MICROBIAL ECOLOGY
BIOL 4115
FALL 2015     12:00-13:20 T/Th     201 Williams Hall

Instructor:  Brent C. Christner
Office:
  282b Life Sciences Building
Phone:
  (225) 578-1734
Email:
  xner@lsu.edu
Office hours:
  W 11:00–12:00
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 relationships between and role of microorganisms in ecological communities.  Course topics are structured to demonstrate the linkages between microbial ecology, diversity, and function. 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.
·  
Community dynamics at both the molecular and the organismal level.
·  
Abiotic and biotic interactions within microbial communities.
·  
Thermodynamic constraints on microbial processes.
·  
Microbial metabolism and biogeochemical cycling.
·  
Molecular and genomic approaches for examining microbial community structure and function.

Text:
Strongly Recommend: Madigan, M.T., J.M. Martinko, K.S. Bender, D.H. Buckley, and D. Stahl. 2015. Brock: Biology of Microorganisms (14th or current eds.), Pearson Education, Inc.
Amazon – 14th ed. (new - $176); 13th ed. (used - $28 and up).

Scientific literature:
Readings from the text will be supplemented with scientific literature 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 (3 September and 12 November), the class period will be dedicated to open discussions of current scientific literature.  Student participation in the discussion sessions will be graded.

Grading:
Exams: There will be 2 exams.  The exams will 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 will cover the same material but will be an essay exam.  The final is cumulative. 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 University Registrar by the specified 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 figures and citations.  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 1 October.  Submit a hard copy of your paper to me in class on 10 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_BIO4115ResPaper.docx). 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 research topics during one of the final class sessions.  Each presentation should be 15 minutes in length, allowing 5 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 presented.

Class participation:  Student participation in class discussions will be graded. 

Literature summary:  A 250-word literature summary is required at the beginning of class on 3 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 22 October at the beginning of the lecture because the answers will be reviewed during that lecture.  Late problem sets will not be accepted.

            Overall grading percentages:

 

Grading scale:

Research paper

30%

 

A+       97-100%

C         73-76%

Mid-term exam

25%

 

A         93-96%

C-        70-72%

Final exam

25%

 

A-        90-92%

D+       67-69%

Oral presentation

10%

 

B+       87-89%

D         63-66%

Class participation

5%

 

B         83-86%

D-        60-62%

Literature summary

2.5%

 

B-        80-82%

F    Below 60%

Problem set

2.5%

 

C+       77-79%

 

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 factored into the final grade.

Code of Student Conduct:
Students are expected to adhere to the Code of Student Conduct, which can be accessed at: http://saa.lsu.edu/code.  University regulations on academic misconduct will be strictly enforced and violators will be referred immediately to the Dean of Students.

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.
·  
Mute cell phones and refrain from any behaviors that might be disruptive to others.
·   If you have trouble concentrating on the lecture because of a distraction, let me know.
·   Contact me immediately if you have any problem which is preventing you from performing satisfactorily in this class.

 TENTATIVE course calendar

(Subject to change)

Class

Date

Activity

Background reading†

1

25 August

Introduction and historical context

1 (1 & 2)

2

27 August

Origin and evolutionary record of life

12 (16)

3

1 September

Microbial diversity and evolution

12 (16)

4

3 September

* Species and speciation
LITERATURE SUMMARY DUE

Fraser et al. (2009) a
Ward (2006) b

5

8 September

Microbe: microbe interactions

7, 19, & 22
(8, 23 & 25)

6

10 September

Microbe: plant/animal interactions

22 (25)

7

15 September

Population ecology

5 (5)

8

17 September

Microbial community structure

18 & 19  (22 & 23)

9

22 September

Physiological microbial ecology

5 & 7 (5, 6, & 8)

10

24 September

Physiological microbial ecology (continued)

5 & 7 (5, 6, & 8)

11

29 September

Biogeochemical cycling

20 (24)

12

1 October

Biogeochemical cycling (continued)
RESEARCH PAPER TOPIC DUE

20 (24)

 

6 October

NO CLASS

 

13

8 October

MID TERM EXAM

 

14

13 October

Thermodynamics and microbial ecology

Thermodyn©

15

15 October

Quantitative ecology: numbers and biomass

18 (22)

16

20 October

Quantitative ecology: metabolic activity

18 (22)

17

22 October

Microbiology’s molecular revolution
PROBLEM SET DUE

18 (22)

 

27 October

NO CLASS

 

 

29 October

FALL HOLIDAY

 

18

3 November

Molecular microbial ecology

18 (22)

19

5 November

Isolating “uncultivable” microbes

Stewart (2012) c

20

10 November

Microbial ecology in the era of genomics
RESEARCH PAPER DUE (in class)

6 & 18  (22)

21

12 November

* Metagenomic analysis of communities

THMPC (2012) d
Rinke et al. (2013) e

22

17 November

Student symposium – Day 1
     Brian Matherne
     Carlie Amore
     Lauren Jimerson

 

23

19 November

Student symposium – Day 2
     Alyssa Chauviere
     Gregory Ware
     Rohit Raina

 

 

24 November

NO CLASS

 

 

26 November

THANKSGIVING HOLIDAY

 

24

1 December

Student symposium – Day 3
     Julianne Martin
     James Ray
     Cullen Hodges

 

25

3 December

Review

 

 

9 December (Wednesday)             FINAL EXAM – 3:00 – 5:00 PM

Unless specified, readings from chapters in Brock Biology of Microorganisms 14th ed (13th ed).
* Dates for in class discussions of specific topics in the scientific literature.            

 Supplemental readings:
a Fraser, F., E. J. Alm, M. F. Polz, B. G. Spratt, and W. P. Hanage (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science 323:741-46.
b
Ward, D.M. (2006) A macrobiological perspective on microbial species. Microbe 1:269-278.
c Stewart, E.J. (2012) Growing unculturable bacteria. Journal of Bacteriology 194:4151-4160.
d The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
e Rinke, C. , Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., Dodsworth, J.A., Hedlund, B. P., Tsiamis, G., Sievert S. M., Liu,W.-T., Eisen, J. A., Hallam, S., Kyrpides, N. C., Stepanauskas, R. , Rubin, E. M., Hugenholtz, P. and Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431-437.