Lab Projects

Wetlands Microbiology

Calumet Wetlands Map

The Calumet Wetlands (N 41°40 W 87°35 ’) are heavy-metal rich alkaline environments located along the southern tip of Lake Michigan. Nearly a century of use as a steel slag dumping site and decades of mineral weathering, especially of calcium silicates, has resulted in an unprecedented alkaline pH exceeding 13 (Roadcap et al., 2005). Additional industry deposits including heavy metals Fe, Zn, Sr, and Pb act as additional stresses to the aerobic and anaerobic microorganisms that survive in this extreme environment (Roadcap et al., 2006).

Study of the microbial communities inhabiting the waters and soils of Calumet is essential to advancing understanding of the on-going biogeochemical processes at this and other hazardous waste sites similar to Calumet. This project addresses microbial diversity in the region by linking geochemical elemental analysis with microbial culturing and sequencing efforts. View a larger version of the map

Geochemical Analysis

  • Analyze the water and soil geochemistry of Calumet sites

Microbial Culturing

  • Cultivate aerobic and anaerobic microorganisms from high-pH Calumet water and soil

Phylogenetic Analysis

  • Sequence and analyze genomic data from Calumet microbes

Microbial Dark Matter

Image of  dark matter

Through cooperation with Brian Hedlund at UNLV, our lab seeks to illuminate microbial taxa that resisted culturing attempts. Even as cultivation -independent approaches have dramatically expanded our view of microbial diversity, they continue to highlight our limitations in isolating novel organisms from the environment. Currently fewer than 50% of Bacterial and Archaeal phylum-level lineages have been cultivated and characterized in the laboratory, leaving the majority of phyla as "biological dark matter" due to our profound ignorance of these groups. Environmenta l genomics (metagenomics) has led to  the recovery of partial or nearly-complete genomes from several candidate phyla in habitats where they are naturally abundant, and the advent of single-cell genomics, where individual cells are isolated and their DNA is amplified and sequenced, has allowed us access to less abundant "dark matter" groups . We have used a synergystic approach to analyze single-cell and metagenome sequencing from Great Basin hot springs and obtain draft genomes from multiple candidate phyla, including Archaeal pSL4 and YNPFFA and Bacterial OP9, EM3, EM19, GAL35, and more. Analysis of these genomes has allowed us to make predictions about the basic biology of these community members, laying the foundation for understanding the ecological role of "dark matter" in not just geotherma systems, but throughout the environment.

Contact:

Photo of Wesley Swingley

Wesley D. Swingley
Department of Biological Sciences
Northern Illinois University
DeKalb, IL 60115
Email: wswingley@niu.edu
Office: MO 333
Phone: (815) 753-7835
Lab: MO 312
Lab Phone: (815) 753-7812