenous peoples in geosciences, and respond to the multicultural and plurilingual educational needs in countries such as Colombia.
ContributorsLondoño Arias, Sandra Carolina (Author) / Williams, Lynda B (Thesis advisor) / Semken, Steven (Thesis advisor) / Brandt, Elizabeth A. (Committee member) / Hartnett, Hilairy H (Committee member) / Raymond, Jason (Committee member) / Arizona State University (Publisher)
Created2016