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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: [email protected].
    • ©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 DJ 1990 Basic local alignment search tool J Mol Biol 215 403 410 10.1016/S0022-2836(05)80360-2 2231712 http://dx.doi.org/10.1016/S0022-2836(05)80360-2
2. Baker GC, Smith JJ, Cowan DA 2003 Review and re-analysis of domain-specific 16S primers J Microbiol Methods 55 541 555 10.1016/j.mimet.2003.08.009 14607398 http://dx.doi.org/10.1016/j.mimet.2003.08.009
3. Emmert EA ASM Task Committee on Laboratory Biosafety 2013 Biosafety guidelines for handling microorganisms in the teaching laboratory: development and rationale J Microbiol Biol Educ 14 78 83 10.1128/jmbe.v14i1.531 23858356 3706168 http://dx.doi.org/10.1128/jmbe.v14i1.531
4. Grau RR, Limansky AS, Ricci JCD, Mendoza Dd 1991 The Winogradsky column: a simple and inexpensive approach to teaching environmental biochemistry Biochem Educ 19 143 147 10.1016/0307-4412(91)90058-G http://dx.doi.org/10.1016/0307-4412(91)90058-G
5. Parales RE 2004 Nitrobenzoates and aminobenzoates are chemoattractants for Pseudomonas strains Appl. Environ. Microbiol. 70 285 292 10.1128/AEM.70.1.285-292.2004 14711654 321308 http://dx.doi.org/10.1128/AEM.70.1.285-292.2004
6. Parks ST 2014 Life in a column: from lab course to a diverse research experience 21st Annual American Society for Microbiology Conference for Educators Danvers, MA
7. Rogan B, Lemke M, Levandowsky M, Gorrell T 2005 Exploring the sulfur nutrient cycle using the Winogradsky column Am Biol Teach 67 348 356 10.1662/0002-7685(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 LB 2003 Promoting student involvement with environmental laboratory experiments in a general microbiology course Microbiol Educ 4 23 29 23653550 3633125

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2015-05-01
2019-01-16

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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