BSC 445/545Microbial Ecology Spring 2008
Instructor:Dr. Charles Somerville Office: S350
Phone:696-2424email:
Office Hours:M2:00-4:00 PM; TR 9:00-10:00 AM, 3:00-4:00 PM; W 10:00 AM-Noon
Classroom:BBSC 102Time:TR 11:00 AM – 12:15 PM
Suggested Text:Atlas, R. and R. Bartha. 1998. Microbial Ecology: Fundamentals and Applications. Benjamin/Cummings Science Publishing, Menlo Park, CA.
Course Overview – Microbial Ecology (BSC445/545) is a senior/graduate level lecture course designed to introduce students of biology to the vital roles that microbes play in sustaining life on Earth. Lecture topics cover a wide range of subjects from the origin of life to biodegradation of natural and man-made compounds. The class begins with broad theoretical concepts and, over the course of the semester, moves to practical applications of microbial activity. See the lecture and exam schedule below for more detail on the topics to be discussed.
Grading and Course Requirements:
Undergraduates - Final grades for undergraduate students will be determined as follows:
1. / Lecture Quizzes (7 @ 25 points each) / = / 175 points2. / Group Mini-Essays (7 @ 10 points each) / = / 70 points
3. / Final Comprehensive Exam (55 points) / = / 55 points
Total Available Points / = / 300 points
Graduate/Honor Students – Final grades for graduate students will be determined as follows:
1. / Lecture Quizzes (7 @ 25 points each) / = / 175 points2. / Group Mini-Essays (7 @ 10 points each) / = / 70 points
3. / Final Comprehensive Exam (55 points) / = / 55 points
4. / Graduate presentations (50 points each) / = / 50 points
5. / Microbiology in the News presentation / = / 10 points
Total Points Available / = / 360 points
1.Lecture Quizzes will include 25multiple choice questions based on material presented and discussed during lectures. Quizzeswill be administered during timed portions of regularly scheduled lecture periods. Quizzes will be closed-book, closed-notes, and non-collaborative. Up to three extra credit questions per exam will be drawn from news articles (see below).
2.Group Mini-Essays will be based on a single question posed to the class, and will be completed in groups composed of one graduate student and three or four undergraduate students. Mini-essays will be completed during timed portions of regularly scheduled lecture periods. Mini-essays will be closed-book and closed-notes, but completion of each assigned essay will be collaborative.
3.Final Comprehensive Exams will include 55 short answer questions. Each student’s final exam will be different, and will be based on questions missed on lecture quizzes. The final exam will be administered during the final exam period (see class schedule, below), and will be closed-book, closed-notes and non-collaborative.
4.Graduate Presentations (Grad/Honors Only). Each graduate orhonors student will make a presentation to the class on an assigned topic. Presentations will be 15 to 20 minutes in length, and each topic will be shared by two students. Additional information on topics and presentation format will be discussed in class. Presentations are worth 55 points toward the final course score.
5.Microbiology in the News (Grad/Honors Only). Each graduate or honors student will collect news or magazine articles from the members of his or her group and summarize the articles for the class. News summaries should take approximately 10 minutes, and will be worth 10 points toward the final course score.
Learning Objectives– by the end of the course students will be able to:
1.Differentiate the chemical structures of DNA and RNA, and describe the structure and function relationship in these nucleic acids.
2.Describe the differences between the “5 Kingdom” and “3 Domain” classification schemes for living organisms.
3.Describe the evolutionary origin of eukaryotic mitochondria and chloroplasts.
4.Describe and differentiate symbiotic relationships along the continuum from parasitism to mutualism.
5.Describe cell to cell communication in bacteria.
6.Describe the formation and ecological importance of biofilms.
7.Identify how bacteria are involved in the geological cycles of carbon, oxygen, hydrogen & nitrogen.
8.Describe how ecological communities can grow in areas where sunlight is not available.
9.Identify the factors that limit the degradation of solid wastes by microbial communities.
10.Describe the processes involved in wastewater treatment, and how those processes work to remove chemical and biological hazards.
Important Policies
Letter Grades will be assigned as follows for undergraduate students: A = 270 to 300 points, B = 240 to 269 points, C = 210 to 239 points, D = 165 to 209 points, F = < 165 points. Grades will be assigned as follows for graduate and honors students: A = 324 to 360 points, B = 288 to 323 points, C = 252 to 287 points, D = 198 to 251 points, F = <198.
Attendance and Participation. Attendance at all scheduled lectures and exams is expected. Material presented and discussed in class will form the basis for lecture quizzes. Discussions will not be repeated outside of course meetings without an excused absence. If you must miss an exam for any reason, it is your responsibility to contact my office prior to the exam period to arrange a make-up test. Failure to do so will result in a score of zero for that exam. Make-up exams will be given in essay format. Written excuses for legitimate absences can be obtained as described below.
Students with Disabilities. The Marshall University H.E.L.P. Program is committed to providing assistance through individual tutoring, mentoring and support, as well as fair and legal access to educational opportunities for students diagnosed with Learning Disabilities (LD) and related disorders such as ADD/ADHD. If you have, or believe you may have, a handicap or learning disability that will make it difficult for you to complete this course as structured, please contact the H.E.L.P. office in Myers Hall at 696-6252 ( The H.E.L.P. program will assess your situation and provide information designed to help me meet your educational needs.
Policy on Academic Dishonesty – Any student suspected of cheating will receive a score of zero for the exercise in question. Repeated cheating will result in a failing score for the course. Appeals can be filed through the BSC Chairperson’s office. Bring as little as possible to class on exam day, and be prepared to stay in the room for the duration of the exam.
Responsibility. This is a senior/graduate level class. Avoid asking what you need to know for an exam - it only demonstrates that your interest is in a grade, not in course content. If we talk about something in class, or it is in a reading assignment, it is fair game. At this point in your education you should no longer be “tape recorders” that are capable of taking up information and repeating it back verbatim. You should also strive to be more than “computers” that are capable of recovering the proper information only if someone taps on the correct keys. It is time to start critically examining the information that you encounter, and incorporating it into the context of your knowledge base. It requires effort on your part. More importantly, it requires that you take full responsibility for your learning experience. The amount that you get out of this course will depend upon the amount of work you are willing to put into it.
“Teaching is not filling a bucket,
it’s lighting a fire.”
John Keats, 1795-1821.
Dropping the Course – I hope every student who enrolls in BSC 445/545 will complete the course. However, I know that may not always be the case. So, be aware that March 21st is the last day to drop a full-semester course. Make sure you know your standing in the class at that point so that you can make an informed decision.
Electronic Devices. Please turn off all cell phones, pagers, and other electronic devices when you enter the classroom. No electronic devices will be needed, and none will be permitted, during exams. The use or access of an electronic device during an exam will be considered academic dishonesty. I reserve the right to answer all cell phones that ring in my class.
Office Hours – Feel free to drop by at any time during posted office hours, however people who call ahead for an appointment will be given priority. An appointment is required if you want to come by outside of posted office hours!
Estimated Class Schedule – Exam/presentation dates are firm. Dates for specific lecture topics may vary.
Mtg.
/Day
/ Date /Lecture Topic
/Slide Set
1 / T / 1/15 / Review Course Philosophy & Syllabus / 1-Introduction2 / R / 1/17 / Chemical Evolution & Early Life on Earth / 2-Origin of Life
3 / T / 1/22 / Bacterial Evolution & the Universal Tree of Life / 3-Tree of Life
4 / R / 1/24 / Cell Architecture – Bacteria, Archaea, Eucarya
5 / T / 1/29 / Quiz 1
The Origin of Eucaryotic Organelles / 4-Evolution of Organelles
R / 1/31 / URDC –CS in Charleston, No Class
6 / T / 2/5 / The Origin of Eucaryotic Organelles – continued
7 / R / 2/7 / Interactions within a population
Quorum Sensing (2 graduate presentations) / 5-Symbioses
8 / T / 2/12 / Quiz 2
Symbioses – Interactions between populations
9 / R / 2/14 / Symbioses (cont)
10 / T / 2/19 / Beneficial Plant-Microbe Interactions / 6-Beneficial Plant-Microbe
11 / R / 2/21 / Beneficial Animal-Microbe Interactions / 8-Beneficial Animal-Microbe
12 / T / 2/26 / Quiz 3
Beneficial Interactions (cont)
13 / R / 2/28 / Biofilms (2 graduate presentations)
Microbial Communities - Structure and Dynamics /
13-Community Dynamics
T / 3/4 / EPA Panel – CS in Washington, DC, No Class14 / R / 3/6 / Microbial Communities (cont)
15 / T / 3/11 / Quiz 4
Physiological Ecology – Adaptation / 14-Physiological Ecology
16 / R / 3/13 / Physiological Ecology (cont)
17 / T / 3/18 / Biogeochemical Cycles (C, O2, H2, N2) / 15 - Geochemical Cycles
18 / R / 3/20 / Biogeochemical Cycles (C, O2, H2, N2) - continued
F / 3/21 / Last Day to Drop Full Semester Class
T / 3/25 / Spring Break – No Class
R / 3/27 / Spring Break – No Class
19 / T / 4/1 / Quiz 5
Atmospheric Microbiology / 16 - Biosphere
20 / R / 4/3 / Aquatic Microbiology – Freshwater, Estuarine, Marine
Hydrothermal Vents (2 graduate presentations)
21 / T / 4/8 / Methane Seeps (2 graduate presentations)
Aquatic Microbiology – continued
22 / R / 4/10 / Soil Microbiology / 17-Soil and Solid Waste
23 / T / 4/15 / Quiz 6
Solid Waste Treatment - Landfills & Composting
24 / R / 4/17 / Liquid Waste Treatment / 18-Liquid Wastes
25 / T / 4/22 / Liquid Waste Treatment – continued
26 / R / 4/24 / Biodegradation / 19-Biodegradation
27 / T / 4/29 / Quiz 7
28 / R / 5/1 / Review for Comprehensive Exam
29 / R / 5/8 / Comprehensive Exam 10:15 - 12 :15
Marshall University Absence from Class Policy
2007 - 2008 Undergraduate Catalog, pages 128-130
It is Marshall University’s policy that each instructor evaluates the importance of student class attendance. In the course syllabus, the instructor must provide his/her policy on class attendance, make-up work, and related matters. If a student is absent from class because of a circumstance that is included in the excused absence policy, the absence can be handled by an arrangement between the student and the instructor or, if either party requests, the student can obtain an official excused absence following the procedure described below. The instructor must honor a university excused absence covered by this policy and allow the student an opportunity to catch up/make up work missed. This policy excludes those academic endeavors that require the completion of a certain number of clock hours, as in clinical experiences, practica or internships. For those courses, the maximum number of absences will be determined by the department chair or program supervisor. This policy does not supersede program accreditation requirements.
Definitions of Excused Absences:
Excused absences fall into five categories:
1. University-sponsored activities:
a. Academic activities including, but not limited to, performing arts, debate and individual events, honors classes, ROTC, and departmental functions.
b. Athletics. Official athletic events sponsored by the Athletic Department.
c. Other University activities, including student government and student organizations. The activity must have a clear educational mission and be closely linked to academic pursuits or to other official University functions.
2. Student Illness or Critical Illness/Death in the Immediate Family – “Immediate Family” is defined as a spouse/life partner, child, parent, legal guardian, sibling, grandparent or grandchild.
a. Student Illness or injury: Absences will be excused only for illnesses or injuries that prohibit students from participating in class.
b. Critical Illness of Immediate Family Member: Absences will be excused if the student documents that he or she had to provide needed care and/or support for a critically ill immediate family member.
c. Death of an Immediate Family Member
3. Short-Term Military Obligation: This is defined as absence as the result of military orders for a short-term period. Note: Students subject to federal activation are covered by a separate policy. Please see the catalog for this policy.
4. Jury Duty or Subpoena for Court Appearance: This applies to absences that are a result of official requests from a court of law.
5. Religious Holidays: This applies to major religious holidays. Please see the Dean of Student Affairs for a list of such holidays.
Process to Secure an Excused Absence
The student who seeks an excused absence must do so immediately after the event/activity/incident by following these guidelines. Whenever time permits, such as for University activities scheduled well in advance, the excuse must be obtained and presented to the instructor prior to the absence.
1. University Sponsored Activities:
a. Academic Activities: These absences are excused by the dean within whose unit the activity is sponsored. The dean must pre-approve any notice that is given or sent to faculty regarding absences of this type.
b. Athletics: These absences are excused by the Provost/Senior Vice President for Academic Affairs who must pre-approve any notice given/sent to faculty.
c. Other University activities: These absences are pre-approved by the Dean of Student Affairs and excused by the Office of Academic Affairs prior to any notice to faculty. The activity and the excused absence must be endorsed in writing by the organization advisor.
2. Student Illness or Critical Illness/Death in the Immediate Family:
a. Student Illness or Injury: The student must submit official documentation of treatment by a medical practitioner to the Dean of Student Affairs as soon as he/she returns to class. Documentation must specify the inclusive dates to be excused. The dean will notify faculty that the absence(s) meets the criteria to be excused.
b. Critical Illness of Immediate Family Member: The student must submit official documentation from the family member’s health care provider that substantiates the critical nature of the illness and the student’s need toprovide the care/support. This documentation is to be submitted to the Dean of Student Affairs upon the student’s return to class. The dean will notify faculty that the absence(s) meets the criteria to be excused.
c. Death of an Immediate Family Member: To obtain an excused absence, the student must submit one of the following to the Dean of Student Affairs upon return to classes: an obituary or a funeral program with the student named as a relative; verification on letterhead stationery of the death andthe relationship by clergy or funeral home personnel. The dean will notify faculty that the absence meets the criteria to be excused.
3. Short-Term Military Obligation: The student who seeks an excused absence for military obligation must present official documentation of his/her orders to duty to the dean of his/her college prior to the absence. The dean will notify faculty that the absences are to be excused.
4. Jury Duty or Subpoena for Court Appearance: The student who seeks an excused absence for jury duty or court appearance must submit his/her subpoena or official notification of jury duty to the dean of his/her college prior to the date of the obligation. The dean will notify faculty that the absence is to be excused.
5. Religious Holidays: Absences resulting from major religious holidays will be excused when the student presents the request in advance of the absence to the Dean of Student Affairs. The dean will indicate his/her approval on the request and forward it to the Office of Academic Affairs for the official excused absence notification to faculty.
Notice: Any student who falsifies information or documentation in order to obtain an excused absence has committed a violation of the Code of Student Rights and Responsibilities and will be referred to Judicial Affairs for appropriate sanctions.
Process to Catch Up/Make Up Missed Work
1. It is the responsibility of the student to request an opportunity to complete missed work.
2. Once the excused absence has been secured, the request to make up work should be made to the instructor at the next available class meeting.
3. Missed activities will be rescheduled or, in the event that rescheduling of an activity is not practical or possible, a fair and equitable alternative way of arriving at the grade for the missed component of the overall grade will be developed by the instructor.
4. Punitive measures must not be taken against students who present an official University excused absence.
5. Students should be aware that excessive absences—whether excused or unexcused— may affect their ability to earn a passing grade.
6. If the faculty member believes that the number of absences accrued under the terms of this policy is such that the student cannot fulfill the learning experience/ mastery that a course requires, he/she may recommend that a student withdraw from the class.
Regardless of the nature of the excused absence, the student is responsible forcompleting all coursework prior to the end of the semester.
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Groups, Presentation Topics, and Presentation Dates
Group # / Undergrad Students / Graduate Student / Presentation Topic / Presentation Date / News Date1 / Amanda Pilbeam
Ashley Straughter
Benjamin Lemon
Brittani Dingess / Danielle Desser / Quorum Sensing / 7 February (Thrs) / 1 May
2 / Brittany Thacker
Candace Radford
Christopher Jones
Chung Kim / Jarrod Pennington / Quorum Sensing / 7 February (Thrs) / 24 April
3 / Daniel Jonas
David Fields
Della Gilman
Douglas White / Jonathan Hart / Biofilms / 28 February (Thrs) / 10 April
4 / Eric Byrge
James Webster
Jamison Radford
Jeremy Wilson / Laura Lynn / Biofilms / 28 February (Thrs) / 20 March
5 / Jesse Pishner
Jody Cox
Justin Hill
Kaitlyn Tinsley / Monique Cameron / Hydrothermal Vents / 3 April (Thrs) / 6 March
6 / Kelly Apgar
Kenneth Oxley
Kenneth Leep
Lacey Wilson / Richard Fulcher / Hydrothermal Vents / 3 April (Thrs) / 21 February
7 / Lauren Bevins
Matthew James
Michaela Rivera
Nicholas Jordan / Tara Braithwaite / Methane Seeps / 8 April (Tues) / 7 February
8 / Robert Nagy
Ryan Hostutler
Tobias Pasquale / Tashina Savilla / Methane Seeps / 8 April (Tues) / 24 January
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