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Microbial Life in a Winogradsky Column: From Lab Course to Diverse Research Experience

    Author: Samantha T. Parks1
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Biology Department, Georgia State University, Atlanta, GA 30303
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 01 May 2015
    • Supplemental materials available at http://jmbe.asm.org
    • Corresponding author. Mailing address: Georgia State University, Biology Department, 161 Jesse Hill Jr. Dr. SE, Atlanta, GA 30303. Phone: 404-413-5884. Fax: 404-413-5301. E-mail: sterris1@gsu.edu.
    • ©2015 Author(s). Published by the American Society for Microbiology.
    Source: J. Microbiol. Biol. Educ. May 2015 vol. 16 no. 1 82-84. doi:10.1128/jmbe.v16i1.847
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    Abstract:

    Many traditional lab courses include both standard and inquiry-based experiments, yet lack cooperative and authentic lab experiences. Such experiences are important for microbiology students and burgeoning researchers. In a novel lab environment, students constructed Winogradsky columns using common soil and water sources. During initial column incubation, students learned methods for identification of microbial isolates including staining, microscopy, biochemistry and 16S-rRNA sequencing. Concurrently, students challenged their columns via varied substrates and contaminants including enrichment with nitro-compounds, hydrocarbons, acids and other environmental stressors. Students were encouraged to use both basic and more advanced identification methods to study the effect of such challenges within their columns. The students were required to maintain lab notebooks and attend weekly lab meetings, which were designed to share progress and facilitate experimentation among their lab-mates. At the end of the semester, students gathered to present their data and conclusions. By engaging in weekly meetings and a final conference, students were able to construct a snapshot of the microbial diversity, including phylogeny and metabolism, in the soil and water used to construct the Winogradsky columns. By using a common source, students were able to observe an array of diversity within individual columns and extrapolate towards the tremendous microbial diversity in the initial soil and water samples. Equally important to the data obtained, the students engaged in a collaborative effort through discussion, trouble-shooting, weekly meetings and the summative conference. Such efforts enabled students to participate in an authentic research experience within a traditional undergraduate laboratory course.

Key Concept Ranking

Biogeochemical Cycle
0.6370819
Chemicals
0.61111116
Soil
0.60416657
Calcium Carbonate
0.5520635
Microbial Diversity
0.5493651
0.6370819

References & Citations

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ1990Basic local alignment search toolJ Mol Biol21540341010.1016/S0022-2836(05)80360-22231712 http://dx.doi.org/10.1016/S0022-2836(05)80360-2
2. Baker GC, Smith JJ, Cowan DA2003Review and re-analysis of domain-specific 16S primersJ Microbiol Methods5554155510.1016/j.mimet.2003.08.00914607398 http://dx.doi.org/10.1016/j.mimet.2003.08.009
3. Emmert EAASM Task Committee on Laboratory Biosafety2013Biosafety guidelines for handling microorganisms in the teaching laboratory: development and rationaleJ Microbiol Biol Educ14788310.1128/jmbe.v14i1.531238583563706168 http://dx.doi.org/10.1128/jmbe.v14i1.531
4. Grau RR, Limansky AS, Ricci JCD, Mendoza Dd1991The Winogradsky column: a simple and inexpensive approach to teaching environmental biochemistryBiochem Educ1914314710.1016/0307-4412(91)90058-G http://dx.doi.org/10.1016/0307-4412(91)90058-G
5. Parales RE2004Nitrobenzoates and aminobenzoates are chemoattractants for Pseudomonas strainsAppl. Environ. Microbiol.7028529210.1128/AEM.70.1.285-292.200414711654321308 http://dx.doi.org/10.1128/AEM.70.1.285-292.2004
6. Parks ST2014Life in a column: from lab course to a diverse research experience21st Annual American Society for Microbiology Conference for EducatorsDanvers, MA
7. Rogan B, Lemke M, Levandowsky M, Gorrell T2005Exploring the sulfur nutrient cycle using the Winogradsky columnAm Biol Teach6734835610.1662/0002-7685(2005)067[0348:ETSNCU]2.0.CO;2 http://dx.doi.org/10.1662/0002-7685(2005)067[0348:ETSNCU]2.0.CO;2
8. Taras LB2003Promoting student involvement with environmental laboratory experiments in a general microbiology courseMicrobiol Educ42329236535503633125
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/content/journal/jmbe/10.1128/jmbe.v16i1.847
2015-05-01
2017-09-26

Abstract:

Many traditional lab courses include both standard and inquiry-based experiments, yet lack cooperative and authentic lab experiences. Such experiences are important for microbiology students and burgeoning researchers. In a novel lab environment, students constructed Winogradsky columns using common soil and water sources. During initial column incubation, students learned methods for identification of microbial isolates including staining, microscopy, biochemistry and 16S-rRNA sequencing. Concurrently, students challenged their columns via varied substrates and contaminants including enrichment with nitro-compounds, hydrocarbons, acids and other environmental stressors. Students were encouraged to use both basic and more advanced identification methods to study the effect of such challenges within their columns. The students were required to maintain lab notebooks and attend weekly lab meetings, which were designed to share progress and facilitate experimentation among their lab-mates. At the end of the semester, students gathered to present their data and conclusions. By engaging in weekly meetings and a final conference, students were able to construct a snapshot of the microbial diversity, including phylogeny and metabolism, in the soil and water used to construct the Winogradsky columns. By using a common source, students were able to observe an array of diversity within individual columns and extrapolate towards the tremendous microbial diversity in the initial soil and water samples. Equally important to the data obtained, the students engaged in a collaborative effort through discussion, trouble-shooting, weekly meetings and the summative conference. Such efforts enabled students to participate in an authentic research experience within a traditional undergraduate laboratory course.

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