Microbiology 101

My Master’s degree research seeks to analyze rock samples to determine whether the structures therein might have been created by life. I’ve looked at various information theoretic approaches to analyzing digital images of samples, and currently I’m testing some texture characterization algorithms to see if they might be useful. It turns out that while there is a lot of existing work debating whether a given rock sample (e.g., stromatolite) was the result of bacterial life or abiotic chemical processes, few people have actually tested biogenic (“created by life”) and abiotic samples side-by-side. One challenge is that stromatolites take a really long time to grow, so it’s not exactly a weekend project.

However, I’ve gotten involved with the USC microbiology lab, and due to the generous assistance of a couple of graduate students, we’re going to do exactly that, but with simple organisms and reactions rather than trying to grow an entire stromatolite. The abiotic samples have already been grown and imaged, and now we’re working on the biogenic ones. To learn how to do this, I reported to the microbiology lab this afternoon and spent two hours trying to absorb a whirlwind of new terminology, procedures, and concepts. Here’s what we did:

  1. Create some “growth medium”. This involves mixing a powder with distilled water to create a “broth” in which bacteria will like to grow. We used “marine broth 2216” and water from the Nanopure Filtration System. We then stirred the mixture, which these days does not mean sticking a rod in and swirling it around manually. No, you put the glass jar on a “stirrer”, which when turned on moves its platform in gentle horizontal circles. That wasn’t enough to get the powder to completely dissolve, so we threw in a magnet (!) which is affected by the stirrer and spins around independently, thoroughly mixing the solution. Very cool.
  2. Sterilize the medium. Here we screwed the lid on the glass jar, stuck “autoclave tape” on it, and then put it in the autoclave. The autoclave is effectively a pressurized oven that (in this case) warms its contents up to a toasty 121 C. (It’s pressurized so that the fluid can be pushed above its boiling point — clever!) It stays at 121 C for 15 minutes and then cools down. The autoclave tape has bands that go black after it’s been cooked, so that you know whether the contents are sterile or not.
  3. Inoculate the medium with bacteria. We’re using a Mn-oxidizing bacteria (an erythrobacter) that is known to generate interesting structures. We pulled some out of cold storage (-80 C!) and pipetted it into the growth medium on a “clean bench”. The clean bench has a constant flow of air coming out to help minimize the chance of you contaminating your own samples. Again, instead of old-time manual pipettes, we had the aid of a “pipet aid”, which is a hand-held device that creates a tiny vacuum and with a push of a button can suck up or release precise quantities of fluid.

We then put everything away (the inoculated samples in a dark closet), and I’ll go back next week to work on the next steps. It turns out that I will also have to take “lab safety” training (certainly not a bad idea) that is spread out over three days, at 2.5 hours each day (!). This is inconvenient, to put it mildly, when one has a day job. :) But regardless, I definitely learned something new today. And there’s more to come.

2 of 2 people learned something from this entry.

  1. jim said,

    March 23, 2007 at 11:21 am

    (Learned something new!)

    This is *so cool*. How much growth are you expecting in one week’s time and how long does the overall case need to run?

  2. wkiri said,

    March 28, 2007 at 8:51 pm

    Right now we’re just cultivating a bunch of bacteria, which we will then put on petri dishes with Mn and let grow into interesting banded structures. I think once we hit that point, it will only take a week? I’m pretty unsure. This is our “test” run. :)

  3. jim said,

    April 12, 2007 at 11:31 am

    (Learned something new!)

    So, is it aliiiiiiive? How is your lab safety training going? (Did you know if you microwave distilled water for a ridiculously long time, it will become superheated. Adding an impurity will result in an explosive fervor. [more info])

  4. Emma said,

    June 20, 2007 at 10:44 am

    where does microbiology take place?

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