BISC209: Lab8

Lab 8: Lab Practical

Today you will have a lab practical exam designed to assess your mastery of basic tools, techniques, and theoretical information on which the field of microbiology is based.

Culturable Bacteria Identification continued

Read last weeks tests, Continue with new tests, add motility and other stains (if useful and not completed yet)

Assignment

Results section with figures/tables:
Identification of Culturable Soil Bacteria by Physical and Metabolic Characteristics

You will write part of the results section for your final paper as a graded assignment to turn in at the beginning of Lab 9. You have worked hard this semester to isolate, characterize and identify some of the thousands of microbes that contribute to the soil community of your habitat. You used DNA sequencing of the 16S rRNA gene to identify a not-completely random sample of bacteria (remember pcr bias and other unavoidable factors that contribute to sampling bias). You also used traditional culture and isolation methods, combined with biochemical and physical tests, to obtain morphologic and metabolic characterizations of a few of the soil community bacteria. Now it's time to start the synthesis of all those results into a cogent and clear analysis of the evidence that answers or sheds some light on our original experimental question: What are the functional roles and phylogenetic relationships among soil bacteria in this community?

You spent many weeks just trying to coax some of these bacteria to grow outside of their soil habitat. You spent additional time separating them from other members of their community. Both of these tasks were difficult and time consuming. Why did we have to do all that when we know that these bacteria exist naturally, quite happily, as part of a large diverse community in the soil? One answer, possibly the most important and difficult, was that we needed to get the bacteria isolated to pure culture to be able to send off an adequate number of separated 16S rRNA genes to serve as the template for DNA sequencing to give us the "name" of our cultured bacteria. Taxonomic identification also allows phylogenetic relationships among bacteria to be explored.

Unlike the relative ease (if we forget how many times we had to repeat our experiments) of using expensive, sophisticated molecular tools (plasmid cloning vectors and genetically modified transformed bacteria) to separate and replicate enough copies of each of the amplified 16s rRNA genes from the culture-independent bacteria that we will study, we also wanted, in the case of our cultured bacteria, to know their genus and species id so that we could determine whether or not our biochemical and physical test results are typical or atypical of their taxonmic group.

Another reason for doing all the morphologic, physical and biochemical tests on your pure cultures was to acquire evidence to explore the possible functional roles of members of the community. For example, if you found out that one or more of your bacteria secret an antibiotic, what might that imply about at least one of that microbe's roles in its community and, possible, in the larger world? If you found out that you have cellulolytic or nitrogen fixing bacteria in your community or that they are highly motile, you are supplying other evidence to prepare the ground for writing an interesting discussion section about the variety, diversity, and possible roles and relationships among the bacteria that were identified either by culture dependent or culture independent means.

You will not write a discussion section for this assignment, but a good results section is crafted to present the evidence for the points you want to make or relationships you want to propose in your discussion. The results section will not propose conclusions as to roles or relationships among memmbers of this soil community since we purposely worked hard to study these bacteria in isolation. Therefore, don't know exactly how they work together. This results section will point out relevant test findings and observations that will allow you to discuss possible roles and relationships in your discussion, including symbioses.

Remember that any results section should start out with a restatement of the experimental goals of this part of the paper: "In order to find out ....". Then it recaps BRIEFLY a summary of what you did, without repeating the whole materials and methods section. The results narrative does not start describing the data until it BRIEFLY frames for the reader how the results you describe were obtained and why. The most important findings are found in two forms in the results section: in a narrative description that describes and analyzes all important findings and in visual representations of some of those data: the figures or tables. There is extensive information about how to write a results section in the Guidelines to Science Writing in the Resources section of the wiki. Remember that you are preparing your reader for your discussion section. Make sure to limit or omit describing results that aren't pertinent to where you think you are going in your discussion of the diversity, functional roles, and phylogenetic relationships of bacteria in a particular soil community.

You will probably not get the sequencing results back until next week. Nevertheless, you can write this results analysis without the complete id of your bacteria. You may, for this assignment, refer to your bacteria by their preliminary group name and by their code names. Who knows, maybe you will discover a previously uncharacterized bacterial species or strain that you can name after yourself! When we know more about the names of our isolates after our sequences are analyzed, you will go back and edit this id information.

Continue to wind down and finalize the classification of your culturable isolates. Start discarding your cultures.

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab11
Lab 12