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Instructor: Brent C. Christner
Office: 282b Life Sciences Building
Phone: (225) 578-1734
Email:
xner@lsu.edu
Office
hours: W 11:00–12:00 or by appointment
Course website:
http://www.brent.xner.net/BIOL4800/index.htm
Prerequisites:
BIOL 2051 – General
Microbiology
BIOL 2153 – Principles of
Genetics
Course objective:
The goal of this course is
to provide a framework for understanding the relationship between and
biogeochemical role of microorganisms in natural communities. Course
topics are structured to demonstrate the linkages between microbial
ecology, diversity, and evolution. The specific objectives of this course
are to expose students to the following topics:
·
Role of microbial life in the evolution and ecology of the
biosphere.
·
Application of classical ecological concepts to microbial
populations and communities.
·
Underlying principles that drive microbial population
structure in the environment.
·
Community function and dynamics at both the molecular and
the organismal level.
·
Abiotic and biotic interactions within microbial
communities.
·
Ecophysiology and thermodynamic constraints on microbial
community structure.
·
Molecular and genomic tools for understanding the physiology
and ecology of microbial communities.
·
Microbial metabolism and biogeochemical cycling.
Text:
Strongly Recommend:
Madigan, M.T., J.M. Martinko, P.V. Dunlap, and D.P. Clark. 2009. Brock:
Biology of Microorganisms (12th or current eds.), Prentice Hall. Amazon – 12th
ed. (new - $170; used - $143 and up); 11th ed. (new - $135;
used - $19 and up).
Tepidly Recommend:
Atlas, R.M., and R. Bartha. 1997. Microbial Ecology: Fundamentals and
Applications, Benjamin Cummings. Amazon (new - $137; used -
$31 and up).
Scientific literature:
Readings from the text will
be supplemented with scientific research papers and reviews that will be
available on the course website (http://www.brent.xner.net/BIOL4800/index.htm).
For many students, these papers will be their first exposure to scientific
literature. Reading a scientific paper is not like reading a text book.
One goal of this course is to develop your ability to digest the content
of and critically evaluate scientific literature. On two occasions during
the semester (11 September and 18 November), the class period
will be dedicated to open discussions of current scientific literature
covering “hot topics” in microbial ecology. Student participation in
these discussion sessions will be graded.
Grading:
Exams: There will be
2 exams. Regular exams consist of multiple choice (60%), short answer
(30%), and essay (10%) questions. If a student misses the mid-term exam
for any reason, there will be one opportunity to makeup the exam at the
end of the course. The makeup exam will cover the same material but will
be in essay format. There will be no early or late finals administered.
The only exception is if a student has 3 or more final exams scheduled in
24 hours and a request is submitted to the Office of the University
Registrar (http://appl003.lsu.edu/slas/registrar.nsf/index)
by the specified university deadline.
Research paper: A
research paper is required for this course. Papers are to be written in
the style of a published minireview (e.g., Applied and Environmental
Microbiology). Paper length should be 10 double-spaced, 12-pt Times New
Roman pages not counting illustrations and citations (15 pages for
graduate students). You are encouraged to explore topics in microbial
ecology not covered in the lecture or assigned readings. Each student
must prepare an outline and meet with the instructor prior to
final approval of a research paper topic. The deadline for submitting a
research paper topic and outline is 9 October. Submit a hard copy
of your paper to me in class on 13 November. DO NOT place your
paper in my mailbox or under the door of my office. In addition to the
hard copy, you must also submit an electronic version of your paper.
Email this file to
xner@lsu.edu with the file named using your first initial and last
name in the file name (e.g. BChristner_BIO4800ResPaper.doc). The penalty
for late turn in of a research paper is deduction of 10 percentage
points per day. See the research paper handout for specific
directions on content and requirements.
Oral presentation:
All students will present their paper topics during one of the final class
sessions. Each presentation should be 12 minutes in length, allowing 3
minutes for questions. The deliverables are the oral presentation and a
hard copy of your slides for the instructor and class. PowerPoint
presentations are fine but not required. Students are responsible for all
material covered in these talks.
Class participation:
Student participation in class discussions will be graded. Attendance may
affect your participation grade.
Literature summary:
A 250-word literature summary is required at the beginning of class on
11 September. In your own words, summarize one of the assigned
scientific readings for this date (see “Course Calendar”) and turn in a
hard copy of this document at the beginning of class. Late assignments
will not be accepted.
Problem set: There
will be a problem set handed out during the semester. You are not
permitted to collaborate with other students on the problem set. The
problem set is due on 4 November at the beginning of the lecture
because the answers will be reviewed during that lecture. Late problem
sets will not be accepted.
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Overall grading percentages: |
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Grading scale: |
|
Research
paper |
30% |
|
A |
100-90% |
|
Mid-term
exam |
25% |
|
B |
89-80% |
|
Final
exam |
25% |
|
C |
79-70% |
|
Oral
presentation |
10% |
|
D |
69-60% |
|
Class
participation |
5% |
|
F |
Below
60% |
|
Literature summary |
2.5% |
|
|
|
|
Problem
set |
2.5% |
|
|
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Additional requirements
for graduate credit: Graduate student exams will be different
(multiple choice 40%, short answer 30%, and essay 30%) and will be graded
on different standards from those designed for undergraduate students.
Graduate students are also required to submit a more substantial 15 page
research paper. As with exams, graduate student research papers and oral
presentations will be evaluated separately from the rest of the class.
Grades for graduate students will be straight scale, meaning there will
be NO adjustment of the final grade. To obtain a passing grade
(i.e., C or higher), graduate students must accrue at least 70% of the
possible points in the course.
Other course information:
Email and internet
access are required for the course. Students should check the course
site and read their email regularly.
Lecture slides: The
instructor will supply a hard copy of the lecture slides for each class.
An electronic copy (pdf version) of these notes will be made available on
the course website (http://www.brent.xner.net/BIOL4800/index.htm).
Attendance will be
documented but is not directly factored into the final grade.
Study hint: The LSU
Center for Academic Success (CAS;
http://appl003.lsu.edu/slas/cas.nsf/index) exists to help students do
well in their classes. At their web site, consider taking their “Test
Your Learning Style” to see how you learn best.
Code of Student Conduct:
Students are expected to
adhere to the Code of Student Conduct, which can be accessed at:
http://appl003.lsu.edu/slas/dos.nsf/$Content/Code+of+Conduct?OpenDocument.
University regulations on academic misconduct will be strictly enforced
and violators will be referred immediately to the Dean of Students.
Plagiarism
examples and
information on proper and improper student writing.
Students with disabilities:
If a student has a disability which may require
accommodation, you should immediately contact the Office of Disability
Services (http://appl003.lsu.edu/slas/ods.nsf/index)
to officially document the needed accommodation. The instructor must be
presented with this documentation during the first week of class.
To make our time together as valuable as possible:
·
Attend all scheduled classes and arrive on time.
·
Come prepared to discuss the material.
·
Please turn off cell phones and refrain from sending text
messages, checking email, or any other behavior that might be disruptive
to other students.
·
If you have trouble concentrating on the lecture because of
a distraction, quietly ask those responsible for the distraction to stop.
If the distraction continues, please let me know.
·
Please contact me immediately if you have any problem which
is preventing you from performing satisfactorily in this class.
course calendar
(Subject to change)
|
Class |
Date |
Activity |
Assigned reading† |
|
1 |
26
August (T) |
Introduction and historical context |
1 (1) |
|
2 |
28
August (Th) |
Origin and evolutionary record of life |
2 & 14 (2 & 11) |
|
|
2
September (T) |
GUSTAV |
|
|
|
4
September (Th) |
GUSTAV |
|
|
3 |
9
September (T) |
Microbial diversity and evolution |
2 & 14 (2 & 11) |
|
4 |
11
September (Th) |
* Species and speciation - Discussion questions
LITERATURE SUMMARY DUE
|
Cohan (2002) a
Ward (2006) b
|
|
5 |
16
September (T) |
Microbe: microbe interactions |
9 & 23 (8 & 19) |
|
6 |
18
September (Th) |
Microbe: plant/animal interactions |
24 (19) |
|
7 |
23
September (T) |
Population ecology |
6 (6) |
|
8 |
25
September (Th) |
Microbial community structure |
22 & 23 (18 & 19) |
|
9 |
30
September (T) |
Physiological microbial ecology |
6, 7 & 9 (6, 7 & 8) |
|
|
2
October (Th) |
NO CLASS |
|
|
10 |
7
October (T) |
Biogeochemical cycling |
24 (19) |
|
11 |
9
October (Th) |
Biogeochemical cycling (cont.)
RESEARCH PAPER TOPIC DUE
|
24 (19) |
|
12 |
14 October (T) |
MID TERM EXAM |
|
|
13 |
16
October (Th) |
Thermodynamics and microbial ecology |
Middleton Library, Room 230-B
THERMODYN |
|
14 |
21
October (T) |
Quantitative ecology: numbers and biomass |
22 (18) |
|
15 |
23
October (Th) |
Quantitative ecology: metabolic activity |
22 (18) |
|
|
28
October (T) |
NO CLASS |
|
|
|
30
October (Th) |
NO CLASS |
|
|
16 |
4
November (T) |
Microbiology’s molecular revolution
PROBLEM SET DUE
|
Pace (1997) c |
|
17 |
6
November (Th) |
Molecular microbial ecology |
22 (18) |
|
18 |
11
November (T) |
Isolating “uncultivable” microbes |
Connon & Giovannoni (2002) d
Zengler (2002) e
Ferrari et al. (2005) f
|
|
19 |
13
November (Th) |
Microbial ecology in the era of genomics
RESEARCH PAPER DUE (in class)
|
Handelsman (2004) g |
|
20 |
18
November (T) |
* Metagenomic analysis of communities |
Hallam et al. (2004) h
Tringe et al. (2005) i
|
|
21 |
20
November (Th) |
Student symposium – Day 1
Jana Robins - Microbes and air quality
Cassie Gray - Subsurface microbiology |
|
|
22 |
25
November (T) |
Student symposium – Day 2
Jason Green - Viral diversity and ecology
Daniel Manieri - Nitrogen cycling in marine systems
Corey Ritts - ??? |
|
|
|
27
November (Th) |
THANKSGIVING BREAK |
|
|
23 |
2
December (T) |
Student symposium – Day 3
Ashlee Clayton - Impact of climate change of polar marine systems
Caitlin King - Chemolithotrophs in volcanic terrestrial systems
Brandi Deamer - Astrobiology and Mars |
|
|
24 |
4
December (Th) |
Student symposium – Day 4
Richshell Smith - Bioflims and periodontal disease
Cori Cooper - Quorum sensing in Pseudomonas
Patrick Swindle - Microbial oil degradation/synthesis
Kristina Dickson - Microbial fuel cells |
|
|
25 |
10
December (W) |
FINAL EXAM – 12:30-14:30 |
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† Unless specified, readings from
chapters in Brock Biology of Microorganisms 12th ed (11th
ed).
* Indicates dates for open discussions of “hot
topics” in microbial ecology.
Disclaimer:
the copyright of the respective articles are with the corresponding
publishers and the files are provided for academic use only.
Supplemental readings:
a
Cohan, F.M.
(2002) What are bacterial species? Annu. Rev. Microbiol. 56:457-87.
b
Ward, D.M.
(2006) A macrobiological perspective on microbial species. Microbe
1:269-278.
c Pace, N.R.
(1997) A molecular view of microbial diversity and the biosphere.
Science 276:734-740.
d
Connon, S.A.,
and S.J. Giovannoni. (2002) High-throughput methods for culturing
microorganisms in very-low-nutrient media yield diverse new marine
isolates. Appl. Environ. Microbiol.
68:3878-3885.
e
Zengler, K. et al.
(2002) Cultivating the uncultured. Proc.
Natl. Acad. Sci. 99:15681-15686.
f
Ferrari, B.C. et al.
(2005) Microcolony cultivation on a soil
substrate membrane system selects for previously uncultured soil bacteria.
Appl. Environ. Microbiol.
71:8714-8720.
g
Handelsman, J.
(2004) Metagenomics: application of genomics to uncultured microorganisms.
Microbiol. Mol. Biol. Rev. 68:669-685.
h
Hallam, S.J. et al.
(2004) Reverse methanogenesis: testing the
hypothesis with environmental genomics. Science 305:1457-1462.
i
Tringe, S.G. et al.
(2005) Comparative metagenomics of microbial
communities. Science, 308:554-557.
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