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- All Subjects: Microbial Ecology
- Creators: Farmer, Jack
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
Creating sustainable alternatives to fossil fuel resources is one of the greatest
challenges facing mankind. Solar energy provides an excellent option to alleviate modern dependence on fossil fuels. However, efficient methods to harness solar energy are still largely lacking. Biomass from photosynthetic organisms can be used as feedstock to produce traditional fuels, but must be produced in great quantities in order to meet the demands of growing populations. Cyanobacteria are prokaryotic photosynthetic microorganisms that can produce biomass on large scales using only sunlight, carbon dioxide, water, and small amounts of nutrients. Thus, Cyanobacteria are a viable option for sustainable production of biofuel feedstock material. Photobioreactors (PBRs) offer a high degree of control over the temperature, aeration, and mixing of cyanobacterial cultures, but cannot be kept sterile due to the scales necessary to meet domestic and global energy demands, meaning that heterotrophic bacteria can grow in PBRs by oxidizing the organic material produced and excreted by the Cyanobacteria. These heterotrophic bacteria can positively or negatively impact the performance of the PBR through their interactions with the Cyanobacteria. This work explores the microbial ecology in PBR cultures of the model cyanobacterium Synechocystis sp. PCC6803 (Synechocystis) using microbiological, molecular, chemical, and engineering techniques. I first show that diverse phylotypes of heterotrophic bacteria can associate with Synechocystis-based PBRs and that excluding them may be impossible under typical PBR operating conditions. Then, I demonstrate that high-throughput sequencing can reliably elucidate the structure of PBR microbial communities without the need for pretreatment to remove Synechocystis 16S rRNA genes, despite the high degree of polyploidy found in Synechocystis. Next, I establish that the structure of PBR microbial communities is strongly influenced by the microbial community of the inoculum culture. Finally, I show that maintaining available phosphorus in the culture medium promotes the production and enrichment of Synechocystis biomass in PBRs by reducing the amount of soluble substrates available to heterotrophic bacteria. This work presents the first analysis of the structure and function of microbial communities associated with Synechocystis-based PBRs.
challenges facing mankind. Solar energy provides an excellent option to alleviate modern dependence on fossil fuels. However, efficient methods to harness solar energy are still largely lacking. Biomass from photosynthetic organisms can be used as feedstock to produce traditional fuels, but must be produced in great quantities in order to meet the demands of growing populations. Cyanobacteria are prokaryotic photosynthetic microorganisms that can produce biomass on large scales using only sunlight, carbon dioxide, water, and small amounts of nutrients. Thus, Cyanobacteria are a viable option for sustainable production of biofuel feedstock material. Photobioreactors (PBRs) offer a high degree of control over the temperature, aeration, and mixing of cyanobacterial cultures, but cannot be kept sterile due to the scales necessary to meet domestic and global energy demands, meaning that heterotrophic bacteria can grow in PBRs by oxidizing the organic material produced and excreted by the Cyanobacteria. These heterotrophic bacteria can positively or negatively impact the performance of the PBR through their interactions with the Cyanobacteria. This work explores the microbial ecology in PBR cultures of the model cyanobacterium Synechocystis sp. PCC6803 (Synechocystis) using microbiological, molecular, chemical, and engineering techniques. I first show that diverse phylotypes of heterotrophic bacteria can associate with Synechocystis-based PBRs and that excluding them may be impossible under typical PBR operating conditions. Then, I demonstrate that high-throughput sequencing can reliably elucidate the structure of PBR microbial communities without the need for pretreatment to remove Synechocystis 16S rRNA genes, despite the high degree of polyploidy found in Synechocystis. Next, I establish that the structure of PBR microbial communities is strongly influenced by the microbial community of the inoculum culture. Finally, I show that maintaining available phosphorus in the culture medium promotes the production and enrichment of Synechocystis biomass in PBRs by reducing the amount of soluble substrates available to heterotrophic bacteria. This work presents the first analysis of the structure and function of microbial communities associated with Synechocystis-based PBRs.
ContributorsZevin, Alexander Simon (Author) / Rittmann, Bruce E. (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Vermaas, Willem Fj (Committee member) / Arizona State University (Publisher)
Created2015