BISC209/S12: Lab8

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(Finding Evidence for Co-operation and Competition Among Cultured Members of a Soil Community)
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(Special Stains:)
 
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==Finding Evidence for Co-operation and Competition Among Cultured Members of a Soil Community==
==Finding Evidence for Co-operation and Competition Among Cultured Members of a Soil Community==
<font size="+1">Complete the Interaction Assays</font size=+"1">  <BR>
<font size="+1">Complete the Interaction Assays</font size=+"1">  <BR>
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Take photos of each of your interaction plates. Make sure that the photos are sharp enough to evaluate later. Download them to your dropbox in Sakai. Email them to yourself and to each of your partners. <BR>
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If you haven't been provided with a digital image, please take a photo of each of your interaction plates. Make sure that the photos are sharp enough to evaluate later. Download them to your dropbox in Sakai. Email them to yourself and to each of your partners. <BR>
A sample completed assay is shown below.<BR>
A sample completed assay is shown below.<BR>
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[[Image:interactions_croppedsm1.jpg]]
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[[Image:interactions_assay_1.jpg]]
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Observe the colonies on your plate, comparing any differences in the appearance of the colony growth of each isolate, alone vs mixed. Note that the inoculum in each of the diagonal spots is a pure culture control as are the spots in the column on the far left. Note the "edge" effect, a difference in the appearance of the colony growth in the spots along the perimeter of the plate as opposed to those growing in a more protected locations (the diagonal control colonies). <br><BR>
 
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==Complete Antibiotic Production & Sensitivity Testing==
 
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'''Week 3 <BR>'''
 
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<UL><LI>
 
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Examine the plates and look for evidence of a zone of inhibition (no growth or reduced growth) of any of the "control" organisms in an area near the putative antibiotic producer's colonial growth. Evidence of antibiotic production should appear as a measurable zone of inhibition (section of a circle of no growth or reduced growth compared to the growth see on the control plate). The size of the zone of inhibition is indicative of the diffusion potential of the antibiotic and/or an indication of how sensitive the test organism is to the secreted inhibitor. Compare your results to other tested isolates in your lab section. Think about why an antibiotic might work differently on a Gram positive vs. a Gram negative organism or between two bacteria that are both Gram positive or Gram negative.  <LI>
 
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Take photos of any plates that show evidence of the presence of antibiotic producers in your soil community. If you found that your isolates did not appear to cause measurable inhibition of growth, does that mean that your isolate does not secrete any antimicrobial compounds? Explain? </LI></UL><BR><BR>
 
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==Motility & MNM TESTS DEVELOPMENT AND ANALYSIS ==
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Observe the colonies on your plate, comparing any differences in the appearance of the colony growth of each isolate, alone vs mixed. Look first at each control culture: the inoculum in each of the diagonal spots is a pure culture control as are the spots in the column on the far left. Compare each "spot" where two isolates are mixed to the control spots where each isolate is growing alone. Is either isolate growing better in combination than alone? If so, you have found a mutualistic (beneficial) interaction. For example, in the assay shown above, isolate #102 appears to have a positive effect on the growth of #101, classified as mutualism. Are there combinations that show a reduction in the amount of growth of either isolate compared to the growth of the control areas? If so, you have found an antagonistic (negative) interaction. An example in the assay plate shown above is between isolates #105 and #102. Number 105 seems to inhibit growth of #102, an example of an antagonistic interaction. Note that there are sometimes "edge" effects, differences in the appearance of the colony growth in the cultures along the perimeter of the plate as opposed to those growing in a more protected locations (such as the diagonal control colonies). Spend some time with these plates, carefully and fully evaluating all possible combinations of your soil community isolates for as many as possible examples of mutualism or antagonism. Record your results in your lab notebook with copies of the photos of your plates. <br><BR>
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'''MOTILITY'''<BR>
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Look for radiating growth around the stab line of inoculation of each isolate in each of your soft agar deeps. Motility detection is possible due to the semisolid nature (low concentration of agar) of these soft agar deeps. '''Growth radiating out from the central stab inoculation line indicates that the test organism is motile.'''  First look at your ''E. coli'' positive control to see an example of what radiating growth may look like. Hold your NA soft agar up to the light so that you can see the difference in the medium and the growth line. Get an uninoculated tube to compare color and turbidity. Motile organisms should exhibit detectable growth radiating from the stab inoculation line towards the periphery. Strictly aerobic organisms may show more growth radiating down from the surface than farther into the stab. Non motile organisms will exhibit growth only along the stab inoculation line. Consult with your instructor if you are having a hard time deciding on the motility results. Would it be useful for some soil community members to be motile? Why? Would having motile members in a soil community be useful to non-motile members, or would that mixture be disadvantageous to one or the other, or could it be both?<BR><BR>
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The NA soft agar deep is used exclusively for motility testing. The MNM tubes can be used for motility testing too but since that medium also tests for other metabolic capabilities, your NA soft agar should be your principle test for motility. If you have time, you can try to confirm that an isolate is motile by doing a flagella stain. See the Protocols section in the wiki on [[BISC209/S12: Motility | Motility Tests]] for directions on performing a flagella stain.<BR><BR>
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'''TEST for MANNITOL as a sole carbon source '''<BR>
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What functional advantage would bacteria have if they are able to use mannitol as their sole carbon source? Would having only some soil community members possess this functional capacity be advantageous to the soil community as a whole? How so? Remember that all metabolic processes are "expensive" in terms of energy and raw materials used. Does this testing give us direct rather than theoretical evidence of a community where members have different metabolic capabilities that contribute to the success of the community? Did the assessment we did previously of community carbon source utilization patterns and diversity provide additional evidence for functional metabolic diversity? Do you understand why we did these tests as part of this investigation?<BR><BR>
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The ability of an isolate to ferment mannitol as its sole carbon source can be assessed as a color change from red to yellow. The MNM medium has a pH indicator that recognizes the acidic byproducts of fermentation and show this as a color change. If this test is positive in an isolate that you originally selected on Azotobacter medium, does that mean that the isolate is more or less likely to be in the Azotobacter group of nitrogen fixing bacteria?
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The motility test and mannitol fermentation tests should be assessed in your MNM tubes before you add the indicator reagent to test for nitrate reduction to nitrite. <BR><BR>
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'''Test for reduction of NITRATE TO NITRITE'''<BR>
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Develop the nitrate to nitrite test in the MNM tube by adding Gries reagent (2 drops of solution A, and then 2 drops of the solution B) to the surface of the medium. Nitrate-negative organisms are unable to reduce nitrates and they yield no color after adding the reagent. Nitrate-positive: The appearance of a pink or red coloration indicates that the nitrates have been reduced to nitrites. Be careful about interpreting negative reactions. It is possible that nitrogen cycling bacteria that reduce nitrate to nitrite may give a negative Gries test because the nitrite produced from reduction of nitrate has been further processed and now is absent by the time we do our testing. A positive test is meaningful but a negative test may not necessarily be evidence of incapability to reduce nitrate to nitrite and, thus, to be component bacteria in the nitrogen cycle.<BR><BR>
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'''Gries reagent''' consists of solutions:<BR>
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'''Solution A'''<BR>
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Sulfanilic Acid 0.8% (v/v) in Acetic Acid 5N<BR>
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'''Solution B'''<BR>
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Alpha-Naphthylamine (0.001% v/v)
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in Acetic Acid 5N
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<BR><BR>
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'''Control Organisms:'''<BR>
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{| border="1"
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! Organism !! ATCC !! Motility !! Mannitol as sole C source !! Nitrate to Nitrite
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|-
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! ''Escherichia coli''
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| 25922
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| +
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| +
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|-
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! ''Klebsiella pneumoniae''
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| 13883
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| -
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| +
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| +
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|-
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! ''Proteus mirabilis''
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| 25933
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| -
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! ''Acinobacter anitrartum''
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| 17924
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| -
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| -
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| -
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|-
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|}
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<br>
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==Assessing Bacterial Morphology:  morphological features visualized by special staining techniques==
==Assessing Bacterial Morphology:  morphological features visualized by special staining techniques==
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Today you will make smear slides (Protocols as Smear Slide Preparation [[BISC209/S12: Smear slide| Smear Slide Preparation]])) to repeat Gram stains and to perform a few special stains to look for spores, capsules, or flagella ([[BISC209/S12: Stains | Stains: Gram Stain]]).<BR><BR>
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Today you will make smear slides (Protocols as Smear Slide Preparation [[BISC209/S12: Smear slide| Smear Slide Preparation]]) to perform a few special stains to look for spores, capsules, or flagella ([[BISC209/S12: Stains | Stains: Gram Stain]]) and to repeat Gram stains (but only if you got ambiguous results on your Gram stains in Lab 7).<BR><BR>
=='''Special Stains:'''==
=='''Special Stains:'''==
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'''Confirmatory Tests for Motility'''<BR>
'''Confirmatory Tests for Motility'''<BR>
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Directions for the Hanging Drop motility test and Flagella stain can be found in the Motility section of Protocols. All bacteria that were positive or ambiguous for motility in SIM medium should be looked at by Hanging Drop technique. Any "swarmers" (bacteria that spread all over the plate when cultured on solid medium)should be looked at by Hanging Drop, too. If the hanging drop test is positive and you have time after you have performed any other confirmation tests or special stains, you could try the Flagella stain, but don't worry if you don't have time for this stain. It is VERY difficult to see flagella even when they are coated with several layers of stain reagent that make the diameter larger. It is hard to get this stain to work well. <BR><BR>
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Directions for the Hanging Drop motility test and Flagella stain can be found in the Motility section of Protocols. All bacteria that were positive or ambiguous for motility in NMN medium should be looked at by Hanging Drop technique. Any "swarmers" (bacteria that spread all over the plate when cultured on solid medium)should be looked at by Hanging Drop, too. If the hanging drop test is positive and you have time after you have performed any other confirmation tests or special stains, you could try the Flagella stain, but don't worry if you don't have time for this stain. It is VERY difficult to see flagella even when they are coated with several layers of stain reagent that make the diameter larger. It is hard to get this stain to work well. <BR><BR>
'''Detecting Capsules by Negative Stain'''<BR>
'''Detecting Capsules by Negative Stain'''<BR>
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Highly mucoid (sticky and wet) colonies could be tested for the presence of a capsule using the capsule stain protocol if you have time. If you don't have time, don't worry. This test isn't particularly useful in acquiring evidence to fulfill the investigative goals of our project. The capsule stain protocol is found in the Special Stains section of PROTOCOLS.<Br><BR>
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Highly mucoid (sticky and wet) colonies could be tested for the presence of a capsule using the capsule stain protocol if you have time. A capsule is a secreted, protective, adhesive, polysacchride envelope layer outside the other parts of the cell envelope. Some, but not all bacteria produce a capsule. It tends to be a virulence factor in bacteria that are human pathogens because it makes it more difficult for the immune system to recognize the bacterium with a capsule as a foreign invader. If you don't have time to perform this stain to check for the presence of a capsule, don't worry. This stain, like the flagella stain, is also difficult to get to work well. If you want to try it, the protocol is found in the Special Stains section of PROTOCOLS.<Br><BR>
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If your Gram stain results were ambiguous or not what you expected from the growth patterns you observed on PEA and EMB media, you should probably repeat those Gram stains.
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'''Repeating Gram Stains''' <BR>
 +
If your Gram stain results were ambiguous or not what you expected from the growth patterns you observed on PEA and EMB media, you should probably repeat those Gram stains. If there are any PEA and EMB plates, consider rechecking the growth of your cultures on these media. Perhaps your earlier cultures were not pure?  How did your stains look?  Is it possible there were more than one organism in what you thought were pure cultures?  If so, what effect might this have on your genomic data?  What other implications might there be?
==Assignment==
==Assignment==
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In Lab 9 you will have a LAB PRACTICAL, an exam that tests your ability to function as a microbiologist in the lab. There will be two main categories of assessment: testing practical skills such as your ability to perform crucial techniques (aseptic transfer, streaking for isolation, performing a Gram stain, micropipetting, etc.) and testing for your understanding of the biological basis behind the work that you've done this semester. For example: we might give you a starch plate flooded with iodine and ask you which, if any, of the bacteria forming colonies on that plate are capable of digesting starch, what metabolic enzyme is produced by these bacteria that allow that digestion and/or what is the ingredient in the medium that allows this evaluation? <BR><BR>
In Lab 9 you will have a LAB PRACTICAL, an exam that tests your ability to function as a microbiologist in the lab. There will be two main categories of assessment: testing practical skills such as your ability to perform crucial techniques (aseptic transfer, streaking for isolation, performing a Gram stain, micropipetting, etc.) and testing for your understanding of the biological basis behind the work that you've done this semester. For example: we might give you a starch plate flooded with iodine and ask you which, if any, of the bacteria forming colonies on that plate are capable of digesting starch, what metabolic enzyme is produced by these bacteria that allow that digestion and/or what is the ingredient in the medium that allows this evaluation? <BR><BR>
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Wondering how to study? A lot of what we will evaluate you on, you already know how to do in your sleep, such as streaking for isolation using proper technique. You do not have to memorize the procedures in the wiki. You will have access to the directions that are printed in the wiki for performing techniques, such as Gram staining; however, you will ''not'' have access to how to read those tests or to the theoretical background information about those tests, such as the cell structural differences that the Gram stain uses as its differentiating principle. You should know that sort of information by studying the background information and protocols found in the Protocols section of the wiki for all the work that have you performed this semester. The protocols in the wiki that describe tests that you have not done  are NOT included in the practical. However, even if you didn't do or get a positive test from those tests performed on your isolates, you should know how to evaluate the tests we all set up, such as the MNM soft agar deeps, eg. how to recognize a positive vs. a negative.<BR><BR>
+
Wondering how to study? A lot of what we will evaluate you on, you already know how to do. (You could probably do some of these techniques,such as streaking for isolation, in your sleep!) You do not have to memorize the steps for each procedure. You will have access to the directions that are printed in the wiki for performing techniques, such as Gram staining; however, you will ''not'' have access to how to read those tests or to the theoretical background information about those tests, such as the cell structural differences that the Gram stain uses as its differentiating principle. You should know that sort of information for each test. Study the background information found in the Protocols section of the wiki and in each lab description. The protocols for which you are responsible include ALL of those that you performed this semester. You should understand how to evaluate these tests (eg. differentiate a positive test from a negative test and how the tests work).<BR><BR>
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Don't forget that understanding of the molecular tools we used for identifying bacteria using their 16srRNA gene sequence. What we can learn from sequencing this gene is practical material. Your homework assignment on the theory behind that work should be a good study guide for that material as is all of the background information in the wiki in LABS 1-8 and in the general information page for our project in the main menu.<BR><BR>
+
Don't forget the molecular tools we used for identifying bacteria using their 16srRNA gene sequence. This process, both the technical aspects and the theory are fair material for this practical. Your homework assignment on the theory behind that work should be a good study guide. Study ALL of the background information in the wiki in LABS 1-8 and in the general information page for our project in the main menu.<BR><BR>
'''Continue to wind down and complete your work on your isolates. Start discarding your cultures.'''
'''Continue to wind down and complete your work on your isolates. Start discarding your cultures.'''

Current revision

Wellesley College-BISC 209 Microbiology -Spring 2012


Contents

LAB 8 Finishing the project!

This is your last wet lab! Please discard all cultures as soon as you have recorded all your results and photographed your evidence. If you have positive antibiotic producers or AI producers, or cool interactions please show them to your lab instructor so they can be shared with the class and saved. Please do not leave any cultures in the lab while we are away for break. You will receive 5 "clean-up points" if we do not find any evidence of your cultures or tests. If we have to discard and clean-up later after you, you will not receive any of those 5 points.

Finding Evidence for Co-operation and Competition Among Cultured Members of a Soil Community

Complete the Interaction Assays
If you haven't been provided with a digital image, please take a photo of each of your interaction plates. Make sure that the photos are sharp enough to evaluate later. Download them to your dropbox in Sakai. Email them to yourself and to each of your partners.
A sample completed assay is shown below.
Image:interactions_assay_1.jpg


Observe the colonies on your plate, comparing any differences in the appearance of the colony growth of each isolate, alone vs mixed. Look first at each control culture: the inoculum in each of the diagonal spots is a pure culture control as are the spots in the column on the far left. Compare each "spot" where two isolates are mixed to the control spots where each isolate is growing alone. Is either isolate growing better in combination than alone? If so, you have found a mutualistic (beneficial) interaction. For example, in the assay shown above, isolate #102 appears to have a positive effect on the growth of #101, classified as mutualism. Are there combinations that show a reduction in the amount of growth of either isolate compared to the growth of the control areas? If so, you have found an antagonistic (negative) interaction. An example in the assay plate shown above is between isolates #105 and #102. Number 105 seems to inhibit growth of #102, an example of an antagonistic interaction. Note that there are sometimes "edge" effects, differences in the appearance of the colony growth in the cultures along the perimeter of the plate as opposed to those growing in a more protected locations (such as the diagonal control colonies). Spend some time with these plates, carefully and fully evaluating all possible combinations of your soil community isolates for as many as possible examples of mutualism or antagonism. Record your results in your lab notebook with copies of the photos of your plates.

Assessing Bacterial Morphology: morphological features visualized by special staining techniques

Today you will make smear slides (Protocols as Smear Slide Preparation Smear Slide Preparation) to perform a few special stains to look for spores, capsules, or flagella ( Stains: Gram Stain) and to repeat Gram stains (but only if you got ambiguous results on your Gram stains in Lab 7).

Special Stains:

Directions for the Schaeffer-Fulton Endospore stain and Capsule negative stain are found in the Protocols section of the wiki.
Stains : Simple, Gram, Endospore, Capsule. The confirmatory tests for motility are found in Protocols under MOTILITY.

Detecting Endospores
All Gram positive bacilli or any bacteria that showed a spore shaped, unstained area in the cells when Gram stained should be stained for endospores. In addition, any Gram positive isolates growing from your dried soil extract on Glyerol Yeast Extract Agar (GYEA) medium should be stained for endospores. There is no need to stain Gram negative isolates for endospores. Would it surprise you to know that most of the spore forming bacteria are common soil organisms? Why would the capacity to form a highly protective, heat tolerant, dessication resistant, non-metabolic spore be useful to soil community microorganisms? Would this capacity give those members a competitive advantage to survive weather extremes? Would you expect a tropical greenhouse habitat to contain relatively fewer or more spore forming members than other habitats?


Confirmatory Tests for Motility
Directions for the Hanging Drop motility test and Flagella stain can be found in the Motility section of Protocols. All bacteria that were positive or ambiguous for motility in NMN medium should be looked at by Hanging Drop technique. Any "swarmers" (bacteria that spread all over the plate when cultured on solid medium)should be looked at by Hanging Drop, too. If the hanging drop test is positive and you have time after you have performed any other confirmation tests or special stains, you could try the Flagella stain, but don't worry if you don't have time for this stain. It is VERY difficult to see flagella even when they are coated with several layers of stain reagent that make the diameter larger. It is hard to get this stain to work well.

Detecting Capsules by Negative Stain
Highly mucoid (sticky and wet) colonies could be tested for the presence of a capsule using the capsule stain protocol if you have time. A capsule is a secreted, protective, adhesive, polysacchride envelope layer outside the other parts of the cell envelope. Some, but not all bacteria produce a capsule. It tends to be a virulence factor in bacteria that are human pathogens because it makes it more difficult for the immune system to recognize the bacterium with a capsule as a foreign invader. If you don't have time to perform this stain to check for the presence of a capsule, don't worry. This stain, like the flagella stain, is also difficult to get to work well. If you want to try it, the protocol is found in the Special Stains section of PROTOCOLS.

Repeating Gram Stains
If your Gram stain results were ambiguous or not what you expected from the growth patterns you observed on PEA and EMB media, you should probably repeat those Gram stains. If there are any PEA and EMB plates, consider rechecking the growth of your cultures on these media. Perhaps your earlier cultures were not pure? How did your stains look? Is it possible there were more than one organism in what you thought were pure cultures? If so, what effect might this have on your genomic data? What other implications might there be?

Assignment

Study for your Lab Practical.

In Lab 9 you will have a LAB PRACTICAL, an exam that tests your ability to function as a microbiologist in the lab. There will be two main categories of assessment: testing practical skills such as your ability to perform crucial techniques (aseptic transfer, streaking for isolation, performing a Gram stain, micropipetting, etc.) and testing for your understanding of the biological basis behind the work that you've done this semester. For example: we might give you a starch plate flooded with iodine and ask you which, if any, of the bacteria forming colonies on that plate are capable of digesting starch, what metabolic enzyme is produced by these bacteria that allow that digestion and/or what is the ingredient in the medium that allows this evaluation?

Wondering how to study? A lot of what we will evaluate you on, you already know how to do. (You could probably do some of these techniques,such as streaking for isolation, in your sleep!) You do not have to memorize the steps for each procedure. You will have access to the directions that are printed in the wiki for performing techniques, such as Gram staining; however, you will not have access to how to read those tests or to the theoretical background information about those tests, such as the cell structural differences that the Gram stain uses as its differentiating principle. You should know that sort of information for each test. Study the background information found in the Protocols section of the wiki and in each lab description. The protocols for which you are responsible include ALL of those that you performed this semester. You should understand how to evaluate these tests (eg. differentiate a positive test from a negative test and how the tests work).

Don't forget the molecular tools we used for identifying bacteria using their 16srRNA gene sequence. This process, both the technical aspects and the theory are fair material for this practical. Your homework assignment on the theory behind that work should be a good study guide. Study ALL of the background information in the wiki in LABS 1-8 and in the general information page for our project in the main menu.

Continue to wind down and complete your work on your isolates. Start discarding your cultures.


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