The Mystery of the Missing Bacteria

First, thank you everyone who took the time to read my last blog post about the activity I designed for my biology class. I really appreciate all of the support and feedback! While last week, I focused on how to get my students into the engineering process, this week I will talk about how I got a taste of the engineering process through my research. Attend the tale of the mysterious vanishing bacteria.

Once upon a time, there was a lab at Rice university using viruses to eliminate harmful bacteria. Every day they would work to test how well these viruses could eliminate bacteria, but never had they imagined they would have to figure out how to grow more bacteria. That is, until the week of June 25th, 2018 when a mystery struck the lab. Dun dun dun! *cue lightning and spooky sound effects*

Normally, when we plate bacteria and our phages in order to count the colonies, we mix planktonic bacteria (meaning, bacteria growing in liquid medium) with the phages and soft agar and then pour it on the plates. In doing so, we get a nice bacterial lawn with a few clear plaques forming where the viruses infect and lyse the bacteria. However, for about the past week and a half this was not going as planned. Rather than forming a bacterial lawn, the bacteria was growing in skinny swirls at best and at worst, it was not growing at all! What could possibly be happening to our bacteria? Well, turning to our handy dandy engineering and design method helped us figure it out.

Each day, we would try adjusting our procedure slightly to see if it would help the bacteria grow.
Define the problem: Bacteria are not growing
Brainstorm Solutions: Maybe we are putting too high of a concentration of viruses, so the bacteria are unable to grow a lawn due to high rates of infection?
Test Our Solution: Adjust the procedure by diluting our viruses 100x
Evaluate Our Solution: Hmm…bacteria still aren’t growing….
Iterate: Let’s try diluting the viruses 1000x and 10000x
Test Our Solution: Still no bacteria…
Brainstorm Solutions: Maybe it’s the temperature of the agar when we pour the bacteria in? If it’s too hot, that would kill the bacteria.
Iterate: Wait longer for the soft agar liquid to cool before adding the bacteria (and fail at this a couple times due to waiting too long and the agar hardening in the tube, sigh.)
Test Our Solution: Still no bacteria… (cries inwardly)
Brainstorm Solutions: Maybe it’s not the temperature of the agar, but the nutrients in the agar? The bacteria is growing just fine in the liquid media, why don’t we try adding some of that media to our agar?
Test Our Solution (crossing our fingers): SUCCESS!! The agar needed more nutrients (see images below). We will have to be sure to add the liquid media any time we are plating this type of bacteria.

Communicate Our Solution: Be sure to label all bottles of soft agar appropriately and only use the ones with media added. Tell labmates that this is the new procedure so that they don’t fall into the same mistake.

Case closed! The mystery of the missing bacteria has been solved all with the help of some engineering.

While going through the engineering process again, and again, and again can feel a bit frustrating sometimes, at the end of the day, figuring out what went wrong and how to fix it was incredibly rewarding. Sometimes in science we forget how much engineering we actually do. Even if it’s not building a device to use, we design and redesign our methods constantly using the engineering design process. I feel even more confident than ever in guiding my students through the engineering process and all of the frustrations and successes that come with it.


4 thoughts on “The Mystery of the Missing Bacteria”

  1. I agree, we must trust the process. Most of this week we have been creating membranes and 4/5 have come out less than ideal. So, we have tweaked the flow, the voltage, and the amount of solution to try and create a great membrane. I am struggling with the amount of time it takes to create one membrane( 3-4 hours). It can be frustrating when it doesn’t come out as expected. How long did it take you all to get it right?

    1. That does sound frustrating! I feel your pain. For us, we don’t know whether our tests work or not until after our plates have incubated overnight, so we basically spent about a week trying to figure out why our bacteria weren’t growing 🙁

  2. One problem that I always encounter in my classes are students that want to skip the “trial and error” part of the design process. They want their designs to work the first time. So, they spend too much time designing, and not actually testing their designs. Showing students how the engineering process actually works, how scientists still have to go through “trials and error”, would definitely help them.

  3. I feel like at this point in time in our research we are all going through similar trials. In fact, this time last year my mentor and I needed to grow a certain amount of bacteria and we actually rejoiced once it did happen. *nerds* 😛 In regards to the process, for example, it seems endless the amount of samples I’m making and it takes 5 hours to cure, then another 5 hours to place in the vacuum and after that I can check it’s properties. We are also stuck because we need another machine to continue other tests. So, it’s frustrating when things aren’t working and I feel like not only do we need to guide our students to not be afraid to fail and try but to also help keep the motivation in a time like this. It’s an important life lesson too. For me, it will be a very vital part in thinking about incorporating this into my lessons at school. Often, we are in such a rush that labs are taken out of the curriculum or made to recipe like.
    Anyway, I’m happy you figured out what was wrong!

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