1887

The CURE for Cultivating Fastidious Microbes

    Authors: Arundhati Bakshi1, Austen T. Webber1, Lorelei E. Patrick1, William Wischusen1, Cameron Thrash1,*
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 29 May 2018 Accepted 15 November 2018 Published 26 April 2019
    • ©2019 Author(s). Published by the American Society for Microbiology
    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.

    • Supplemental materials available at http://asmscience.org/jmbe
    • *Corresponding author. Mailing address: University of Southern California, Department of Biological Sciences, 3616 Trousdale Pkwy., AHF107, Los Angeles, CA 90089. E-mail: [email protected].
    Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1635
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • PDF
    481.49 Kb
  • HTML
    77.28 Kb
  • XML
    97.98 Kb

    Abstract:

    Course-Based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.

References & Citations

1. Lopatto D 2007 Undergraduate research experiences support science career decisions and active learning CBE Life Sci Educ 6 297 306 10.1187/cbe.07-06-0039 18056301 2104507 http://dx.doi.org/10.1187/cbe.07-06-0039
2. Brownell SE, Hekmat-Scafe DS, Singla V, Chandler Seawell P, Conklin Imam JF, Eddy SL, Stearns T, Cyert MS 2015 A high-enrollment course-based undergraduate research experience improves student conceptions of scientific thinking and ability to interpret data CBE Life Sci Educ 14 2 ar21 10.1187/cbe.14-05-0092 26033869 4477737 http://dx.doi.org/10.1187/cbe.14-05-0092
3. Olimpo JT, Fisher GR, DeChenne-Peters SE 2016 Development and evaluation of the tigriopus course-based undergraduate research experience: impacts on students’ content knowledge, attitudes, and motivation in a majors introductory biology course CBE Life Sci Educ 15 4 ar72 10.1187/cbe.15-11-0228 27909022 5132369 http://dx.doi.org/10.1187/cbe.15-11-0228
4. Linn MC, Palmer E, Baranger A, Gerard E, Stone E 2015 Undergraduate research experiences: impacts and opportunities Science 347 1261757-1-6 10.1126/science.1261757 http://dx.doi.org/10.1126/science.1261757
5. Shapiro C, Moberg-Parker J, Toma S, Ayon C, Zimmerman H, Roth-Johnson EA, Hancock SP, Levis-Fitzgerald M, Sanders ER 2015 Comparing the impact of course-based and apprentice-based research experiences in a life science laboratory curriculum J Microbiol Biol Educ 16 186 197 10.1128/jmbe.v16i2.1045 http://dx.doi.org/10.1128/jmbe.v16i2.1045
6. Spell RM, Guinan JA, Miller KR, Beck CW 2014 Redefining authentic research experiences in introductory biology laboratories and barriers to their implementation CBE Life Sci Educ 13 102 110 10.1187/cbe.13-08-0169 24591509 3940451 http://dx.doi.org/10.1187/cbe.13-08-0169
7. Thompson SK, Neill CJ, Wiederhoeft E, Cotner S 2016 A model for a course-based undergraduate research experience (CURE) in a field setting J Microbiol Biol Educ 17 469 471 10.1128/jmbe.v17i3.1142 http://dx.doi.org/10.1128/jmbe.v17i3.1142
8. Cotner S, Hebert S 2016 Bean beetles make biology research sexy Am Biol Teach 78 233 240 10.1525/abt.2016.78.3.233 http://dx.doi.org/10.1525/abt.2016.78.3.233
9. Miller CW, Hamel J, Holmes KD, Helmey-Hartman WL, Lopatto D 2013 Extending your research team: learning benefits when a laboratory partners with a classroom BioScience 63 754 762 10.1093/bioscience/63.9.754 http://dx.doi.org/10.1093/bioscience/63.9.754
10. Bakshi A, Patrick LE, Wischusen EW 2016 A framework for implementing course-based undergraduate research experiences (CUREs) in freshman biology labs Am Biol Teach 78 448 456 10.1525/abt.2016.78.6.448 http://dx.doi.org/10.1525/abt.2016.78.6.448
11. Staley JT, Konopka A 1985 Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats Ann Rev Microbiol 39 321 346 10.1146/annurev.mi.39.100185.001541 http://dx.doi.org/10.1146/annurev.mi.39.100185.001541
12. Connon SA, Giovannoni SJ 2002 High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates Appl Environ Microbiol 68 3878 3885 10.1128/AEM.68.8.3878-3885.2002 12147485 124033 http://dx.doi.org/10.1128/AEM.68.8.3878-3885.2002
13. Button DK, Schut F, Quang P, Martin R, Robertson BR 1993 Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results Appl Environ Microbiol 59 881 891 16348896 202203
14. Henson MW, Pitre DM, Weckhorst J, Lanclos VC, Webber AT, Thrash JC 2016 Artificial seawater media facilitate cultivating members of the microbial majority from the Gulf of Mexico mSphere 1 e00028 16 27303734 4894692
15. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ 2002 Cultivation of the ubiquitous SAR11 marine bacterioplankton clade Nature 418 630 633 10.1038/nature00917 12167859 http://dx.doi.org/10.1038/nature00917
16. Stingl U, Tripp HJ, Giovannoni SJ 2007 Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site ISME J 1 361 371 10.1038/ismej.2007.49 18043647 http://dx.doi.org/10.1038/ismej.2007.49
17. Song J, Oh HM, Cho JC 2009 Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean FEMS Microbiol Lett 295 141 147 10.1111/j.1574-6968.2009.01623.x 19459973 http://dx.doi.org/10.1111/j.1574-6968.2009.01623.x
18. Henson MW, Lanclos VC, Faircloth BC, Thrash JC 2018 Cultivation and genomics of the first freshwater SAR11 (LD12) isolate ISME J 12 1846 1860 10.1038/s41396-018-0092-2 29599519 6018831 http://dx.doi.org/10.1038/s41396-018-0092-2
19. Marshall IPG, Blainey PC, Spormann AM, Quake SR 2012 A single-cell genome for Thiovulum sp Appl Environ Microbiol 78 8555 8563 10.1128/AEM.02314-12 23023751 3502928 http://dx.doi.org/10.1128/AEM.02314-12
20. Yang SJJ, Kang I, Cho JCC 2016 Expansion of cultured bacterial diversity by large-scale dilution-to-extinction culturing from a single seawater sample Microb Ecol 71 29 43 10.1007/s00248-015-0695-3 http://dx.doi.org/10.1007/s00248-015-0695-3
21. Cho JC, Giovannoni SJ 2004 Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria Appl Environ Microbiol 70 432 440 10.1128/AEM.70.1.432-440.2004 14711672 321273 http://dx.doi.org/10.1128/AEM.70.1.432-440.2004
22. Thrash JC, Weckhorst JL, Pitre DM 2015 Cultivating fastidious microbes 57 58 McGenity TJ, Timmis KN, Nogales B Hydrocarbon and Lipid Microbiology Protocols: Isolation and Cultivation 4 Springer-Verlag Berlin, Heidelberg 10.1007/8623_2015_67 http://dx.doi.org/10.1007/8623_2015_67
23. Emmert EAB 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
24. Kuh GD 2008 High-impact educational practices: what they are, who has access to them, and why they matter Association of American Colleges and Universities Washington, DC
25. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO 2013 Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies Nucleic Acids Res 41 e1 10.1093/nar/gks808 3592464 http://dx.doi.org/10.1093/nar/gks808
26. Bergkessel M, Guthrie C 2013 Chapter 25: Colony PCR Meth Enzymol 529 299 309 10.1016/B978-0-12-418687-3.00025-2 http://dx.doi.org/10.1016/B978-0-12-418687-3.00025-2
27. Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk HP, Gophna U, Ruppin E 2015 Harnessing the landscape of microbial culture media to predict new organism-media pairings Nature Comm 6 8493 10.1038/ncomms9493 http://dx.doi.org/10.1038/ncomms9493
28. Garcia SL, McMahon KD, Grossart HP, Warnecke F 2014 Successful enrichment of the ubiquitous freshwater acI Actinobacteria Environ Microbiol Rep 6 21 27 10.1111/1758-2229.12104 24596259 http://dx.doi.org/10.1111/1758-2229.12104

Supplemental Material

Loading

Article metrics loading...

/content/journal/jmbe/10.1128/jmbe.v20i1.1635
2019-04-26
2019-08-24

Abstract:

Course-Based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

/deliver/fulltext/jmbe/20/1/jmbe-20-10.html?itemId=/content/journal/jmbe/10.1128/jmbe.v20i1.1635&mimeType=html&fmt=ahah

Figures

Image of FIGURE 1

Click to view

FIGURE 1

Flowchart of the mCURE background and experimental design. Using this flowchart, students are guided through the scientific process to gain an understanding of the relevance and importance of the project. Various segments of the course are color-coded (grey, orange, green, blue, and yellow), corresponding to Table 1 , where the week-by-week activities for each of these segments are described. This flowchart may be modified as needed to suit alternative projects using a similar protocol.

Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1635
Download as Powerpoint
Image of FIGURE 2

Click to view

FIGURE 2

Grade distributions for two sections of mCURE students during each of two semesters in the 2015–2016 school year. Fall 2015 consisted of ~50 Honors college students majoring in biology. The topics for the five quizzes (Q1–Q5) were as follows: Q1 = Safety, Controls; Q2 = Experimental design, Scientific writing; Q3 = DNA extraction; Q4 = PCR; Q5 = Gel electrophoresis, Purpose of sequencing, Primer design. Spring 2016 consisted of ~60 mostly nonbiology major students. The topics for the five quizzes (Q1–Q5) were as follows: Q1 = Dilutions, Pipetting, Safety, Controls, Scientific writing; Q2 = Experimental design, Dilution, Pipetting, Controls; Q3 = DNA extraction; Q4 = PCR, Primer selection/design, Gel electrophoresis; Q5 = Purpose of sequencing, Sequence analysis. The grades for both semesters were assigned based on the following score criteria: A = 90%–100%; B = 80%–90%; C = 70%–80%; D = 60%–70%; F = <60%.

Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1635
Download as Powerpoint
Image of FIGURE 3

Click to view

FIGURE 3

Example gel electrophoresis image of a successful 16S rRNA gene PCR amplification from fall 2015. Lanes labeled according to contents: “Sample A11–22” is the amplicon from isolate DNA (expected size 1,466 bp); “Ladder” is Lambda HindIII digest ladder (NEB N3012S), with the lowest visible band at 2,027 bp; “Control” is the negative control (water).

Source: J. Microbiol. Biol. Educ. April 2019 vol. 20 no. 1 doi:10.1128/jmbe.v20i1.1635
Download as Powerpoint

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error