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Syllabus

• Agar slant tubes
• Aseptic technique
• Assays
• Assays Illustrated
• Colony morphology
• Gram stain
• Isolating colonies
• Making serial dilutions
• Culture media
• Preparing spread plates
• Relationship to oxygen
• Viewing Gram stains
• Viewing living bacteria

• Characterization writeup
• Lab responsibilities
• Project proposal guidelines
• Using Bergey's

Supplemental pdfs

• Inoculating sticks
• Microscopy procedures

Welcome to BIOC 318, Laboratory Studies in Applied Microbiology

In fall 2016 we significantly revised the content of this course to focus on a single, albeit ambitious, project to characterize the resident flora (primarily bacteria) of a local water source. The changes were very well received and the benefits of the new course design far outweighed the bumps in the road that are inevitable when one makes major changes to an established course design.

Example of some of the work you will conduct in this course. (A) Agar plates with bacterial unknowns, 72h following aerobic incubation at 30˚C. (B) Identically streaked agar plates incubated anaerobically for 72h, revealing relationship to oxygen.

Our project

Many studies of samples taken from a wide variety of sources have revealed that only 0.01 to 0.1% of all bacterial cells that can be seen in a light microscope are actually "cultivable" in the laboratory.¹ This means that for every bacterial species successfully isolated from an environmental sample, as many as 10,000 species remain undetected. Our project seeks to find and characterize some of this "dark matter" of environmental microbiota. Our overall goals are:

• to estimate how many bacterial species can be cultured from an environmental source using conventional methods
• to establish a starting point by identifying and characterizing the "cultivable" species from the source
• to isolate currently "uncultivable" species by (1) applying recently developed published methods and (2) developing and applying methods of our own

Scientists have estimated that up to one trillion microbial species exist on Earth, about 0.001% of which are actually known.² If the one trillion estimate is accurate, then if 100 Rice students each discover 100 new species every year (obviously not a realistic expectation), it will take 100 million years to discover all of them. Realistically, we'll be very happy if we discover even one new species or strain of bacteria. Achieving our second project goal, especially part 2, will be challenging, and success is not guaranteed. In fact, most scientific experiments result in failure. What we have to keep in mind is that each step that we take, whether or not it succeeds, is a step that we will not have to repeat. Even a failed attempt represents progress.

Why pursue this project? What good will it do anyone to discover new species of bacteria? We have no idea. What we do know is that most of the world's greatest discoveries did not come about through targeted research. They came about when scientists (including quite ordinary people like ourselves) asked questions just for the sake of knowing. We have no idea where the next great idea or discovery will come from. 

Objectives and learning outcomes

The main goal of this course, as must be true for any experiential course, is personal development. We want you to build on skills that you've already acquired and learn new ones. Below we summarize our most important learning objectives and outcomes.

1. Learn to work as a productive member of a research team on a long term project
2. Be able to access and employ published reference materials, current primary literature, and other information sources in order to advance your understanding of the properties of bacteria and how to isolate and characterize them
3. Learn to integrate your previous and newly acquired experience into development of new techniques and strategies
4. Improve your powers of observation, such as the ability to use physical and metabolic differences to distinguish strains and species of bacteria and to draw information from microscopic observations
5. Learn to make the decisions that are necessary in order to conduct a systematic open-ended investigation
6. Learn to make your work accessible to yourself and others by documenting your activities and findings in a well organized laboratory notebook, by contributing to our laboratory's database, and by summarizing your work in a clearly written report
7. Learn and practice good laboratory "citizenship," including respect for people, the facility, and equipment
8. Acquire proficiency in essential methodologies and use your newly acquired skills to advance our project
9. Learn to appreciate the value and potential of pure science, that is, the pursuit of knowledge for its own sake

Please see the Syllabus for course details, course timetable, and a list of assignments with due dates.

¹D'Onofrio, Anthony, Jason M. Crawford, Eric J. Stewart, Kathrin Witt, Ekaterina Gavrish, Slava Epstein, Jon Clardy, and Kim Lewis . "Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria." Chemistry & Biology (2010): 254-64.

²Offord, Catherine. "Earth: Home to 1 Trillion Microbial Species." The Scientist (2016): http://www.the-scientist.com/?articles.view/articleNo/46016/title/Earth--Home-to-1-Trillion-Microbial-Species/