All Things Microbial Group


The Geo- Environmental- Microbiology (G.E.M.) Laboratory comprises a collection of talented scientists and engineers with a multitude of experiences. We have varied backgrounds in life and in education. To us, this brings strength to what we share--an interest in figuring out some component(s) of information about the microbial world.

Some of us work on the microbiota associated with engineered systems for water and wastewater treatment. Some, on the diversity of microbial life and their novel enzymes in Yellowstone National Park hotsprings. Others, on the complexity of microbial life in 6 cm thick microbial mats from Guerrero Negro, Baja California Sur. Some, on how to stimulate energy production for renewable energy use. And others, on the development of robotic explorers to sample and better understand microbial ecosystems that have forever been out of reach to human understanding. We work and collaborate with people across the CSM campus, the State and University of Colorado systems, other universities around the USA and the world; and local, state and federal agencies. We do microbial based research and collaborate with people in locations around the world.

Dr. John R. Spear


  • Postdoctoral Research Associate, University of Colorado, Boulder 1999 - 2005 Molecular, Cellular and Developmental Biology, Laboratory of Dr. Norman R. Pace
  • Ph.D., Colorado School of Mines, Division of Environmental Science and Engineering, 1999
  • M.S., Colorado School of Mines, Division of Environmental Science and Engineering, 1994
  • B.A., University of California, San Diego
  • Curriculum Vitae available upon request

Research Interests

  • Geobiology
  • Environmental Microbiology
  • Molecular Microbial Ecology
  • Microbiology of 'Extreme' Environments - Any Environment
  • Bioremediation of Metals
  • Bio / Renewable Energy
  • Microbiology of Caves and Karst

The great majority of life on Earth is microbial in size, things only visible through the microscope. Almost all of these microbes are harmless to humans and in fact, provide vital ecosystem services to just about every habitat on the planet - including our own bodies. We are interested in the who, what, when, where, why and how questions about microbial lifeā€”in essence, microbial ecology. Who are they? - We are interested in the diversity of this microbial life in all three domains of life-Eucarya, Bacteria and Archaea. What do they do? - Are they interacting and / or changing their environment? What can they do for us? - Can we learn how to optimize a microbial process for bioremediation or for bioenergy? When are the microbiota of a particular environment active? - Can we manipulate that activity for stimulation in an engineered system or process? Where are they?-Is a certain microbe only found in one place or throughout the ecosystem / world? Why are they there? Why do they do what they do? This leads us to ask "how?" Do microbiota interact with their world? Do microbiota use energy flow in novel ways? Do microbiota process metal and /or heavy metals? Are these processes beneficial to humanity?

Teaching Philosophy

My first real teaching experience began twenty-five years ago. I worked for an outdoor education school where the outdoors is the classroom. It was not typical teaching. Being able to talk about glaciology in front of a glacier, cave formation 10 miles underground, climbing 1500 feet up a wall, or group dynamics and teamwork during a mock rescue are all uniquely advantageous to both the student learning and the teacher teaching. The most important thing that I learned by teaching in this fashion is not only that I have a wide variety of ideas to convey but that I have new ideas to learn from those that I am teaching. To be a good teacher is not to have a one way flow of ideas; there needs to be an effective interchange of ideas between both the student and the teacher.

Outdoor education was an excellent way for me to learn a personal philosophy of teaching. Outside, there is no chalk board, no overhead projector, no climate controlled venue, and no roof over your head. This means that you talk in a normal tone of voice in one instant, and in the next, scream at the top of your lungs so the person in the back can hear you over the wind or the rain. It also means creative improvisation to convey a point with only what you have in front of you. For example, I have pulled some needles off of a pine bow (needles representing hydrogen atoms) to demonstrate the single / double bond characteristics of saturated verses unsaturated fatty acids for a nutrition class. Teaching outside means being able to convey a complex topic without the use of much visual aid. You have to paint a verbal picture from which the student can take away the message.

Why talk about all of this here? Because a college classroom is no different. You still have to paint a verbal picture, you still have to improvise and work with what is in front of you. You still have to understand your students. To an extent the classroom provides an extra benefit because you have access to the technology of a chalkboard, an overhead projector, and a non-variable climate. With these tools present however, I still like to concentrate on the fundamentals of good teaching. For example, when I am asked a question after explaining a point, I always think of another example to get the point across. Students have a wide range of learning styles (i.e., auditory, visual, kinesthetic) so I try to present information from several different perspectives and appeal to multiple intelligences. Being able to teach means knowing the subject, being able to talk about the subject, and understanding the audience who is listening.

Listening is a problem in our society. We live in a sound-bite society where people have developed short attention spans. I feel that most people are willing to talk, some quite a bit more than others, but not many people care to listen and to listen carefully. This is where the two way exchange of ideas comes into focus. A good teacher needs to get to know the audience. For me, that means listening. That in turn leads me to be able to facilitate individual learning - which is the heart of education. We all must have the ability to, and desire for, lifelong learning.

In all of the classes I teach I employ the above philosophy, and from past evaluations, my students have respected my teaching philosophy. I am a believer in the premise that you cannot know a subject until you teach the subject. I also feel that you cannot just keep teaching the same subject; if you do, then you should always change the class. With the way research is progressing in nearly every area today, this is not hard. By accepting new ideas, learning about new subjects, and teaching new classes, there is a lot of learning to be done! I believe that daily current events can play a role in every class. There is not a day that goes by that I do not find some biologically related piece of news for relevant to Environmental Biology, or a statistical point that I can incorporate into a graduate data analysis class. Not only does this allow for a further understanding of the class material, it allows for a further understanding of the world happening around us. This is what the college experience is all about.


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"Cause when you showed me myself, you know, I became someone else..."
- Joseph Arthur, In The Sun