Soil Ecology
ESS 573
Spring 2014
We know more about the movement of celestial bodies than about the soil underfoot.
Leonardo da Vinci
Professor: Dr. Rachel K. Thiet, Phone: (603) 283-2337, E-mail: rthiet@antioch.edu. Office
hours by appointment.
Teaching Associate: Ms. Ju Kim. E-mail: jkim5@antioch.edu. Ju will be working with us
throughout the semester in class and during our lab exercises. Her primary role in the course is to
work with you closely as you develop, conduct, and write up your soil ecology research projects.
Required textbooks:
Ashman, M.R. and Purti, G. 2002. Essential Soil Science. Blackwell Science Ltd., Oxford, UK.
Nardi, J.B. 2007. Life in the Soil: A Guide for Naturalists and Gardeners. The University of
Chicago Press, Chicago and London.
We will also draw from the primary literature and other texts; each article is available in the
Readings folder in Sakai. You may also want to have on hand a general chemistry book, as we
will be talking in some depth about soil and global biogeochemistry. Some of the general
references listed at the end of the syllabus may also aid your understanding of chemistry and
biogeochemistry. General biology and microbiology books may also help, as we will be
discussing microbial physiology and soil food web organisms.
Course description: In this course, you will learn about the ecological relationships between soil
organisms and their biotic and abiotic environments, with emphasis on the role of soil organisms
in biogeochemical cycling, ecosystem structure and function, long-term ecosystem sustainability,
and global environmental change. Specific objectives are to examine (1) the physical processes
of soil formation and development; (2) the biodiversity of soil ecosystems; (3) the biotic and
abiotic factors controlling soil community diversity and structure; (4) the linkages between soil
communities, soil physical properties, and soil organic matter and nutrient cycling; and (5)
several contemporary topics in soil ecology such as aboveground-belowground dynamics, global
environmental change, and special seminar topics chosen by student pairs.
Student learning outcomes:
By the end of this course, you will be able to: (1) through written and verbal work, demonstrate
understanding of the linkages among soil formation and development, local and regional climate
and soil characteristics, and soil organisms; (2) through written and verbal work, demonstrate an
understanding of the relationships between soil organisms, soil physical properties,
biogeochemical cycling, ecosystem functioning, and global environmental change; (3)
independently design and execute a scientific experiment in soil ecology; (4) write a research
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proposal and scientific paper about your soil ecology experiment; (5) conduct laboratory assays
of various soil physical and biological properties; (6) facilitate an effective graduate seminar
discussion about a soil ecology topic of your choice; and (7) characterize and identify terrestrial
and hydric soil types in the field.
Methods of instruction and student performance objectives: This course meets for one threehour session per week. We will use this time to combine lecture, instructive activities, laboratory
exercises, discussions of the readings, and work on your research projects. The research project
is designed to introduce you to research methods currently used by soil ecologists and to provide
you with a complete soil research experience including hypothesis generation, experimental
design, proposal writing, data collection and analysis, and preparation of a research paper and
presentation.
Evaluation of student work: In this course, each of you is expected to (1) do all the reading and
participate in classroom discussions of assigned reading material; (2) conduct a Mystery Soil Lab
project with your lab group; (3) complete an in-class midterm essay exam; (4) lead a graduate
seminar about a chosen topic in soil ecology; (5) prepare a research proposal for a short-term soil
ecology research project; and (6) conduct and present the results of your research project in an
oral presentation and written research paper. Evaluations of your work will be on a continuum
ranging from unsatisfactory to outstanding. You will be evaluated on your class participation,
performance on the midterm exam, the quality of your Mystery Soil Lab project, the quality of
your leadership during your chosen graduate seminar, and the strength of your research proposal,
paper, and presentation.
Attendance: The attendance policy of Antioch University New England expressly states that a
student may miss no more than two class periods per semester; a third missed class may result in
“no credit” for the course. I will make exceptions to this policy on a case-by-case basis and only
under extreme and unexpected student circumstances.
Course outline and required reading schedule: Do the reading corresponding to each class
before coming to class that day. This will allow you to interact deeply with the course material,
to ask questions that clarify confusing information, and to participate effectively in discussions
with your colleagues.
Dates, themes, and readings:
Key:
ESS = Essential Soil Science (Ashman and Purti)
LITS = Life in the Soil (Nardi)
January 24
Themes:
Course introduction
Soil formation and development I: This buzzing biomantle
Lab: Begin Mystery Soil Lab
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Readings:
1. This syllabus in its entirety
2. ESS Chapter 1: Rocks to Soil (pp 1-25)
3. LITS How to Use this Book; Preface; and Part One pp 1-8 only
4. Logan, W.B. 1995. The Circulation of Stone. In: Dirt: The Ecstatic Skin of the Earth, The
Berkley Publishing Group, NY. Pp 95-97.
January 31
Themes:
Soil formation and development II: Deeper than Dokuchaev
Soil taxonomy and global soil distribution
Lab: Mystery Soil Lab in-class work
Readings:
1. ESS Chapter 5: Soil Survey, Classification and Evaluation (pp 100-105 only)
2. Glanz, J. 1995. Earthworms, Charles Darwin, and Soil Formation Theory. Chapter 6 in:
Saving Our Soil: Solutions for Sustaining Earth’s Vital Resource. Johnson Books, Boulder.
(pp 83-103).
3. Johnson, D.L., J.E.J. Domier, and D.N. Johnson. 2005. Reflections on the nature of soil and its
biomantle. Annals of the Association of American Geographers 95(1):11-31.
4. Meysman, F.J.R., J.J. Middelburg, and C.H.R. Heip. 2006. Bioturbation: a fresh look at
Darwin’s last idea. Trends in Ecology and Evolution 21(12): 688-695.
5. Logan, W.B. 1995. Underground Horizons. In: Dirt: The Ecstatic Skin of the Earth, The
Berkley Publishing Group, NY. Pp 177-181.
6. Hillel, D. 2008. Soil Classification, Chapter 4 in Soil in the Environment: Crucible of
Terrestrial Life, Elsevier, Oxford, UK (pp 27-53; mostly pictures!).
Mark your calendars now for a midterm review session on Thursday evening, March 27, from
4:30-6:30 PM
February 7
Themes:
The soil habitat I: Home is where the pore is
Lab: Laboratory skills module I; Mystery Soil Lab in-class work
Readings:
1. ESS Chapter 2: Particles, Structures, and Water (pp 25-44)
2. LITS Part One (pp 8-45 only)
3. Hillel, D. 2008. Soil Physical Attributes, Chapter 5 in Soil in the Environment: Crucible of
Terrestrial Life, Elsevier, Oxford, UK (pp 55-77).
4. Logan, W.B. 1995. Kaolin. In: Dirt: The Ecstatic Skin of the Earth, The Berkley Publishing
Group, NY, pp 129-132.
5. This reading is not required but may be helpful for your Mystery Soil Lab:
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Langley-Turnbaugh, S.J. and D.R. Keirstead. 2005. Soil properties and land use history: A
case study in New Hampshire. Northeastern Naturalist 12(4):391-402.
February 14
Themes:
Soil habitat II: Arriving at the intact aggregate
The soil biota I: Breathing belowground
Lab: Laboratory skills module II; Mystery Soil Lab final in-class day
Readings:
1. ESS Chapter 3: Soil Surfaces, Acidity, and Nutrients (pp 46-66)
2. ESS Chapter 4: Soil Microbes and Nutrient Cycling (pp 67-77 only)
3. LITS, Part Two (pp 47-87 only)
4. Hillel, D. 2008. Soil Biodiversity, Chapter 12 in: Soil in the Environment, Crucible of
Terrestrial Life, Elsevier, Oxford, UK (pp 163-174)
February 21
Themes:
Soil biota II: Food webs: creepies, crawlies, and creatures that just cyst around
Lab: The soil biota
Readings:
1. LITS Part Two, pp 87-197 only
Assignment due today: Mystery soil lab presentations (see project guidelines for details)
February 28
Themes:
The ecology of soil organisms: creatures and their comforts
Experimental design techniques I
Lab: Soil food web exercise; begin discussing research projects
Readings:
1. LITS Collecting and Observing Life in the Soil (pp 257-268; this chapter should give you
some ideas for your research projects).
2. Bardgett, R.D. and D.A. Wardle. 2010. Biotic interactions in soil as drivers of ecosystem
properties, sections 2.1 through 2.4 (pp 15-45) in: Aboveground-Belowground Linkages:
Biotic Interactions, Ecosystem Processes, and Global Change, Oxford University Press.
Assignment due: Brief summary of a possible ecological question and two specific soil
properties you are interested in researching for your research project, and a possible study
location (see project guidelines for details). Post your possible question and soil properties in the
folder titled, “Research project ideas” in Sakai; then, read others’ posts to see if you share
interests with one of your peers and might benefit from working together.
March 7
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Themes:
Soil organisms and C cycling: pay dirt!
Experimental design techniques II
Lab: Continue planning research projects
Reading:
1. ESS Chapter 4: Soil Microbes and Nutrient Cycling (pp 77-81 only)
2. Hillel, D. 2008. Soil Chemical Attributes and Processes, Chapter 10 in Soil in the
Environment: Crucible of Terrestrial Life, Elsevier, Oxford, UK (pp 135-138 only).
3. White, R.E. Soil Organisms and Organic Matter, Chapter 3 (pp. 34-58) in: Principles and
Practice of Soil Science: The Soil as a Natural Resource (4th ed.), Blackwell Publishing.
March 21
Themes:
Soil organisms and N cycling: enough’s enough
Lab: Continue planning research projects
1. ESS Chapter 4: Soil Microbes and Nutrient Cycling (pp 81-89 only)
2. Aber, J.D., K.J. Nadelhoffer, P. Steudler, and J.M. Melillo. 1989. Nitrogen saturation in
northern forest ecosystems. BioScience 39(6):378-387.
3. LITS Part Two, pp 197-238 only
Assignment due: Finalize and turn in your research project proposal (see project guidelines for
details).
March 28
Midterm essay exam (you will need all three hours to complete this in-class exam)
April 4
Themes:
Contemporary issues in soil ecology: Plant-soil and aboveground consumer-soil interactions
Special topics seminar I: topic and paper TBD by student pairs
Lab: Begin work on your research projects
Readings:
1. Seminar leaders paper of choice.
2. Bonkowski, M., C. Vilenave, and B. Griffiths. 2009. Rhizosphere fauna: the functional and
structural diversity of intimate interactions of soil fauna with plant roots. Plant and Soil
321:213-233.
3. Bohlen, P.J., S. Scheu, C.H. Hale, M.A. McLean, S. Migge, P.M. Groffman, and D.
Parkinson. 2004. Non-native invasive earthworms as agents of change in northern temperate
forests. Frontiers in Ecology and the Environment 8:427-435.
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4. Wardle, D.A. and R.D. Bardgett. 2004. Human-induced changes in large herbivorous mammal
density: the consequences for decomposers. Frontiers in Ecology and the Environment 3:145153.
5. Bardgett, R.D. and D.A. Wardle. 2010. Sections 3.4 through 3.6 (pp 85-110) in:
Aboveground-Belowground Linkages: Biotic Interactions, Ecosystem Processes, and Global
Change, Oxford University Press.
6. You should now be reading a few papers every week about your chosen research topic
April 11
Themes:
Contemporary issues in soil ecology: Soil ecology and global environmental change
Special topics seminar II: topic and paper TBD by student pairs
Statistics module
Lab: In-class research workday – research project consult
Readings:
1. Seminar leaders paper of choice.
2. Hillel, D. 2008. The Role of Soil in the Mitigation of Global Warming. Appendix A in: Soil in
the Environment: Crucible of Terrestrial Life, Elsevier, Oxford, UK (pp 233-251).
3. Bardgett, R.D. and D.A. Wardle. 2010. Biotic interactions in soil as drivers of ecosystem
properties, section 2.5 (pp 45-59) in: Aboveground-Belowground Linkages: Biotic
Interactions, Ecosystem Processes, and Global Change, Oxford University Press.
4. Davidson, E.A. and I.A. Janssens. 2006. Temperature sensitivity of soil carbon decomposition
and feedbacks to climate change. Nature 440:165-173 (March 9, 2006).
5. Wieder, W.W., G.B. Bonan, and S.D. Allison. 2013. Global soil carbon projections are
improved by modeling microbial processes. Nature Climate Change 3:909-912.
6. Schimel, J. 2013. Soil carbon: Microbes and global carbon. Nature Climate Change 3:867868.
7. Continue reading papers about your chosen research topic
April 18
Themes:
Special topics seminar III: topic and paper TBD by student pairs
Field day! Characterizing soils in the field I: terrestrial soils
Readings:
1. Seminar leaders paper of choice.
2. Field trip handouts.
3. Continue reading papers about your chosen research topic.
April 25
Themes:
Special topics seminar IV: topic and paper TBD by student pairs
Field day! Characterizing soils in the field II: hydric soils
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1. Seminar leaders paper of choice.
2. Field trip handouts.
3. Continue reading papers about your chosen research topic.
May 2
Research presentations Day I
May 9
Research presentations Day II; wrap up, evaluations, and celebrate!
Assignment due: Research papers (see project guidelines for details)
PROJECTS AND ASSIGNMENTS
Mystery Soil Lab project
The Mystery Soil Lab project is a four-week project in which you and your lab group
characterize the physical and biological properties, landscape position, and land use history of a
Mystery Soil given specifically to your group. Your group will have several in-class lab periods
and whatever time you need outside of class to work on the project, and you will present your
Mystery Soil to the class on February 21 in whatever format you’d like. I will distribute specific
guidelines for the project early in the semester.
Research project
In the latter half of the course, you will be spending considerable time working on an
independent research project; you may work individually or with a research partner. My goals
for this project are to: (1) challenge you with an opportunity to conduct a scientific research
project from conceptualization to presentation; and (2) provide you with an opportunity to
integrate concepts and methodological approaches from soil ecology into your own area of
interest in this field. My learning objectives for the research project are that you will learn to: (1)
conceptualize and defend a meaningful soil ecological question given your new knowledge and
skills in soil ecology; (2) develop a laboratory- and/or field-based experiment to address your
ecological question and scale the experiment properly in time and space; (3) independently or
collaboratively conduct a scientific experiment; (4) learn and develop lab and field skills in soil
ecology; (5) write a scientific paper that effectively communicates your ideas and study findings;
(6) present your ideas and findings clearly and effectively in an oral presentation, and; (7) gain a
deeper appreciation for the complexity and nuance of soils and soil organisms. I will distribute
specific guidelines for the research project early in the semester.
Graduate seminars
Later in the semester we will be exploring various compelling and contemporary themes in soil
ecology through discussions of recent publications about the topics. During these class periods,
each of you will work in pairs to structure and lead a one-hour graduate seminar discussion about
a relevant paper of your choice pertaining to your chosen topic. Just prior to the midterm exam
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you will choose your seminar topic and I will distribute specific guidelines for leading an
effective seminar.
VARIOUS COURSE REFERENCES
General references
Bardgett, R.D. and D.A. Wardle. 2010. Aboveground-belowground Linkages: Biotic
Interactions, Ecosystem Processes, and Global Change. Oxford University Press, USA.
Bardgett, R.D. 2005. The Biology of Soil: A Community and Ecosystem Approach. Oxford
University Press, USA.
Baskin, Y. 2005. Under Ground: How Creatures of Mud and Dirt Shape Our World. Island Press,
Washington, D.C.
Brady, N.C. and Weil, R.R. 1998. The Nature and Property of Soils 12th edition. Prentice Hall,
Upper Saddle River, NJ.
Buol, S.W., Southard, R.J., Graham, R.C., and McDaniel, P.A. 2003. Soil Genesis and
Classification (5th ed.). Iowa State Press, Ames, IA.
Coleman, D.C., Crossley, D.A., and Hendrix, P.R. 2004. Fundamentals of Soil Ecology (2nd ed.).
Academic Press, San Diego, CA.
Glanz, J. 1995. Saving our Soil: Solutions for Sustaining Earth’s Vital Resource. Johnson Books,
Boulder, CO.
Hillel, D. 1991. Out of the Earth: Civilization and the Life of the Soil. University of California
Press, Berkeley, Los Angeles, CA.
Killham, K. 1994. Soil Ecology. Cambridge University Press, Cambridge, UK.
Kormondy, E.J. 1996. Concepts of Ecology 4th edition. Prentice Hall, Upper Saddle River, NJ.
Lal, R. and Stewart, B.A. (eds.) 2009. Soil Quality and Biofuel Production. CRC Press.
Logan, W.B. 1995. Dirt: The Ecstatic Skin of the Earth. Riverhead Books, The Berkeley
Publishing Group, NY, NY.
Paul, E.A. and Clark, F.E. 1996. Soil Microbiology and Biochemistry. Academic Press, San
Diego.
Schinner, R., Ohlinger, R., Kandeler, E., and Margesin, R. (eds.). 1996. Methods in Soil Biology.
Springer-Verlag, Berlin.
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Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change (2nd ed.). Academic
Press, San Diego.
Stewart, A. 2004. The Earth Moved: On the Remarkable Achievements of Earthworms.
Algonquin Books of Chapel Hill, Chapel Hill, NC.
Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G., and Zuberer, D.A. (eds.). 1999. Principles and
Applications of Soil Microbiology. Prentice Hall, Upper Saddle River, NJ.
Tate, R.L. 1995. Soil Microbiology, John Wiley & Sons, Inc., NY.
USDA Soil Conservation Service and NH Dept. of Environmental Services Water Supply and
Pollution Control Division. 1991. Soil Manual for Site Evaluations in New Hampshire (2nd
ed.). Rockingham County Conservation District, Exeter, NH.
Wardle, D. 2002. Communities and Ecosystems: Linking the Aboveground and Belowground
Components. Princeton University Press, Princeton, NJ and Oxford, UK.
White, R.E. 2006. Principles and Practice of Soil Science: The Soil as a Natural Resource (4th
ed.). Blackwell Publishing, Malden, MA, Oxford, UK, Victoria, Australia.
Soil-specific scientific journals (will be useful for your research projects)
Agricultural Systems
Applied Soil Ecology
Biology and Fertility of Soils
Canadian Journal of Soil Science
Communications in Soil Science and Plant Analysis
Journal of Soil Science
Mycorrhiza
Plant and Soil
Soil Biology and Biochemistry
Soil Science Society of America Journal
Scientific journals that are not soil-specific, but which publish papers about soils
Canadian Journal of Botany
Canadian Journal of Forest Research
Ecological Applications
Ecological Monographs
Ecology
FEMS Microbial Ecology
Forest Science
Frontiers in Ecology and the Environment
Journal of Applied Ecology
Microbial Ecology
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Microbios
Natural Areas Journal
Nature
Oecologia
Restoration Ecology
Ecological Restoration
Science
Trends in Ecology and the Environment
Fun soil websites
USDA soil surveys on the web: http://websoilsurvey.nrcs.usda.gov/app/HomePage.htm
Biological Soil Crusts: http://www.soilcrust.org/
Microbe World: http://www.microbeworld.org/mlc/
Microbe Zoo: http://commtechleb.msu.edu/sites/dlc-me/zoo/
General microbiology: http://www.microbes.info/
Fungi: http://www.wisc.edu/botany/fungi/volkmyco.html
More fungi: http://botit.botany.wisc.edu/toms_fungi/
Mycorrhiza Information Exchange: http://mycorrhiza.ag.utk.edu/
Famous Protozoa Posters: http://www.mbl.edu/html/LEUCKART/index.html
Tree of Life phylogenies: http://phylogeny.arizona.edu/tree/phylogeny.html
Mites: http://www.uq.edu.au/entomology/mite/mitetxt.html
Collembola and springtails: http://www.ams.rdg.ac.uk/zoology/hopkin/
Nematodes: http://nematode.unl.edu/Wormhome.htm
USDA Soil Biology Primer:
http://soils.usda.gov/sqi/soil_quality/soil_biology/soil_biology_primer.html
Various soil ecology images and videos: http://www.agron.iastate.edu/~loynachan/mov/
Learning disabilities and special needs
In accordance with Section 504 of the Rehabilitation Act of 1973, the Americans with
Disabilities Act, and simple justice and decency, AUNE does not exclude or discriminate against
otherwise qualified students with disabilities. Students with physical or learning disabilities that
are diagnosed by a qualified professional and disclosed to the Student Disability Services
Coordinator may request and receive reasonable accommodations that will allow them to
participate in their graduate program fully. If you have a documented learning disability, need
special accommodation to optimize your learning, and/or need special accommodation for any
class activity, please talk with me as soon as possible. This information will remain
confidential. For more information, please contact Fran Ziperstein, Director of Disability
Services, at 603-283-2438 or by email at fziperstein@antioch.edu.
An invitation
Antioch New England Graduate School is unique in its ability to attract students from myriad life
experiences. This creates a wonderful opportunity to learn from each other as we earnestly and
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respectfully discuss course material and as we sort through our contributions to making the Earth
a better place to live for all living beings. This diversity of life experiences also means that
students will inevitably experience course material differently; this same material may at once be
very difficult to some and be review to others. It is important to me that each of you is
challenged to integrate new material and ways of seeing into your worldview and into your
professional aspirations. Please communicate with me throughout the semester about how you
are experiencing the course material and its presentation. If you do not understand a term,
definition, or concept, please let me know. Conversely, if this material is familiar to you and you
are not sufficiently challenged, please see me so we can find ways to enhance your learning
experience.
Remember: the first three letters of ‘fungi’ are ‘fun’!
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