Dissertation/Thesis Abstract

Genome-Resolved Meta-Omics Analyses of Microbial Interactions in Mining-Impacted Systems
by Kantor, Rose Simone, Ph.D., University of California, Berkeley, 2016, 125; 10251153
Abstract (Summary)

Microbial communities play important roles in natural, engineered, and anthropogenically altered systems. Specifically, microorganisms can metabolize contaminants and contribute to nutrient cycling. These processes can be achieved by one species or by the combined effects of multiple species. Hence, communities can possess emergent properties that are not always obvious from work on isolates or taxonomic profiling. Furthermore, the majority of microorganisms have not been cultivated in the laboratory and even for cultivated species, the full metabolic capacity may not be known. Examining genomes, the blueprints for life, and proteomes, the parts assembled from these blueprints, can provide insight into microbial physiologies and their roles in systems of interest. A more detailed understanding of which organisms are responsible for key processes could improve monitoring of in situ bioremediation, allow better targeted biostimulation, and even direct the manipulation of applied microbial systems to be more efficient.

Genome-resolved metagenomics and metaproteomics (“meta-omics”) techniques are approaches that sample biomolecules (DNA and protein) from an intact microbial community, sequence or identify these molecules, and assign the sequences to specific populations. Analysis of the resulting data can yield a species-resolved view of the metabolic potential present in a community. These methods were used to investigate the structure and functioning of microbial communities in mining-contaminated systems. Bioinformatic analyses across three different systems sought to elucidate ecological roles for members of novel bacterial phyla and identify organisms that contributed to contaminant transformation. Contaminant studies focused on removal of common mining-related compounds including thiocyanate, cyanide, and reduced sulfur species. Metagenomes taken in series were used to examine the stability of consortia over time and increased thiocyanate loading while metagenomes taken across a mining landscape were used to assess the diversity, metabolic potential, and seasonal variation of microbial communities.

Most microbial communities include bacteria from major branches of the tree of life with no cultivated representatives. These lineages are referred to as Candidate Phyla (CP), and in the absence of complete genomes or cultivated representatives, many aspects of their biology and ecological roles remained unclear. Extensive characterization of sediment- and groundwater-associated microbial communities in Rifle, Colorado, USA, provided some of the first genomic observations of these CP. The site of a former uranium and vanadium mill in Rifle has been the subject of in situ biostimulation experiments, most notably, acetate addition to increase uranium reduction by the native microbial community. A series of metagenomes from acetate-amended aquifer sediment yielded three complete and one near-complete bacterial genomes from CP, some of the first ever reported. Subsequent exploration of microbial communities involved in thiocyanate remediation and acid mine drainage also recovered genomes from the CP. Metabolic analyses based on the four Rifle genomes revealed the lack of an electron transport chain and pointed to energy generation based on fermentation of organic substrates including sugars, organic acids, amino acids, and DNA. A significant portion of genes in the unusually small genomes were involved in attachment, motility, and cell surface modification. Perhaps most importantly, none of the four genomes contained genes required for the complete biosynthesis of nucleic acids and amino acids. Taken together, all evidence suggests an obligately symbiotic or parasitic lifestyle for all four organisms.

Thiocyanate (SCN-) is a common industrial contaminant produced at high quantities in gold mining. Chemical degradation of this compound is expensive and can produce other toxic byproducts, whereas biological treatment produces sulfate, ammonium, and carbon dioxide. Thiocyanate bioremediation has been successful at the pilot and industrial scale, but the biological underpinnings of the process were not well understood. In order to identify key pathways and organisms involved in thiocyanate degradation, microbial communities of two laboratory-scale continuous flow bioreactors were studied. The first reactor was a long-running system fed at high thiocyanate loadings whereas the second, inoculated with mixed culture from the first, was fed both thiocyanate and cyanide. Metagenomic sequencing and analysis of the two reactor communities resulted in a total of 93 bacterial and two eukaryotic genome bins. Based on coverage, the most abundant organisms in both reactors belonged to the genus Thiobacillus. Importantly, the genomes for these organisms encoded the enzyme thiocyanate hydrolase, located in an operon with cyanase and a predicted thiocyanate transporter. Other organisms in the reactor were predicted to oxidize sulfur or ammonium produced during thiocyanate degradation, and some possessed genes encoding denitrification. Whereas prior culture-based approaches had suggested heterotrophic organisms were responsible for thiocyanate degradation and that this process requires oxygen, the Thiobacillus spp. genomes encoded autotrophic metabolism and anaerobic respiration using nitrate. (Abstract shortened by ProQuest.)

Indexing (document details)
Advisor: Banfield, Jillian F.
Commitee: Firestone, Mary K., Nelson, Kara L.
School: University of California, Berkeley
Department: Microbiology
School Location: United States -- California
Source: DAI-B 80/08(E), Dissertation Abstracts International
Subjects: Microbiology
Keywords: Bacteria, Bioremediation, Genomes, Metagenomics, Mining, Thiocyanate
Publication Number: 10251153
ISBN: 978-1-392-03469-9
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