BISC209: Lab5

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Wellesley College-BISC 209 Microbiology -Spring 2010


LAB 5: Getting the 16S rRNA genes from the Soil Genomic DNA in the E. coli clones ready to send away for DNA sequencing

Preparing your clones to send away for sequencing analysis of your 16S rRNA gene
When you examine your transformation plates after their initial overnight incubation, there should have been hundreds of well isolated colonies. In theory, each of them should contain the vector plasmid with an insert of the 16s rRNA gene from one of your soil sample bacteria. Since the vector plasmid contains a kanamycin resistance gene, kanamycin resistance is a selectable marker. The genetically engineered strain of E. coli that we transformed is sensitive to kanamycin UNLESS it is expressing the kanamycin resistance gene on the plasmid. E. coli that did not take up a cloning vector plasmid and express its genes do not form colonies on media with kanamycin. Kanamycin is an antimicrobial compound that disrupts bacterial protein synthesis and kill the cells.

We know each of the vector plasmids in the transformed E. coli growing on the plate contains a 16S rRNA gene insert from the genomic DNA isolated from your soil sample for two reasons. First, there is a ccdB gene in the insertion region of the vector plasmid. That gene, ccdB, means "control of cell death". That gene, when not disrupted, expresses the ccdB protein that poisons bacterial DNA gyrase, causing degradation of the host chromosome and cell death. But the presence of your 16S rRNA gene insert has disrupted the ccdB gene and turned off the protein that inhibits DNA gyrase, allowing the cell to live, replicate and form a colony that should appear white, NOT blue. The second reason that we know the white colonies are transformed with the vector plasmid and that the plasmid contains our insert is that there is a lacZ gene positioned next to the ccdB gene in the insert area and when it is disrupted by insertion of your 16s rRNA gene, it turns off expression of the lacZ gene product, beta-galactosidase. Beta-gal is in enzyme that catalyzes the breakdown of several substrates, including lactose and X-gal. X-gal is a colorless substrate that is is cleaved into a blue colored product by beta-galactosidase. Your Luria-Bertoni agar medium contains both kanamycin and Xgal. If you saw blue colonies, those bacteria are daughter cells from a vector transformed E. coli, BUT the vector plasmid probably does not contain the 16s DNA insert we seek. Therefore, you only want to pick "not-blue" colonies to send away for sequencing of the insert. We hope that there are hundreds of these not-blue colonies on your plate (but not so many that they are not well separated from each other). Our goal is to find 16s rRNA gene fragments from DIFFERENT soil bacteria in many transformed clones, but we have no way of detecting right now which colonies contain a 16s rRNA gene from different soil bacterial species because all will be identical looking non-blue colonies on these plates.

You and your partner will be given a 96 well sterile block. You will use your P1000 to inoculate 1 ml (1000μL) of LB broth with 0.25-0.50 μL/ml kanamycin (NO X-gal) into each well of your block. Then follow the directions below, carefully, to inoculate each well with a different, well isolated non-blue colony.

Preparing Over-night Cultures to send away for 16s rRNA gene sequencing

1. Find well-spaced, white, colonies on your transformation plates.
2. Use the flat end of a sterile toothpick to pick up a single colony. Be careful NOT to touch any of the area of the plate around the colony with your toothpick! Place the toothpick in a singe well of your 96 well block. Leave the toothpick in the well so you will know which wells have been inocuated!!!!
3. Once you and your partner have inoculated the whole block and all the wells are filled with toothpicks, carefully pull out each toothpick by wiping it on the edge of the well (to scrape off the organism) on a side of the well that will allow you to discard the toothpick without the chance of dripping this well's contents into another well. BE CAREFUL not to cross-contaminate your wells!!! Discard the toothpicks in the autoclave bag. Apply the sterile sealing mat carefully and label a piece of your team color tape to put on your block. Label should include your lab section, team color, and initials of partners, data. Take your block to the 37C room and place it carefully on the plateform shaker. Your block will incubate at 37C overnight with shaking.

Preparing Glycerol Stocks from your Overnight Cultures(Your instructor will do this part for you so make sure that your plate and wells are clearly identified!)

1. Pipet 50 μL of 50% glycerol in each well a 96 well Costar round bottom plate.
2. Mix each overnight culture from the 96 well block by pipetting up and down and transfer 50 μL of each culture into a separate well of Costar plate. Mix well.
3. Seal the plate with an aluminum foil special seal and label the plate clearly: Wellesley College, BISC209, T or W (for lab day), Team color code: Y, O, R, B, G, P and the date.
4. Freeze at -80C and send away for sequencing on dry ice.
The sequences should come back in a week or two.

Culturable Bacteria Characterization continued

Activity 1
Interpreting Selective/Differential PEA and EMB plates.

  • Use a fresh stock slant or a colony from your newest isolation streak plate to make a replacement stock slant. Careful attention to replacing stocks will ensure that your cultures remain pure and grow satisfactorily.
  • Complete, continue, or repeat work started previously.
  • Check all tests in progress and record results or observations on your latest isolation streak plates and stocks of your soil bacteria isolates.
  • Examine and record the growth and appearance of soil bacteria isolates inoculated to PEA and EMB plates last week. See the description in the Protocol BISC209: Selective,and/or Differential, and/or Enriched media to help you with the evaluation of cell wall type and other information you might glean from growth appearance on these selective and differential media. Are your Gram stain findings supported? If not, explain why and/or repeat your Gram-stain.

Activity 2:
Morphologic tests Special stains and Motility tests.
At this point, you should have significant knowledge about the cell wall type, the characteristic microscopic appearance of the bacteria (individual, chains, pleomorphic, dimorphic, etc.), and colony growth information. You should also find out whether or not each of your organisms of interest has a capsule, flagella, makes endospores, or might be acid-fast.

To do these stains, follow the appropriate Protocols for Stains and Motility testing in the Prtocols section: Special Stains: Endospore, Acid fast, Capsule, and Flagella and Motility Tests.

The flagella stain is tricky and may not always work. Remember that flagella are bacterial motility organelles. Therefore, if you get a positive motility test from inoculation of a SIMS tube or from the results of a hanging drop test but a negative flagella stain test, you should doubt the stain result and call your isolate motile.

The pattern of results from these tests for morphologic characteristics might allow you a preliminary identification for some of your organisms of interest. Use the Link to the electronic edition of | The Prokaryotesthrough Springer ebooks and the Link to the electronic edition of | Bergey's Manuals to try to determine the taxonomic grouping of each bacteria strain.

Activity 3
Metabolic Activity Tests & Tests for Antibiotic Production
Check for the presence or absence of the following enzymes:
Catalase and oxidase. Enzyme tests

Activity 4
Follow the instructions in Protocols for determining the roles of soil isolates in the soil to begin or perform the following tests:

4A. Inoculate tubes of OF-Glucose medium (2 per organism) to determine whether an organism is oxidative or fermentative using the carbohydrate glucose.

4B. Start the protocol to examine cellulose degradation. This will examine the ability of your isolates to participate in carbon recycling through the digestion of leaf cellulose. This protocol involves collecting leaf discs from your team habitat in the greenhouse. You will use a microfuge tube to "punch" the discs from leaves. It is preferable to use fallen leaves collected from the soil surface, if you need to use leaves still on the plants in the greenhouse check with your instructor and avoid noticeable damage to the plants.

4C. Begin or continue the protocol for Antibiotic Production by testing your isolates for antibiotic producer and for susceptibility of control bacteria (Staph, E. coli, Micrococcus) to antibiotics. If you like, you can set up to test your isolates for antibiotic production against your other isolates as possibly susceptible.

4D. Begin the protocol to test for Ammonification by soil microbes.

4E. Examine starch digestion by your isolates by inoculating starch plates. If time is limited today you may omit this activity.


1. All culture plates that you are finished with should be discarded in the big orange autoclave bag near the sink next to the instructor table. Ask your instructor whether or not to save stock cultures and plates with organisms that are provided.

2. Culture plates, stocks, etc. that you are not finished with should be labeled on a piece of your your team color tape. Place the labeled cultures in your lab section's designated area in the incubator, the walk-in cold room, or at room temp. in a labeled rack. If you have a stack of plates, wrap a piece of your team color tape around the whole stack.

3. Remove tape from all liquid cultures in glass tubes. Then place the glass tubes with caps in racks by the sink near the instructor's table. Do not discard the contents of the tubes.

4. Glass slides or disposable glass tubes can be discarded in the glass disposal box.

5. Make sure all contaminated, plastic, disposable, serologic pipets and used contaminated micropipet tips are in the small orange autoclave bag sitting in the plastic container on your bench.

6. If you used the microscope, clean the lenses of the microscope with lens paper, being very careful NOT to get oil residue on any of the objectives other than the oil immersion 100x objective. Move the lowest power objective into the locked viewing position, turn off the light source, wind the power cord, and cover the microscope with its dust cover before replacing the microscope in the cabinet.

7. If you used it, rinse your staining tray and leave it upside down on paper towels next to your sink.

8. Turn off the gas and remove the tube from the nozzle. Place your bunsen burner and tube in your large drawer.

9. Place all your equipment (loop, striker, sharpie, etc) including your microfuge rack, your micropipets and your micropipet tips in your small or large drawer.

10. Move your notebook and lab manual so that you can disinfect your bench thoroughly.

11. Take off your lab coat and store it in the blue cabinet with your microscope.

12. Wash your hands.


Write two Materials and Methods Sections for your final paper: Isolation of soil bacteria to pure culture
and Identification of bacteria by 16S rRNA gene sequencing from soil genomic DNA

The M&M section that you wrote previously, Amplification of 16S rDNA in a soil sample, can be revised and used as the first part of the more complete Materials and Methods section you will write this week, Identification of bacteria by 16S rRNA gene sequencing from soil genomic DNA. Please use the feedback you received on your previous M&M to improve this Methods submission. Both of the M&M sections that you will write for this assignment should have multiple subsections. Although it is unlikely that you know the genus and species name of the bacteria you have cultured and isolated by this point in our project; you probably do know to which of our desired bacterial groups each is likely to belong. Therefore, when you write this M&M section on Isolation of soil bacteria to pure culture, you should, at an appropriate point, divide it into subsections, each describing the different enrichment protocols you followed to culture and isolate a specific bacterial group. You do not have to write up all 11 groups, but only those protocols that you used to isolate your part of your group's work.

Continue monitoring and following the appropriate protocols to enrich and isolate the culturable bacteria.
Actively begin/continue to research how the morphologic, metabolic, biochemical, and other test results on your bacterial isolates fits with your expectations for the group you enriched for based on the guidance of The Prokaryotes and Bergey's Manual. Link to the new interface for electronic access to the e-book form of The Prokaryotes and Bergey's Manual at |

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10

Lab 12
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