This project was prepared as part of a BioQUEST faculty development workshop entitled ASM/BioQUEST Bioinformatics Institute at American Society for Microbiology in March 2007. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

Upcoming events               BEDROCK Problem Spaces

Student Research in Microbial Biogeography: Introducing Bioinformatics Tools
Authors          Audiences          Overview           Materials          Resources           Future Directions



Gary Kuleck
Loyola Marymount University

Jason Tor
Hampshire College

Cynthia Liebert
National Institutes of Health


Possible Audiences:

Faculty and students at colleges and universities teaching research-based courses in microbial ecology, and environmental microbiology, and molecular biology.



Brief Overview:

Microbial communities exist in spatially distinct environments. Undergraduates participate in research that takes them into the field and laboratory to study the communities. We describe two student-directed research projects that highlight the effect of environmental variation on microbial diversity. Bioinformatics tools are critical in analyzing the large amount of molecular data arising from such analysis.



Project Materials:

Computer based: NCBI web site, Biology Workbench, IMG-JGI
Environment: Arsenic-contaminated soils in New England; Ballona Wetlands, Los Angeles
Laboratory: Molecular biology supplies, reagents, and protocols



Resources and References:

Martiny et al. 2006. Microbial biogeography: putting microorganisms on the map Nature Reviews Microbiology 4:102-112.

California Regional Water Quality Control Board, State Water Resources Control Board and U.S. Environmental Protection Agency. 2002. DRAFT Strategy for Developing TMDLs and Attaining Water Quality Standards in the Los Angeles Region. Public Review Draft, December 2002. Report available at:

A.M. Osborn, E.R.B. Moore and K.N. Timmis. 2000. An evaluation of terminalrestriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics Environ. Micro. 21(1): 39-50.

Manfred G. Höfle, Sébastien Flavier, Richard Christen, Julia Bötel, Matthias Labrenz, Ingrid Brettar. 2005. Retrieval of nearly complete 16S rRNA gene sequences from environmental DNA following 16S rRNA-based community fingerprinting. Env. Micro. 7(5): 670–675.

Macur, R. E., H. W. Langner, et al. (2004). "Linking geochemical processes with microbial community analysis: successional dynamics in an arsenic-rich, acid-sulphate-chloride geothermal spring." Geobiology 2: 163-177.

Joynt, J., M. Bischoff, et al. (2006). "Microbial Community Analysis of Soils Contaminated with Lead, Chromium and Petroleum Hydrocarbons." Microb. Ecol. 51: 209-219.



Future Directions:

Writing collaborative grants

Development of a collaborative website to highlight student research and serve as a resource of information

Development of a new project-based research course in Microbial Biogeography.

Undergraduate research projects using bioinformatics in 4 upper division lab courses throughout the college: biology, chemistry, engineering, natural sciences.

New bioinformatics course centered on microbial genome annotation.

A network of research collaborators with locally available metal contaminated soil, sediments, and surface waters.

Construction of a web-based network where research groups could post information about their research sites.




- JMT24.ppt
- GK2.ppt
- BallonaWS.jpg