Publication Date


Document Type


First Advisor

Swingley, Wesley D.

Degree Name

M.S. (Master of Science)

Legacy Department

Department of Biological Sciences


Microbiology; Bioinformatics; Ecology


The Calumet Wetlands, located in southern Chicago, Illinois, USA, is a historical steel waste site that was created through the dumping of steel mill slag waste, which was used until the middle of the 20th century to turn the wetlands into buildable land. The weathering of the steel slag has led to a highly alkaline (up to pH 13.4), non-saline environment due to the release of Ca(OH)2 into the groundwater flow. While there are many chemical similarities to natural alkaline systems, such as serpentinizing sites, Calumet is distinct in that its extreme pH is a result of anthropogenic processes. Preliminary16S rDNA sequence analysis of these sites revealed that the microbial community was low in microbial diversity, and a significant portion of the community, particularly at the most alkaline sites, contained divergent sequences possibly representing some novel bacterial clades. The alkalinity of this site makes cultivation of these bacteria difficult and current ex situ culturing attempts have not yielded novel clades. As an alternative to the cultivation of these divergent taxa, we performed metagenomic sequencing and taxonomic binning to examine the genomes through computational analyses. Microbial DNA was sequenced from three samples taken from a single sediment core and assembled using a de novo metagenomic sequence assembler (SPAdes). Taxonomic bins were created using tetramer frequency and coverage values to separate contigs (Anvi'o). Nine robust genomes were identified within the Calumet metagenome dataset and were taxonomically placed using protein and 16S rRNA gene analyses and annotated using online tools (KEGG and RAST). Of the nine highest quality bins, four belonged to known genera and two to the novel Firmicutes from previous genetic surveys. Several of these genomes showed uncommon metabolic pathways, including nitrogen oxidation and hydrogen utilization that all for energy production in the harsh environmental conditions. Analysis also revealed very few proteins that are typically implicated in high pH adaptation and tolerance.


Advisors: Wesley D. Swingley.||Committee members: Melissa Lenczewski; Yanbin Yin.||Includes bibliographical references.||Includes illustrations.


ix, 84 pages




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