1887

Metagenomic Approaches to Identify Novel Organisms from the Soil Environment in a Classroom Setting

    Authors: Sadia J. Rahman1, Trevor C. Charles2, Parjit Kaur1,*
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biology, Georgia State University, Atlanta, GA, 30303, USA; 2: Department of Biology, University of Waterloo, Waterloo, ON N2V 2P1, Canada
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 02 December 2016
    • ©2016 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: Department of Biology, Georgia State University, 58 Edgewood Ave., Atlanta, GA 30303. Phone: 404-413-5405. Fax: 404-413-5301. E-mail: pkaur@gsu.edu.
    Source: J. Microbiol. Biol. Educ. December 2016 vol. 17 no. 3 423-429. doi:10.1128/jmbe.v17i3.1115
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • HTML
    51.17 Kb
  • XML
  • PDF
    1.46 MB

    Abstract:

    Molecular Microbial Metagenomics is a research-based undergraduate course developed at Georgia State University. This semester-long course provides hands-on research experience in the area of microbial diversity and introduces molecular approaches to study diversity. Students are part of an ongoing research project that uses metagenomic approaches to isolate clones containing 16S ribosomal ribonucleic acid (rRNA) genes from a soil metagenomic library. These approaches not only provide a measure of microbial diversity in the sample but may also allow discovery of novel organisms. Metagenomic approaches differ from the traditional culturing methods in that they use molecular analysis of community deoxyribonucleic acid (DNA) instead of culturing individual organisms. Groups of students select a batch of 100 clones from a metagenomic library. Using universal primers to amplify 16S rRNA genes from the pool of DNA isolated from 100 clones, and a stepwise process of elimination, each group isolates individual clones containing 16S rRNA genes within their batch of 100 clones. The amplified 16S rRNA genes are sequenced and analyzed using bioinformatics tools to determine whether the rRNA gene belongs to a novel organism. This course provides avenues for active learning and enhances students’ conceptual understanding of microbial diversity. Average scores on six assessment methods used during field testing indicated that success in achieving different learning objectives varied between 84% and 95%, with 65% of the students demonstrating complete grasp of the project based on the end-of-project lab report. The authentic research experience obtained in this course is also expected to result in more undergraduates choosing research-based graduate programs or careers.

Key Concept Ranking

Bacteria and Archaea
0.59849423
16s rRNA Sequencing
0.51974165
0.59849423

References & Citations

1. Amann RI, Ludwig W, Schleifer KH1995Phylogenetic identification and in situ detection of individual microbial cells without cultivationMicrobiol Rev5911431697535888239358
2. American Association for the Advancement of Science2011Vision and change in undergraduate biology education: a call to action: a summary of recommendations made at a national conference organized by the American Association for the Advancement of ScienceJuly 15–17, 2009Washington, DC
3. Beja O, et al2000Bacterial rhodopsin: evidence for a new type of phototrophy in the seaScience28954861902190610.1126/science.289.5486.190210988064 http://dx.doi.org/10.1126/science.289.5486.1902
4. Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM1997Molecular phylogeny of Archaea from soilProc Natl Acad Sci USA94127728210.1073/pnas.94.1.277899019919314 http://dx.doi.org/10.1073/pnas.94.1.277
5. Donato JJ, Kllimstra MA, Byrnes JR, White RJ, Marsh TC2012The introduction of metagenomics into an undergraduate biochemistry laboratory course yielded a predicted reductase that decreases triclosan susceptibility in Escherichia coliDNA Cell Bio31696897310.1089/dna.2011.1512 http://dx.doi.org/10.1089/dna.2011.1512
6. Fuhrman JA2012Metagenomics and its connection to microbial community organizationF1000 Biol Rep41510.3410/B4-15229126493410722 http://dx.doi.org/10.3410/B4-15
7. Gasper BJ, Gardner SM2013Engaging students in authentic microbiology research in an introductory biology laboratory course is correlated with gains in student understanding of the nature of authentic research and critical thinkingJ Microbiol Biol Educ141253410.1128/jmbe.v14i1.460238583513706163 http://dx.doi.org/10.1128/jmbe.v14i1.460
8. Gibbens BB, Scott CL, Hoff CD, Schottel JL2015Exploring metagenomics in the laboratory of an introductory biology courseJ Microbiol Biol Educ161344010.1128/jmbe.v16i1.780259497554416502 http://dx.doi.org/10.1128/jmbe.v16i1.780
9. Handelsman J2004Metagenomics: application of genomics to uncultured microorganismsMicrobiol Mol Biol Rev68466968510.1128/MMBR.68.4.669-685.200415590779539003 http://dx.doi.org/10.1128/MMBR.68.4.669-685.2004
10. Hugenholtz P, Pace NR1996Identifying microbial diversity in the natural environment: a molecular phylogenetic approachTrends Biotechnol14619019710.1016/0167-7799(96)10025-18663938 http://dx.doi.org/10.1016/0167-7799(96)10025-1
11. Kaur P, Rahman SJ2015Molecular microbial metagenomicsBIOL 4905 laboratory manualUniversity Readers, Georgia State UniversityAtlanta, GA
12. Muth TR, McEntee CM2014Undergraduate urban metagenomics research moduleJ Microbiol Biol Educ151384010.1128/jmbe.v15i1.645248395174004741 http://dx.doi.org/10.1128/jmbe.v15i1.645
13. Neufeld JD, et al2011Open resource metagenomics: a model for sharing metagenomic librariesStand Genomic Sci5220321010.4056/sigs.1974654221808233235511 http://dx.doi.org/10.4056/sigs.1974654
14. Pace NR1997A molecular view of microbial diversity and the biosphereScience276531373474010.1126/science.276.5313.7349115194 http://dx.doi.org/10.1126/science.276.5313.734
15. Rios-Velazquez C, et al2011Summer workshop in metagenomics: one week plus eight students equals gigabases of cloned DNAJ Microbiol Biol Educ12212012610.1128/jmbe.v12i2.177236537553577266 http://dx.doi.org/10.1128/jmbe.v12i2.177
16. Russell SH, Hancock MP, McCullough J2007Benefits of undergraduate research experienceSci Educ Forum316548549
17. Sanders ER, Hirsch AM2014Immersing undergraduate students into research on the metagenomics of the plant rhizosphere: a pedagogical strategy to engage civic-mindedness and retain undergraduates in STEMPlant Sci515714
18. Sharpton TJ2014An introduction to the analysis of shotgun metagenomic dataFront Plant Sci520910.3389/fpls.2014.00209249826624059276 http://dx.doi.org/10.3389/fpls.2014.00209
19. Ward BB2002How many species of prokaryotes are there?Proc Natl Acad Sci USA9916102341023610.1073/pnas.16235919912149517124894 http://dx.doi.org/10.1073/pnas.162359199
20. Weaver GC, Russell CB, Wink DJ2008Inquiry-based and research-based laboratory pedagogies in undergraduate scienceNat Chem Biol41057758010.1038/nchembio1008-57718800041 http://dx.doi.org/10.1038/nchembio1008-577
21. Whitman WB, Coleman DC, Wiebe WJ1998Prokaryotes: the unseen majorityProc Natl Acad Sci USA95126578658310.1073/pnas.95.12.6578961845433863 http://dx.doi.org/10.1073/pnas.95.12.6578
22. Zarraonaindia I, Smith DP, Gilbert JA2013Beyond the genome: community-level analysis of the microbial worldBiol Philos28226128210.1007/s10539-012-9357-8234828243585761 http://dx.doi.org/10.1007/s10539-012-9357-8
jmbe.v17i3.1115.citations
jmbe/17/3
content/journal/jmbe/10.1128/jmbe.v17i3.1115
Loading

Citations loading...

Supplemental Material

Loading

Article metrics loading...

/content/journal/jmbe/10.1128/jmbe.v17i3.1115
2016-12-02
2017-03-23

Abstract:

Molecular Microbial Metagenomics is a research-based undergraduate course developed at Georgia State University. This semester-long course provides hands-on research experience in the area of microbial diversity and introduces molecular approaches to study diversity. Students are part of an ongoing research project that uses metagenomic approaches to isolate clones containing 16S ribosomal ribonucleic acid (rRNA) genes from a soil metagenomic library. These approaches not only provide a measure of microbial diversity in the sample but may also allow discovery of novel organisms. Metagenomic approaches differ from the traditional culturing methods in that they use molecular analysis of community deoxyribonucleic acid (DNA) instead of culturing individual organisms. Groups of students select a batch of 100 clones from a metagenomic library. Using universal primers to amplify 16S rRNA genes from the pool of DNA isolated from 100 clones, and a stepwise process of elimination, each group isolates individual clones containing 16S rRNA genes within their batch of 100 clones. The amplified 16S rRNA genes are sequenced and analyzed using bioinformatics tools to determine whether the rRNA gene belongs to a novel organism. This course provides avenues for active learning and enhances students’ conceptual understanding of microbial diversity. Average scores on six assessment methods used during field testing indicated that success in achieving different learning objectives varied between 84% and 95%, with 65% of the students demonstrating complete grasp of the project based on the end-of-project lab report. The authentic research experience obtained in this course is also expected to result in more undergraduates choosing research-based graduate programs or careers.

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

Full text loading...

/deliver/fulltext/jmbe/17/3/jmbe-17-423.xml.a.html?itemId=/content/journal/jmbe/10.1128/jmbe.v17i3.1115&mimeType=html&fmt=ahah

Figures

Image of FIGURE 1

Click to view

FIGURE 1

Flow of experiments in the project and analyses of PCR-amplified DNA. (A) Progression of experiments. A simplified flowchart of the experiments for identifying 16S rRNA gene-containing clones from the metagenomic library by a stepwise process of elimination. Red plus sign indicates the presence of a positive 16S-containing clone in the batch. (B) Isolation of pooled DNA and PCR analysis. This flowchart shows the experimental steps corresponding to each blue asterisk in panel A. DNA = deoxyribonucleic acid; rRNA = ribosomal ribonucleic acid; PCR = polymerase chain reaction; RDP = ribosomal database project.

Source: J. Microbiol. Biol. Educ. December 2016 vol. 17 no. 3 423-429. doi:10.1128/jmbe.v17i3.1115
Download as Powerpoint
Image of FIGURE 2

Click to view

FIGURE 2

Learning gains evident from pre/post-class surveys given during the Summer Pilot Program. A pre-class survey ( Appendix 3 ) was given on the first day of the program to test knowledge of the topics related to the course. The same survey was provided to the students at the end of the program. The surveys were completed by five students and were evaluated on accuracy as well as the extent of knowledge displayed. Blue = pre-class survey; red = post-class survey; RNA = ribonucleic acid; PCR = polymerase chain reaction; DNA = deoxyribonucleic acid.

Source: J. Microbiol. Biol. Educ. December 2016 vol. 17 no. 3 423-429. doi:10.1128/jmbe.v17i3.1115
Download as Powerpoint
Image of FIGURE 3

Click to view

FIGURE 3

Assessment of learning gains from two semester-long courses with a total of 16 students. (A) Average scores on all assessment methods ( 1 6 ) and the average overall course grade over two semesters ( 7 ). (B) Average scores on selected quiz questions (provided in Appendix 4.1 ). (C) Detailed assessment of student lab reports: writing style follows scientific paper (1); abstract summarizes purpose of the project (2); introduction includes appropriate content (3); method section provides concise narrative (4); results include rationale and summary of experiments (5); figures and tables are included in results (6); discussion includes analysis of results (7). (D) Overall assessment of the lab reports using a two-point rubric: i) understanding flow of the project, and ii) understanding central concepts. BLAST = basic local alignment search tool.

Source: J. Microbiol. Biol. Educ. December 2016 vol. 17 no. 3 423-429. doi:10.1128/jmbe.v17i3.1115
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