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June 09, 2011

Preaching to a Prokaryotic Choir

by Mark Martin


At my small liberal arts undergraduate institution, there is only one microbiology course, and it is generally taken by seniors. Here is an image of my Spring 2011 students, and below is the logo that the talented artist Kaitlin Reiss came up for our class T-shirts. One of my frustrations as an educator is how much I would like to tell students about microbiology, and how little time exists in my one course; if it were up to me, there would be a great deal more microbiology in freshman and sophomore biology courses. There is a reason that my students often call me a “microbial supremacist,” I suppose. Guilty as charged!


I find that, at institutions like my own, students really enjoy hearing about microbiology, and how it relates to their other courses in biology and biochemistry. No textbook can keep up with the ferment (if you will excuse the pun) of change that is an ongoing characteristic of this Golden Age of microbiology. Thus, I work hard to remind students not only of the basic framework of microbiology, but also enthusiastically bring up the cutting edge and wonderful discoveries that take place nearly daily (with a healthy dose from Small Things Considered, among other sources, of course!).

I am interested in how the students perceived my microbiology course, and what they valued about it. This feedback might be useful for modifying not only my senior level course, but prerequisite courses as well. To that end, I asked three questions of my microbiology students near the end of my course, and I would like to share their responses.

Question #1: What is ONE thing you have learned in this course that you did not know when you started?

  • That the majority of microbes aren’t good (mutualists) or bad (pathogens). Most “don’t care” and see us as a surface, if that.
  • Prokaryotic enzymes are vital to the planet: rubisco to fix carbon and nitrogenase to make nitrogen bioavailable. Without prokaryotes, the planet would die!
  • The importance of biofilms in the environment and to human disease.
  • Anything about the Archaea; they are really important to the biosphere (element cycling, symbioses, etc). I hadn’t heard much about them before!
  • Quorum sensing is widespread and important to bacteria and their gene regulation.
  • That only archaea can do methanogenesis.
  • Growing bacteria in the laboratory—domesticating them—leads to genetic changes in the organism. (Does studying “lab rats” help us understand the real microbial world?)

Question #2: What is ONE thing that you believe freshmen students should learn about microbiology during their first year biology courses?

  • That most microbes don’t cause disease (“germ” doesn’t mean “bad”).
  • Spend more time on the Woese Tree of Life.
  • That microbes are more powerful and prevalent than we thought: not just how they act on people, but how they control the biosphere!
  • Really focus on the differences between Archaea and Bacteria. Structure and function!
  • Extremophiles and how their adaptations to those environments are related to changes in their biochemistry and composition. “Ecophysiology.”
  • The definition of prokaryote and the controversy surrounding that concept.
  • Group activities of microbes: biofilms and quorum sensing. (There should be a lab exercise for freshmen on these ideas!)
  • Antibiotic resistance in bacteria and how that relates to evolution.

Question #3: What is the most exciting thing you have learned from this class about microbiology?

  • Cellular microbiology: by learning about how microbes interact with eukaryotic cells, we learn more about how eukaryotic cells work. Examples: antibiotics and ribosomes, cytoskeleton and Listeria (that cool video of Listeria trucking around inside of a cell using actin rockets), fusion of lysosomes and Mycobacterium.
  • The positive interactions between humans and their microbiota (gut and skin communities).
  • Biofilms are related to human diseases and pathogenesis (80%).
  • Some pathogens can make eukaryotes do things: Salmonella induces inflammation so that the gut cells make a special terminal electron acceptor that only Samonella can use. Crazy coevolution there!
  • Bacteriophages can be used to fight infections, and why that might be an alternative to antibiotics.
  • Deinococcus radiodurans: its genome is blasted to tiny bits by radiation, but can regenerate itself overnight! Conan the microbe!
  • The many symbioses between microbes and animals and plants—I want to know more!
  • MAMPs and what that tells us about coevolution: if our cells can recognize parts of bacteria specifically, we have been interacting with them a long, long time.
  • Innate immunity: there should be a whole course on immunology!
  • Nanowires and respiration over a distance. Can bacteria act like a computer network?
  • Horizontal gene transfer is EVERYWHERE among microbes. Prokaryotic genomes are plastic and mobile, much more so than us!

I had fun teaching microbiology this Spring, and it seems as if the students enjoyed it. What are your students learning—what mattered the most to them, and why? What did they know about microbiology entering class, and what do they take away at the end? These questions and answers certainly help me plan for my classes in the Fall, and have given me some insights into my freshman introductory courses in biology.

What have been your experiences when you either taught or took microbiology?

Mark is associate professor in the Department of Biology, University of Puget Sound, an Associate Blogger for STC, and a passionate advocate for the Small Things.

Editor's Note: That "micro" class member in the front row bears a striking resemblance to the author of this post.


Dear Dr. Yarmolinsky: I don't mean to go all Santayana on you, but there is not much interest in history among my microbiology students (not entirely true; I get one or two each year who find it as interesting as I do). Anyway, your point is *supremely* important.

In fact, as a well known microbial supremacist, I have pointed out to all of my students over the years (to the patient head shaking of my colleagues) that microbiology has *driven* the major advances in biology. What would biochemistry be without microbes? I certainly teach how Kluyver pushed the "comparative biochemistry" concept on science---that what was relevant to us, biochemically, was relevant to other microbial systems, and vice versa. The same thing is true of genetics; I appreciate pea plants and Drosophila as much as the next geneticist, but microbial systems led to a quantum leap in our understanding of genetics (mad props to the Lederbergs for leading the way). Ditto the very fabric of molecular biology, ranging from the structure of TMV to Taq polymerase and all points in between. And now...we are starting to see how microbial systems inform and advance ecological and evolutionary questions.

So...even if the students didn't bring this up, I proselytized to them often about the debt that all of biology owes the Small Masters (which is what I call the microbes). I wish there were more courses that I could teach...the history of microbiology is important, indeed! Thanks for your comment.

Mark Martin’s enthusiasm for microbiology and his interest in the students he teaches are evident and praiseworthy. But I am troubled by the absence among the student replies to his good questions of any mention of the contributions to our understanding of fundamental biological processes that microbiology made possible. A lack of appreciation of those contributions may account for the inadequate coverage of microbiology in the undergraduate curriculum.

I usually ask my undergraduate microbiology courses what they learned in the course that they believe will be the most important in their future. I get some interesting replies. Most of them are nursing students.

My most sincere thanks to Mark Martin. The detailed consideration of his contribution can be of much help to those of us teaching microbiology at high school, of course, but at the university too!!!!: New ideas for the teacher, yes, but also a lot of useful spontaneous, inspiring and fresh contributions from the students point to specific learning demands. Certainly a bonus for any vocational microbiologist that loves teaching and wants to improuve his/her courses year after year.

I think it's great that you're doing your own evaluations of the class. Too often, professors believe their students' input is irrelevant. Yay for student-centered directions for college teaching.

Author's reply: the Tiny Microbiologist in the front row is indeed my youngest F1, Zachary Vincent Quinn Martin, who exemplifies many admirable and dominant traits derived from his maternal parent. He was ill the day before, and came with me to class that day...and insisted on wearing his "microbiology uniform," as he calls it. Thus, I suspect I preach at home as well as the classroom!

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