Microbial Ecology, Marine Microbiology, Microbial Diversity

Courses Taught

MICR 401 Marine Microbiology (3 credits)

Evolution, ecology, biochemistry, genetics and physiology of marine bacteria by examining defined systems and organisms. Pre: BIOL 265/265L and 275/275L and 301/301L, and OCN 201; or 351/351L or consent. Meets M/W/F mornings in the spring semester.

Subjects covered include 1. Ocean evolution and marine chemistry 2. Ocean physics, with emphases on temperature, heat capacity, currents, salinity, density, light 3. History of marine microbiology 4. Metabolic groups 5. Habitats in marine microbiology 6. Sampling considerations and methods 7. Structure and physiology of marine bacteria (Archaea and Bacteria) 8. Marine microbial DNA & taxonomy 9. Phylogenetic diversity of marine prokaryotes 10. Enzymes in aquatic environments 11. Cultivation methods in marine microbiology 12. Oligotrophy 13. Primary production 14. Secondary production 15. Molecular methods in marine microbiology 16. Marine Fungi and yeasts 17. Marine viruses 18. Marine biotechnology. In spring 2005, four guest lecturers described their work in different marine environments.

Here is how the grade for the course was determined in spring, 2005. This will likely change for 2006, but not significantly.

  • Analysis of set papers.
    You will receive several papers from the peer-reviewed literature on one aspect of marine microbiology. You should write a 500 word summary of the papers. You must not plagiarize text from the papers given to you, nor should you cut and paste text from web sites. The rationale behind this piece of work is that we are often required to summarize large pieces of work, or several short pieces of work, into succinct accounts for colleagues, including lab managers/professors. The abstract on each published paper provided to you will be 'masked' out. You should aim to pick out the 'message' of each paper, or the unifying theme, and highlight common grounds or different points of view. Be prepared to say what are the merits (if any) of the arguments presented? This piece of work will be worth 15% of your final grade.

  • Mid-term exams
    Two mid-term exams will be set. Questions will take the form of short answers or multiple choice. These exams will allow you to demonstrate your familiarity with the concepts and terminology in the field. You will be given plenty of notice of when the exams are to be held. Each exam will be worth 15% of your final grade. (Note: Student feedback on these exams has been very positive.)

  • Presentation
    You will give a short PowerPoint presentation on a marine microbiology topic of your choice. (The duration will depend on course enrolment.) Advice will be given on how to structure such a presentation. You must consult with the instructor before starting work to ensure your selected title or field is appropriate. Your presentation will be 'judged' by the instructor and your fellow students; everyone will have a comments sheet and must complete that for each presenter. Return the sheets to the instructor at the end of class. Your comments will be considered, but the instructor will have the final say on a grade. The rationale of this work is that presentations in your office, laboratory, or at scientific meetings attended by thousands of people, are often restricted to minutes. You will deliver pertinent information in a short time, and in a way that people unfamiliar with the field will understand. You will receive a summary of all comments, with constructive advice on how to improve your future presentations. Time limits will be enforced. Your presentation will be worth 15% of your final grade. (Note: This may seem daunting, but student feedback has always been very encouraging, especially from students who have given their presentation and can sit back and watch their colleagues!)

  • Final exam
    One final exam will be set. This will be worth 40% of your final grade.

    Before each exam I have an 'open' class, during which I answer questions and clarify any material we have covered. I answer all questions 'equally', and make no distinctions based on whether or not the question will be on the exam ☺

MICR 401L Marine Microbiology Laboratory (1 credit) (1 3-hr Lab)

Laboratory to accompany 401. Pre: BIOL 265/265L and BIOL 275/275L and BIOL 301/301L and OCN 201; or 351/351L; 401 or concurrent; or consent. Meets Monday afternoon in the spring semester.

We focus on techniques widely used in the field, although some are also used outside marine microbiology. Early in the course we take a morning 'cruise' on the RV Klaus Wyrtki to collect samples, and you see and use some of the equipment we discuss during MICR401; we process the samples throughout the semester. Some of the techniques we use are: 1. Membrane filtration 2. Colony selection, description and purification 3. Gram stain and DNA extraction 4. DNA detection & PCR 5. Clone library construction and plasmid purification 6. DNA sequencing (we have a MegaBACE 1000 DNA sequencer in the lab' for student use) 7. Analysis of DNA sequences, phylogenetic tree construction 8. Physiology of marine bacteria (Biolog, API) 9. FISH/DAPI 10. Live/Dead stain 11. Flow cytometry 12. Ectoenzyme activities 13. ATP analysis 14. LPS/endotoxin assay. The grade for this course is based on attendance and participation, plus one essay from a choice of several titles (in marine microbiology) provided by the instructor.


BIOL 404W Advanced Topics in Marine Biology, writing intensive (3 credits)

Current themes in marine biology and experience in scientific assessment. Repeatable two times. A-F only. Pre: 301/301L or consent.

Taught jointly with Dr. Cindy Hunter in alternate (odd numbered) years. My lectures include: 1. History of marine biology and microbiology 2. Marine microbial diversity 3. Large marine ecosystems 4. Noise pollution in the ocean 5. Non-acoustic marine pollution 6. Marine biotechnology and bioremediation 7. Domain (regime) shifts 8. Ecotourism 9. International law and the oceans. Dr. Hunter and I require students to submit three essays for our review; we return the essays to the students who should then take into account our comments before submitting a final version for grading. Each student also writes and presents a research proposal of their choice. The course is taught jointly in alternate (even numbered) years by Dr. Dave Carlon (Zoology) and Dr. Alison Sherwood (Biology).


MICR 314 Research Ethics (1 credit)

An introduction to the ethical issues faced by individuals and institutions involved in scientific research. Based on case studies in an ethics text, students discuss ethical issues in research. Issues include humans and animals in research, mentoring, authorship, ownership of data, genetic technologies and record keeping. This course is designed for students with majors in the natural sciences. A-F only. Pre: BIOL 172 (or concurrent), or MATH 321 (or concurrent), or PHYS 170 (or concurrent), or CHEM 272 (or concurrent); or consent.

Course URL:: http://www2.hawaii.edu/~patek/ethics/index.htm

Team taught in spring 2005 with Dr. Paul Patek and Dr. Sean Callahan. My lectures focused on 1. Authorship and peer review 2. Conflicts of interest 3. Ownership of data and intellectual property 4. Scientific record keeping.