Teach the Earth > Undergraduate Research > 2014 Workshop > Activities > Genomics of microbial communities in Thermopolis Hot Springs

Genomics of microbial communities in Thermopolis Hot Springs

Suzanne M (Suki) Smaglik, Central Wyoming College
Author Profile

This activity has benefited from input from faculty educators beyond the author through a review and suggestion process. This review took place as a part of a faculty professional development workshop where groups of faculty reviewed each others' activities and offered feedback and ideas for improvements. To learn more about the process On the Cutting Edge uses for activity review, see http://serc.carleton.edu/NAGTWorkshops/review.html.


This page first made public: Aug 8, 2014

Summary

The hot springs (52°C) in Thermopolis, WY contain abundant microbial mats, including mineral-rich filamentous bacteria. While cooler than nearby Yellowstone, Thermopolis contains a number or rare or unique organisms.

This activity begins with a field exploration, then includes DNA extraction and preparation for sequencing of the 16S rRNA gene, genomic determination of resulting sequences andstatistically analyzing the resulting sequence data.

Context

Audience

Research on the microbial life of Thermopolis is included in our GEOL 2000 Earth System Science Course. This is a sophomore-level course in
geobiochemistry.

Skills and concepts that students must have mastered

The prerequisites for this course are a 1000-level chemistry course plus, a 1000-level geology course or a 1000-level biology course. Since it is a sophomore-level course, sophomore level written and oral communications skills are expected.

How the activity is situated in the course

The thermophile project is a culminating project that dominates the second half of the course. In lieu of a final exam, students must present their research projects as either poster or oral, at the Wyoming State Undergraduate Research Day, held at the University of Wyoming at the end of April.

Goals

Content/concepts goals for this activity

  • evolution of life with Earth and search for possible life on other planets
  • effect of life on atmospheric, hydrospheric and lithospheric processes
  • field data collection: water chemistry and microbial mat sample description
  • protocol for DNA extraction from difficult samples
  • behavior of scientists as professionals

Higher order thinking skills goals for this activity

  • critical evaluation of field area, defining problem statements and formulating hypotheses
  • statistical analysis of data and interpretation of results

Other skills goals for this activity

  • team decision-making and planning
  • confidence with chemical and or biological lab work
  • genomic searches using BLAST web-based software
  • creation of simple pie charts, bar charts and histograms of genetic data
  • online search for literature describing microbes discovered Thermopolis
  • writing and artistic creation of professional size poster and or powerpoint preseantation

Description and Teaching Materials

This has been presented verbally in class up to this point. Its time to
create some more detailed descriptions.

For the DNA extractions and bioinformatics, I rely heavily on the
Discover the Microbes Within: The Wolbachia Project and the HHMI
Biointeractive Resources, as well at the SERC Microbial Life pages

To be continued...

Teaching Notes and Tips

The papers that students are required to read in preparation for their research are listed in the Resources section below.

Assessment

The assessment consists of two parts:

  1. presentation at Undergraduate Research Day, individually or with team
  2. essay directed at summarizing the relationship of their research project with the textbook chapters that correspond to biogeochemical systems

References and Resources

Discover the Microbes Within!: The Wolbachia Project
http://discover.mbl.edu/labs.htm

HHMI Biointeractives - Bacterial Identification Virtual Lab
http://www.hhmi.org/biointeractive/bacterial-identification-virtual-lab

Brock, Thomas D.
Thermophilic microorganisms and life at high temperatures
Springer-Verlag, 1978
http://digicoll.library.wisc.edu/cgi-bin/Science/Science-idx?id=Science.BrockTher

Ch.4 Thermophiles in NPS Yellowstone Research Journal (this site has most images removed to facilitate faster down loading but I can provide a complete version upon request) http://lasp.colorado.edu/home/wp-content/uploads/2011/07/thermophiles.pdf
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