1887

Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

    Authors: SARAH M. BOOMER1,*, DANIEL P. LODGE1, BRYAN E. DUTTON1
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Western Oregon University, Department of Biology, Monmouth, Oregon 97361
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • *Corresponding author. Mailing address: Western Oregon University, Department of Biology, 345 Monmouth Ave., Monmouth, OR 97361. Phone: (503) 838-8209. Fax: (503) 838-8072. E-mail: [email protected].
    • Copyright © 2002, American Society for Microbiology. All Rights Reserved.
    Source: J. Microbiol. Biol. Educ. May 2002 vol. 3 no. 1 18-25. doi:10.1128/154288102X14285807655107
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • PDF
    286.24 Kb
  • HTML
    47.90 Kb
  • XML

    Abstract:

    We have developed a ten-week curriculum for molecular biology that uses 16S ribosomal RNA genes to characterize and compare novel bacteria from hot spring communities in Yellowstone National Park. The 16S rRNA approach bypasses selective culture-based methods. Our molecular biology course offered the opportunity for students to learn broadly applicable methods while contributing to a long-term research project. Specifically, students isolated and characterized clones that contained novel 16S rRNA inserts using restriction enzyme, DNA sequencing, and computer-based phylogenetic methods. In both classes, students retrieved novel bacterial 16S rRNA genes, several of which were most similar to Green Nonsulfur bacterial isolates. During class, we evaluated student performance and mastery of skills and concepts using quizzes, formal lab notebooks, and a broad project assignment. For this report, we also assessed student performance alongside data quality and discussed the significance, our goal being to improve both research and teaching methods.

Key Concept Ranking

Restriction Fragment Length Polymorphism
0.4429262
Environmental Microbiology
0.4421141
0.4429262

References & Citations

1. Amann R, Ludwig W, Schleifer KH 1995 Phylogenetic identification and in situ detection of individual microbial cells without cultivation Microbiol Rev 59 143 169 7535888
2. Ausubel F, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K 1997 Short protocols in molecular biology 3rd ed John Wiley and Sons, Inc New York, N.Y.
3. Boomer SM, Lodge DP, Dutton BE, Pierson B 2002 Molecular characterization of novel red green nonsulfur bacteria from five distinct hot spring communities in Yellowstone National Park Appl Environ Microbiol 68 346 355 10.1128/AEM.68.1.346-355.2002 11772644 http://dx.doi.org/10.1128/AEM.68.1.346-355.2002
4. Boomer SM, Pierson BK, Austinhirst R, Castenholz RW 2000 Characterization of novel bacterio-chlorophyll-a-containing red filaments from alkaline hot springs in Yellowstone National Park Arch Microbiol 174 152 161 10.1007/s002030000189 11041345 http://dx.doi.org/10.1007/s002030000189
5. Committee on Development of an Addendum to the National Science Education Standards on Scientific Inquiry 2000 Inquiry and the National Science Education Standards, a guide for teaching and learning National Academy Press Washington D.C.
6. Hanada S, Takaichi S, Matsuura K, Nakamura K Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium which lacks chlorosomes Int. J. Syst. Bacteriol. 52 187 93
7. Hugenholtz P, Goebel BM, Pace NR 1998 Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity J Bacteriol 180 4765 4774 9733676
8. Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD 2002 Manual of environmental microbiology 2nd ed ASM Press Washington D.C.
9. Pace NR 1997 A molecular view of microbial diversity and the biosphere Science 276 734 740 10.1126/science.276.5313.734 9115194 http://dx.doi.org/10.1126/science.276.5313.734
10. Reysenbach AL, Wickham GS, Pace NR 1994 Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park Appl Environ Microbiol 60 2113 2119 7518219
11. Sanger F, Nicklen S, Coulson AR 1977 DNA sequencing with chain-terminating inhibitors Proc Natl Acad Sci USA 74 5463 5467 10.1073/pnas.74.12.5463 271968 http://dx.doi.org/10.1073/pnas.74.12.5463
12. Winfrey MR, Rott MA, Wortman AT 1997 Unraveling DNA molecular biology for the laboratory Prentice-Hall, Inc Upper Saddle River, N.J.
13. Woese CR 1987 Bacterial evolution Microbiol Rev 51 221 271 2439888

Supplemental Material

No supplementary material available for this content.

Loading

Article metrics loading...

/content/journal/jmbe/10.1128/154288102X14285807655107
2002-05-01
2019-04-22

Abstract:

We have developed a ten-week curriculum for molecular biology that uses 16S ribosomal RNA genes to characterize and compare novel bacteria from hot spring communities in Yellowstone National Park. The 16S rRNA approach bypasses selective culture-based methods. Our molecular biology course offered the opportunity for students to learn broadly applicable methods while contributing to a long-term research project. Specifically, students isolated and characterized clones that contained novel 16S rRNA inserts using restriction enzyme, DNA sequencing, and computer-based phylogenetic methods. In both classes, students retrieved novel bacterial 16S rRNA genes, several of which were most similar to Green Nonsulfur bacterial isolates. During class, we evaluated student performance and mastery of skills and concepts using quizzes, formal lab notebooks, and a broad project assignment. For this report, we also assessed student performance alongside data quality and discussed the significance, our goal being to improve both research and teaching methods.

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

Full text loading...

/deliver/fulltext/jmbe/3/1/jmbe-3-1-18.xml.a.html?itemId=/content/journal/jmbe/10.1128/154288102X14285807655107&mimeType=html&fmt=ahah

Figures

Image of FIG. 1

Click to view

FIG. 1

Student-generated flow chart depicting large-scale plasmid isolation procedures, Unit 1. This component of the prelab assignment comprised 10% of each Unit Lab grade. Evaluation notes in upper right corner are instructors additions.

Source: J. Microbiol. Biol. Educ. May 2002 vol. 3 no. 1 18-25. doi:10.1128/154288102X14285807655107
Download as Powerpoint
Image of FIG. 2

Click to view

FIG. 2

Phylogenetic tree using representative class data. The tree was generated using maximum parsimony methods against a dataset of known bacteria (indicated in italics with accession number in parentheses). The bar indicates 10 nucleotide changes. Branch numbers indicate percent support for that branch. Bacterial lineages are indicated in brackets.

Source: J. Microbiol. Biol. Educ. May 2002 vol. 3 no. 1 18-25. doi:10.1128/154288102X14285807655107
Download as Powerpoint
Image of FIG. 3

Click to view

FIG. 3

Representative PCR data. Panel A was generated using general bacterial 16S primers. Panel B was generated with GNS-specific primers. Lane 1 in both A and B is marker standards (Lambda/HindIII), and lanes 2 through 12 were representative products using different PCR buffers. The arrows at the right indicate the target fragment. PCR product was separated using 1% agarose with standard TAE running buffer.

Source: J. Microbiol. Biol. Educ. May 2002 vol. 3 no. 1 18-25. doi:10.1128/154288102X14285807655107
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