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Microbial Ecology
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Dept of Microbiology


Instructor: Professor Schloss

Room:  N319 Morrill I

Time:  MWF 10:10-11:00 (3 credits)

Office hours:  MW 4:00-5:00 and by appointment


Course website:

Ereserve password:  microbes


Motivation of course

"By ecology, we mean the body of knowledge concerning the economy of nature -- the investigation of the total relations of the animal both to its organic and to its inorganic environment; including above all, its friendly and inimical relation with those [microbes,] animals and plants with which it comes directly or indirectly into contact -- in a word, ecology is the study of all the complex interrelationships referred to by Darwin as the conditions of the struggle for existence."

- Ernst Haeckel, 1870


"Anything that is true of Escherichia coli must be true of elephants, only more so."

- Jacques Monod, 1954


"Nothing in biology makes sense except in the light of evolution."

- Theodosius Dobzhansky, 1973


"Very little in evolution makes sense, except in the light of ecology."

- Begon et al., 1990



Course format

Overview:  Traditional ecology courses emphasize theory and sprinkle in examples of where the theory either fits or needs to be revisited.  Traditional environmental microbiology courses stress physiological and environmental diversity with ecological theory sprinkled in.  This course will follow the traditional ecology model with examples drawn primarily from microbiology (i.e. viruses, bacteria, archaea, and microeukaryotes), some examples from macroecology, and discussion of where the two don't seem to fit.  Overall, this course has an extra goal of exposing and helping to form you for a graduate-level education.


Class:  Each class will follow a similar three-part format consisting of an inquiry-based/active learning exercise, mini-lecture, and discussion of an example from the microbial ecology literature.  Since there is no textbook for this class, review articles will be assigned for reading prior to the presentation of material in class.  These readings are available through E-reserve at the library.  These are to be printed and read ahead of and brought to class.


Course learning goals and expectations for meeting goals


Learning goal

Level of Performance



Needs Improvement


Learn what science is and how it is done

Develops an insatiable appetite to learn and apply material

Beginning to form ideas of how to test hypotheses

Shows interest in material, but thinks the answers are in a book somewhere

Is apathetic about material and is only taking the course for 3 credits

Appreciate the interconnectedness of life from viruses to humans

Can integrate concepts to describe interaction of organisms and their environment from genes to ecosystems

Can integrate concepts at the microbial level or the macroscopic level, but has difficulties synthesizing across levels

Cannot connect microbial and macroscopic life or the role of microbes in ecosystem functioning

Cannot adequately distinguish between various forms of life

Describe the relationship between evolution and ecology

Can take any ecological concept and interpret it in light of evolutionary theory

Can interpret many ecological theories in light of evolution

Has a working knowledge of evolution and ecology, but cannot synthesize the two

Cannot articulate the key concepts in ecology or evolution

Apply macro-ecological theory to microbial communities

Has no problem seeing how to apply ecological theory to microbes and can identify limitations of theory

Has no problem seeing how to apply ecological theory to microbes, but cannot identify limitations

Has basic knowledge of ecological concepts but not theories or how they are applied

Cannot articulate the reasoning behind key ecological theories

Describe how science is done and how a hypothesis is formed and tested

Can formulate and propose a realistic means of testing an ecological theory for microbes or macroorganisms

Can formulate and propose a realistic means of testing an ecological theory for macroorganisms

Can formulate a hypothesis and method of testing, but has difficulties applying to ecology

Cannot formulate a hypothesis or method of testing a hypothesis

Understand that ecology is a quantitative science

Can flexibly use and implement simple simulation software, tools for sequence analysis, and statistics

Can understand the theory behind various models, but has difficulties with their implementation

Can understand basic conceptual models used in ecology, but cannot grasp the mathematical underpinnings

Is petrified of anything involving models, statistics, mathematics or computers



Students will demonstrate that they have achieved the learning goals through:

  • 60% of grade – Three exams over each of the three themes in the class (20% each).
  • 10% of grade – Write 5 hypothetical letters to investigators profiled in separate Microbe World Radio podcasts.
  • 10% of grade – Read a popular science book and write a reflection and chapter.
  • 10% of grade – Complete 5 homework assignments that stress quantitative skills.  May be done collaboratively – work with partner, but write individually.
  • 10% of grade – Class participation.  To be judged by turning in index card at end of class.  Students can miss 4 before losing points.
  • Academic integrity: Late papers will be docked 5 points per day.  Cheaters will be drawn, quartered according to university policies.



A:         93-100

A-:       90-93

B+:       87-90                                       Boarderline calls will be based on general level of

B:         83-87                                       participation in classes and is left to the discretion

B-:       80-83                                       of Dr. Schloss

C+:      77-80

C:        73-77

C-:       70-73




Course packet.  Most classes will have one or two assigned readings for the following class.  It is essential that you read these to adequately participate in class discussions and activities.  Some of these papers are quirky and some are more serious.  These readings have been compiled are available through E-reserve at the library.  You need to print these yourself [a course packet would have cost over $100!].


1.     Mayr, E.  1998.  Two empires or three?  Proceedings of the National Academy of Sciences USA 95:9720-3.

2.     Woese, CR.  1998.  Default taxonomy: Ernst Mayr’s view of the microbial world.  Proceedings of the National Academy of Sciences USA 95:11043-6.

3.     Rennie, J.  2002.  15 answers to creationist nonsense.  Scientific American.  June 2002:78-85.

4.     Bennett, CH, Li, M, and Ma, B.  2003.  Chain letters and evolutionary histories.  Scientific American  June 2003:76-81

5.     Metzker, ML, Mindell, DP, Liu, X-M, Ptak, RG, Gibbs, RA, and Hillis, DM.  2002.  Molecular evidence of HIV-1 transmission in a criminal case. Proceedings of the National Academy of Sciences USA 99:14292-7.

6.     Otto, SP and Gerstein, AC.  2006.  Why have sex? The population genetics of sex and recombination.  Biochemical society transactions  34:  519-22.

7.     Zimmer, C.  2005. Testing Darwin. Discover  26: 28-35.

8.     Elena, SF & Lenski, RE.  2003.  Evolution experiments with microorganisms:  the dynamics and genetic bases of adaptation.  Nature Reviews Genetics  4:457-9.

9.     Liu, R & Ochman, H.  2007.  Stepwise formation of the bacterial flagellar system. Proceedings of the National Academy of Sciences USA  104:7116-21.

10.  Wong, T, Amidi, A. Dodds, A, Siddiqi, S, Wang, J, Yep, T, Tamang, DG, and Saier, MH Jr.  2007.  Evolution of the bacterial flagellum.  Microbe  2:335-340.

11.  Smith, EE, Buckley, DG, Wu, Z, Saenhimmachak, C, Hoffman, LR, D’Argenio, DA, Miller, SI, Ramsey, BW, Speert, DP, Moskowitz, SM, Burns, JL, Kaul, R, Olson, MV.  2006. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients.  Proceedings of the National Academy of Sciences USA 103:8487-92.

12.  Warmflash, D & Weiss, B.  2005.  Did life come from another world?  Scientific American  October 2005.

13.  Pace, NR.  2006.  Time for a change.  Nature  441:289.

14.  Martin, W & Koonin, EV.  2006.  A positive definition of prokaryotes.  Nature  442:868.

15.  Dolan, MF & Margulis L.  2006.  Advances in biology reveal truth about prokaryotes.  Nature  445:21.

16.  Skerker, JM & Laub, MT.  2004.  Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus.  Nature Reviews Microbiology 2:325-37.

17.  Ridley, M.  2004.  The Agile Gene.  HarperCollins Publishers, Inc.  New York.  Chapter 1: The Paragon of Animals; pgs. 7-37.

18.  Valentine, DL.  2007.  Adaptations to energy stress dictate the ecology and evolution of the Archaea.  Nature Reviews Microbiology  5:316-323.

19.  Angert, ER.  2005.  Alternatives to binary fission in bacteria.  Nature Reviews Microbiology 3:214-224.

20.  Fraser CM.  2004.  A genomics based approach to biodefense preparedness.  Nature Reviews Genetics  5:23-33.

21.  Hardin, G.  1968.  The tragedy of the commons.  Science  162:1243-48.

22.  Nyholm, SV & McFall-Ngai, MJ.  2004.  The winnowing: establishing the squid-vibrio symbiosis.  Nature Reviews Microbiology  2:632-42.

23.  Nowak, MA & Sigmund, K.  2004.  Evolutionary dynamics of biological games.  Science  303:793-9.

24.  Turner, PE.  2003.  A virus booster for game theory.  ASM News  69:289-95.

25.  West, SA, Griffin, AS, Gardner, A, and Diggle, SP.  2006.  Social evolution theory for microbes.  Nature Reviews Microbiology  4:597-607.

26.  Nowak, MA.  2006.  Five rules for the evolution of cooperation.  Science  314:1560-3.

27.  Pernthaler, J.  2006.  Predation on prokaryotes in the water column and its ecological implications.  Nature Reviews Microbiology  3:537-546.

28.  Bazinet, C.  2004.  Endosymbiotic origins of sex.  Bioessays  26:558-66.

29.  Walker, A & Crossman, L.  2007.  This place is big enough for both of us.  Nature Reviews Microbiology  5:90-2.

30.  Crossman, L. & Thomson, N.  2006.  Peddling the nitrogen cycle.  Nature Reviews Microbiology  4:494-5.

31.  Currie, CR, Wong, B, Stuart, AE, Schultz, TR, Rehner, SA, Mueller, UG, Sung G-H, Spatafora, JW, Straus, NA.  2003.  Ancient tripartite coevolution in the attine ant-microbe symbiosis.  Science.  299:386-8.

32.  Ley, RE, Peterson, DA, and Gordon, JI.  2006.  Ecological and evolutionary forces shaping microbial diversity in the human intestine.  Cell  124:837-48.

33.  Eckburg, PE, Lepp, PW, and Relman, DA.  2003.  Archaea and their potential role in human disease.  Infection and Immunity.  71:591-6.

34.  Schloss, PD & Handelsman, J.  2007.  The last word:  Books as a statistical metaphor for microbial communities.  Annual Reviews in Microbiology. 61:23–34.

35.  Tilman, D, Reich, PB, Knops, JMH.  2006.  Biodiversity and ecosystem stability in a decade-long grassland experiment.  Nature  441:629-32.

36.  Bezemer, TM & van der Putten, WH.  2007.  Diversity and stability in plant communities.  Nature  446:E6-E7.

37.  Tilman, D, Reich, PB, Knops, JMH.  2007.  Tilman et al. reply.  Nature  446:E7-E8.

38.  Ives, AR & Carpenter, SR.  2007.  Stability and diversity of ecosystems.  Science  317:58-62.

39.  Whitfield, J.  2005.  Biogeography: Is everything everywhere?  Science  310:960-1.

40.  O’Malley, MA.  2007.  The nineteenth century roots of ‘everything is everywhere’.  Nature Reviews Microbiology. 5:647-51.

41.  Balser, TC, McMahon, KD, Bart, D, Bronson, D, Coyle, DR, Craig, N, Flores-Mangual, ML, Forshay, K, Jones, SE, Kent, AE, and Shade, AL.  2006.  Bridging the gap between micro- and macro-scale perspectives on the role of microbial communities in global change ecology.  Plant Soil  289:59-70.

42.  Brooks, TM, Mittermeier, RA, da Fonseca, GAB, Gerlach, J, Hoffman, M, Lamoreux, JF, Mittermeier, CG, Pilgrim, JD,  Rodrigues, ASL.  2006.  Global biodiversity conservation principles.  Science  313:58-61.

43.  Yim, G, Wang, HH, and Davies, J.  2006.  The truth about antibiotics.  International Journal of Medical Microbiology  296:163-70.


Text book references.  This course does not have an assigned textbook.  The books below will be reserved at the W.E.B. Du Bois library to supplement assigned readings and class activities and lectures.


Madigan, M. T., J. M. Martinko, and T. D. Brock. 2006. Brock biology of microorganisms, 11th ed, Pearson Prentice Hall, Upper Saddle River, NJ.


Any edition will do.  Hopefully you still have your copy from MICRO 310.  This is a good resource that has broad information about microbial physiology and diversity and a superficial coverage of microbial ecology.  If you are serious about pursuing a career related to microbiology, you should have a copy of this book.


Begon, M., J. L. Harper, and C. R. Townsend. 1996. Ecology: Individuals, Populations, and Communities. 3rd ed. Blackwell Science, Malden, MA.


Any edition will do.  The Ecology textbook used in most ecology courses.  Significant bias towards plants and animals, but it represents much of the basic ecological theory that is important for our purposes.


Atlas, R. M., and R. Bartha. 1993. Microbial Ecology:  Fundamentals and Applications, 3 ed, The Bengamin/Cummings Publishing Company, Inc., Redwood City, CA.


Probably the most popular microbial ecology textbook; however, it is really an environmental microbiology textbook.  Many of the methods are out of date and it lacks an evolutionary perspective.


McArthur, J. V. 2006. Microbial ecology: an evolutionary approach, Elsevier/Academic Press, Burlington, MA.


This is a recent attempt to synthesize microbial ecology and evolution.  Poorly organized and has a bias towards "natural" ecosystems.


Hartl, D. L., and A. G. Clark. 1997. Principles of population genetics, 3rd ed, Sinauer Associates, Sunderland, MA.


A mathematically oriented treatment of population genetics, with some treatment of haploid organisms, but mostly focused on sexually reproducing populations.


Hedrick, P. W. 2000. Genetics of populations, 2nd ed, Jones and Bartlett Publishers, Sudbury, Mass.


A mathematically oriented treatment of population genetics, with some treatment of haploid organisms, but mostly focused on sexually reproducing populations.



Microbe World Radio Podcast Letters

In an effort to make the public more aware of the critical role that microbes play in the biosphere the American Society for Microbiology has launched the Microbe World website.  Part of this effort is a daily 90-second podcast that is available through services such as iTunes (  Throughout the semester you will listen to at least 5 of these broadcasts and write a 500-word letter to the scientists profiled in the podcast.  Pretend that you are a prospective graduate student that would like to work with the profiled investigator and write them a letter.  Your letters will be evaluated based on the following:


  • Format (5 pts):  450 to 550 words, Arial 12 pt, 1 in margins, single-spaced, correct formatting of a letter, professionalism, and date and title of podcast
  • Summary of podcast (15 pts):  Summarize what you learned from the podcast and how it relates to microbial ecology
  • Pitch (15 pts):  If you were to join this investigator’s lab as a graduate student, what would be an extension of this work that you would like to work on?
  • Follow-up (10 pts):  What is one burning question that you would like to ask the investigator?
  • Convincing (5 pts):  Convince the investigator that you want to work in their lab


These letters will be due as indicated on the course schedule.



Popular Science Chapters

Background.  Microbes get pretty short shrift in popular science books and when they are discussed, the discussion pertains to pathogens.  No doubt, publishers think that human evolution is far more interesting than bacterial evolution and that gore sells.  Matt Ridley has written a number of books on evolution and ecology and they are quite popular and engaging.  Unfortunately, he also largely ignores bacteria.  Your charge is to read one of these books with your group:


Ridley, M. 1997. The origins of virtue: human instincts and the evolution of cooperation.  Viking, New York.

Ridley, M. 2003.  The red queen: sex and the evolution of human nature.  Harper Perennial, New York.

Ridley, M. 2003.  The agile gene: how nature turns on nurture.  Harper Perennial, New York.

Ridley, M. 2006.  Genome: the autobiography of a species in 23 chapters.  Harper Perennial, New York.


Individual Assignment.  You are expected to read the entire book that you have chosen.  Based on the reading there are two individual assignments.  First, you will write a one page (1" margins, 11 point arial font, single spaced) reflection on the biases and opinions posed by Ridley in the book you have read.  Second, you will write a test question for the other people in the class that read the same book.  One of the questions will show up on the 3rd exam.  Both of these assignments are due on 10/26/2007 at 5 pm.


Group Assignment.  In a group of 3-4 people, chapter for a Ridley book that takes on a problem that either directly or tangentially relates to the existing chapters, but must emphasize and use examples drawn from microbes.  It should be written in the style of Ridley – mature yet basic, referenced, analogies, etc.  Think outside the box – the goal isn’t to get THE answer, but to provide text that shows depth of thought, creativity, knowledge of underlying theory, and ability to digest some examples from the literature. Your group needs to "clear" your idea with Dr. Schloss by 10/26/2007 and submit the paper by 5 pm on 12/7/2007.


Specifications for chapter.  When I write a white paper for a grant competition, it is essential that I follow the guidelines and that I adequately address the interests of the funding agency.  Failure to do so can have my white paper or proposal returned to me without being read or will severely affect my chances of receiving funding.  Here are the guidelines for your chapters


  • Individual contribution (10 pts):  Depth of thought put into individual reflection and test question
  • Format (10 pts; all or none):  9,000-11,000 words, Arial 11 pt, 1" margins, single-spaced; provide a paper and electronic copy.
  • Flow (15 pts):  Everyone should contribute to writing the chapter, but it should not be obvious that it was written by a group.
  • Research (15 pts): Cite at least five peer-reviewed journal articles (no websites!)
  • Evolutionary and Ecological Ideas (25 pts):  You need to show a firm grasp of the evolutionary and ecological ideas presented in class.
  • Knowledgeable (25 pts):  You have gone beyond the material presented in the class to provide a compelling story about an interesting problem.



Fine Print

Workload.  This class may require more effort than a typical 300-level course; however, based on my experience at various universities, the workload is appropriate.  This means that you will need to use foresight in planning your reading, study, and work schedule.  The rewards for exhibiting the necessary level of fortitude will help you to learn and love microbial ecology.


Classroom decorum.  Students are expected to assist in maintaining a classroom environment that is conducive to learning.  In order to assure that all students have the opportunity to gain from time spent in class, I propose certain basic standards of classroom respect be adhered to.  Respect does not eliminate appropriate humor, enjoyment, or other indications of a comfortable and pleasant classroom community.  However, there is an expectation that all participants in this course will:

  • Attend and participate in lectures, group discussions, and other classroom activities.
  • Avoid negative language that is considered racist, sexist, or homophobic or in other ways may exclude members of our campus and classroom community.
  • Avoid unnecessary disruptions during class such as private conversations, reading newspapers, checking or speaking on cell phones, using a laptop for something other than current classroom work, arriving late or leaving early, eating, drinking, sleeping during class, and wearing inappropriate clothing.

Failure to comply with these fundamental principles of classroom decorum will result in students being asked to leave class and tests.


Contacting Professor.  Do not wait until the last minute to contact me; I have a busy schedule and some weeks I will be traveling between classes.  Also, if you think your grade is in peril, contact me immediately.  E-mail is appropriate to schedule an appointment or for short questions to clarify class assignments or specific items from a lecture.  E-mail is not appropriate to deliver the following:

  • Messages with inappropriate language or anything you would not be willing to communicate to me in person.
  • Junk mail, internet jokes, chain letters, etc.
  • Excuses to miss class, requests for my lecture notes or asking if you "missed anything" when you miss a class. It is your responsibility to attend class and obtain notes. If you miss a class, obtain notes from a fellow student or the website.  Outlines and slides will be posted on the course website.

Email is frequently not a good substitute for meeting with me.  This is why I have office hours. Office visits are the best way to ask questions about course material, and to discuss classroom issues or any other special concerns you may have about your class performance.  Also, do not contact me by phone.


Office hours.  I am very generous with my time.  In addition to the two hours per week that are available to meet, I am available outside of these times if you contact me via email to schedule a time to meet.  I am more that willing to answer any questions you have about class, microbiology, careers, or just life in general.  One thing I ask is that you come to office hours prepared.  My time and your classmates' time are very valuable; do not waste it by showing up without thinking or trying to understand first.  How is this done?  Bring your notes from class, diagrams you have drawn of processes, preliminary attempts to solve problems.  You may make use of each other for help in understanding class and in solving problems; however, you must acknowledge your comrades' contributions.  Also, one way of aiding the learning process is by reading each other's writing (this is something I do with my students and colleagues!).  I would encourage anyone that has difficulty writing to consult with members of the Writing Center on campus (  I will be grading for content, not grammar and spelling; however, if your grammar and spelling are poor it will affect your grade because it will make it too distracting to understand the content and will affect the ability to transmit your message.


Academic integrity.  Please be aware of your rights and responsibilities as a student at UMass.  Academic dishonesty will not be tolerated.  I will not tolerate any cheating in my class.  If I catch you cheating in my class, I will report you to the administration and request that you receive the most severe punishment from the university.

Course Outline



1.       9/5        Orientation – What is ecology?  What is microbial ecology?



2.       9/7        Introduction – Introduction to evolution

3.       9/10      Introduction – Natural selection

4.       9/12      Introduction – Phylogeny

5.       9/14      Mechanisms – Sources of variation; Letter #1 due

6.       9/17      Mechanisms – Horizontal gene transfer and sex

7.       9/19      Mechanisms – Selection

8.       9/21      Adaptation – Studying evolution via artificial life

9.       9/24      Adaptation – Studying evolution in the lab

10.    9/26      Adaptation – Studying evolution in the world

11.    9/28      History of life – Speciation and species definitions; Letter #2 due; HW #1 due

12.    10/1      History of life – Genesis theories

13.    10/3      History of life – Biodiversity and the Tree of Life

   10/5      EXAM 1


Life within Populations

14.    10/9      Introduction – Habitats, individuals, and populations

15.    10/10    Autecology – Nature vs. nurture

16.    10/12    Autecology – Responses to stress; HW #2 due

17.    10/15    Autecology – Shape, size, reproduction, death

18.    10/17    Population ecology – Analysis of populations

19.    10/19    Population ecology – Intra-species competition; Letter #3 due

20.    10/22    Population ecology – Inter-species competition

21.    10/24    Microbial behavior – Communication

22.    10/26    Microbial behavior – Game theory

23.    10/29    Microbial behavior – Cooperation; HW #3 due

24.    10/31    Microbial behavior – Cheating

25.    11/2      Microbial behavior – Altruism

26.    11/5      Microbial behavior – Predation; Letter #4 due

        11/7      EXAM 2


Life within Communities and Ecosystems

27.    11/9      Symbiosis – Coevolution; Deadline for meeting with Dr. Schloss

28.    11/14    Symbiosis – Nitrogen fixation

29.    11/16    Symbiosis – Social insects; HW #4 due

30.    11/19    Symbiosis – Human microbiome

31.    11/21    Symbiosis – Polymicrobial infections

32.    11/26    Community ecology – Analysis of communities; Letter #5 due

33.    11/28    Community ecology – Food chains and webs

34.    11/30    Community ecology – Disturbances, colonization and succession

35.    12/3      Community ecology – Biogeography

36.    12/5      Ecosystem ecology – Nutrient cycling

37.    12/7      Ecosystem ecology – Integrating microbial and macro-ecology; Paper due

38.    12/10    Ecology synthesis – Conservation

39.    12/12    Ecology synthesis – Antibiotic resistance; HW #5 due

        12/14    EXAM 3

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Patrick D. Schloss --
Department of Microbiology, UMASS AMHERST