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Laboratory Activity to Effectively Teach Introductory Geomicrobiology Concepts to Non-Geology Majors

    Authors: Massimiliano Marvasi1,*, Yarely C. Davila-Vazquez2, Lilliam Casillas Martinez2
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Soil and Water Science Department, University of Florida, Gainesville, FL 32610-3610; 2: Biology Department, University of Puerto Rico-Humacao, Humacao, PR 00791
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 02 December 2013
    • Supplemental materials available at http://jmbe.asm.org
      During our experiment we trained students in making Standard B4. The experience was successful but it was very time consuming. Consequently, during the preparation of the manuscript we decided to exclude this part, suggesting the instructor prepare the media for the students.
    • *Corresponding author. Mailing address: Soil and Water Science Department, University of Florida, 2033 Mowry Road – Room 330E, PO Box 103610, Gainesville, FL 32610-3610. Phone: 352-273-8195. Fax: 352-273-5645. E-mail: [email protected].
    • ©2013 Author(s). Published by the American Society for Microbiology.
    Source: J. Microbiol. Biol. Educ. December 2013 vol. 14 no. 2 206-212. doi:10.1128/jmbe.v14i2.578
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    Abstract:

    We have designed a three-week experiment that can complement any microbiology course, to teach main geomicrobiology concepts for non-geology majors. One of the most difficult concepts for non-geology majors to comprehend is how bacteria serve as a platform for different mineralization reactions. In our three-week laboratory practice, students learn the main principles and conditions required for an induced bacterial mineralization. Upon completion of the laboratory experience, students will: 1) learn how microbial-induced mineralization (such as calcium carbonate formation) is affected by differential media and growth conditions; 2) understand how bacterial physiology affects any induced in situ or in vitro mineralization; 3) comprehend how growing conditions and bacterial physiologies interrelate, resulting in differential crystal formation. The teaching-learning process was assessed using a pre-/posttest with an increase from 26% to 76% in the number of positive answers from the students. We also measured the students’ proficiency while conducting specific technical tasks, revealing no major difficulties while conducting the experiments. A final questionnaire was provided with satisfactory evaluations from the students regarding the organization and content of the practices. 84–86% of the students agreed that the exercises improved their knowledge in geomicrobiology and would like to attend similar laboratories in the future. Such response is the best indicator that the laboratory practice can be implemented in any undergraduate/graduate microbiology course to effectively teach basic geomicrobiology concepts to non-geology majors.

Key Concept Ranking

Microbial Ecology
1.295725
Environmental Microbiology
1.2885664
Optical Microscopes
0.636872
Calcium Carbonate
0.6097461
Chemicals
0.58731186
Crystal Violet
0.54406136
Gram Staining
0.5325518
1.295725

References & Citations

1. Benzerara K, et al 2006 Nanoscale detection of organic signatures in carbonate microbialites PNAS 103 9440 9445 10.1073/pnas.0603255103 16772379 1480426 http://dx.doi.org/10.1073/pnas.0603255103
2. Boquet E, Boronat A, Ramos-Cormenzana A 1973 Production of calcite (calcium carbonate) crystals by soil bacteria is a general phenomenon Nature 246 527 529 10.1038/246527a0 http://dx.doi.org/10.1038/246527a0
3. Dupraz C, Reid RP, Braissant O, Decho AW, Norman RS, Visscher PT 2009 Processes of carbonate precipitation in modern microbial mats Earth-Sci Rev 96 141 162 10.1016/j.earscirev.2008.10.005 http://dx.doi.org/10.1016/j.earscirev.2008.10.005
4. Dupraz S, Parmentiera M, Méneza B, Guyota F 2009 Experimental and numerical modeling of bacterially induced pH increase and calcite precipitation in saline aquifers Chem Geol 15 44 53 10.1016/j.chemgeo.2009.05.003 http://dx.doi.org/10.1016/j.chemgeo.2009.05.003
5. Ehrlich HL 1999 Microbes as geologic agents: their role in mineral formation Geomicrob J 16 135 153 10.1080/014904599270659 http://dx.doi.org/10.1080/014904599270659
6. Hernández-Machado B, Casillas-Martínez L 2009 Design and assessment of an introductory geomicrobiology course for non-geology majors J Geosci Educ 57 23 32 10.5408/1.3544225 http://dx.doi.org/10.5408/1.3544225
7. Lowenstam HA, Weiner S 1989 On biomineralization Oxford University Press New York, NY
8. Madigan MT, Martinko JM, Dunlap JM, Clark DP 2009 Brock, Biology of Microorganisms Twelfth edition 669 Pearson San Francisco, CA
9. Marvasi M, Visscher PT, Perito B, Mastromei G, Casillas L 2010 Physiological requirements for carbonate precipitation during biofilm development of Bacillus subtilis etfA mutant FEMS Microbiol Ecol 71 341 350 10.1111/j.1574-6941.2009.00805.x 20059546 http://dx.doi.org/10.1111/j.1574-6941.2009.00805.x
10. Marvasi M, et al 2012 Importance of B4 medium in determining organomineralization potential of bacterial environmental isolates Geomicrobiol J 29 916 924 10.1080/01490451.2011.636145 http://dx.doi.org/10.1080/01490451.2011.636145
11. Morse JW, Arvidson RS, Luttge A 2007 Calcium carbonate formation and dissolution Chem Rev 107 342 381 10.1021/cr050358j 17261071 http://dx.doi.org/10.1021/cr050358j
12. Powers E 1995 Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts Appl Environ Microbiol 61 3756 3758 7487012 167675
13. Ries JB, Anderson MA, Hill RT 2008 Seawater Mg/Ca controls polymorph mineralogy of microbial CaCO 3: a potential proxy for calcite-aragonite seas in Precambrian time Geobiology 6 106 119 10.1111/j.1472-4669.2007.00134.x 18380873 http://dx.doi.org/10.1111/j.1472-4669.2007.00134.x
14. Rios-Velazquez C, Casillas-Martínez L, Visscher PT 2007 Learning geomicrobiology as a team using microbial mats, a multidisciplinary approach J Microbiol Biol Educ 8 28 35 23653817 3577146

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/content/journal/jmbe/10.1128/jmbe.v14i2.578
2013-12-02
2019-10-14

Abstract:

We have designed a three-week experiment that can complement any microbiology course, to teach main geomicrobiology concepts for non-geology majors. One of the most difficult concepts for non-geology majors to comprehend is how bacteria serve as a platform for different mineralization reactions. In our three-week laboratory practice, students learn the main principles and conditions required for an induced bacterial mineralization. Upon completion of the laboratory experience, students will: 1) learn how microbial-induced mineralization (such as calcium carbonate formation) is affected by differential media and growth conditions; 2) understand how bacterial physiology affects any induced in situ or in vitro mineralization; 3) comprehend how growing conditions and bacterial physiologies interrelate, resulting in differential crystal formation. The teaching-learning process was assessed using a pre-/posttest with an increase from 26% to 76% in the number of positive answers from the students. We also measured the students’ proficiency while conducting specific technical tasks, revealing no major difficulties while conducting the experiments. A final questionnaire was provided with satisfactory evaluations from the students regarding the organization and content of the practices. 84–86% of the students agreed that the exercises improved their knowledge in geomicrobiology and would like to attend similar laboratories in the future. Such response is the best indicator that the laboratory practice can be implemented in any undergraduate/graduate microbiology course to effectively teach basic geomicrobiology concepts to non-geology majors.

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Figures

Image of FIGURE 1.

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FIGURE 1.

Example of workflow of the experiments conducted over the three-week period to introduce main geomicrobiology concepts. Characterization of soil microorganisms based on Gram type, morphology and pigmentation. Unique morphotypes were streaked on different B4 media. An example is provided of possible results: strain A is grown on both Standard B4 and Buffered B4. When strain A is grown on Standard B4 it can modify the pH by itself, inducing alkalization and fostering precipitation. Below, when the same strain is grown on a buffered acidic environment (Buffered B4), the precipitation does not occur. A similar but opposite example is shown for strain B. Students discriminated between acid/alkaline conditions and presence or absence of crystal precipitation. Crystals and their matrices were collected from the biofilms and analyzed using the optical microscope.

Source: J. Microbiol. Biol. Educ. December 2013 vol. 14 no. 2 206-212. doi:10.1128/jmbe.v14i2.578
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Image of FIGURE 3.

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FIGURE 3.

Box-and-wisher plot showing the median of 25th to 75th percentile of positive responses in the pre- and posttests to assess student learning in geomicrobiology after the three-week laboratory experiment.

Source: J. Microbiol. Biol. Educ. December 2013 vol. 14 no. 2 206-212. doi:10.1128/jmbe.v14i2.578
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Image of FIGURE 4.

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FIGURE 4.

Assessment for student performance. The scale ranges from very good ( 5 ), to good ( 3 ), to poor ( 1 ). Tasks assigned: (A) The student is able to prepare the B4 medium as instructed . (B) The student uses aseptic techniques to streak the isolates on B4 media plates. (C) The student can discriminate among alkaline (red) and acidic (yellow) conditions in the B4 media plates. (D) The student is able to associate acidic conditions on B4 plates with impairment of crystal formation. (E) The student discriminates among different crystal morphologies using the microscope. (F) The student is able to visualize the EPS matrix using the microscope. (G) The student properly identifies the crystals on the biofilm.

Source: J. Microbiol. Biol. Educ. December 2013 vol. 14 no. 2 206-212. doi:10.1128/jmbe.v14i2.578
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Image of FIGURE 2.

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FIGURE 2.

Main findings reported after the three-week laboratory experience to introduce geomicrobiology concepts. On panels A and B, two different morphotypes were grown on standard B4 plates with Phenol Red as indicator and incubated for 7 days at 40°C. Biofilms in panel A were alkaline (see red coloration, indicative of pH ≥ 8.2 with an arrow indicating the crystals). In panel B, we show a strain with a more acidic metabolism and, consequently, no crystals were formed (yellow, indicative of pH ≤ 6.4). Panels C and D demonstrate the observation of CaCO crystals (see arrows) with the stereomicroscope (magnification 4X). Panels E and F show examples of CaCO crystals observed with the optical microscope (magnification 100X). Panel G shows the matrix stained with crystal violet associated with the carbonate crystals that are progressively dissolved after 0.1 N HCl treatments.

Source: J. Microbiol. Biol. Educ. December 2013 vol. 14 no. 2 206-212. doi:10.1128/jmbe.v14i2.578
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