ENVS
164: Projects and Practices in Soil Ecology (5 credits)
Class meetings: 9:50-11:25 am
Tuesdays & Thursdays in 431 ISB (or the lab:468 NS2)
Instructor: Weixin Cheng
Office Hours: 9:45-11:45 am,
Monday at 416 ISB
Email: wxcheng@ucsc.edu; Office phone:
831-459-5317
Course
Caption:
Learning soil ecological principles by carrying out
inquiry-based projects and practices in land ecosystems (agroecosystems,
forests and grasslands). UCSC reserves, farms, gardens and greenhouses are the
default living laboratories for the course. The emphasis is on experiential
learning of practical and technical skills in using soil methods. Prior
enrollment in 161 is preferred. Prerequisite(s): Previous or concurrent
enrollment in ENVS 100/L required, or by permission of instructor.
Course
Evaluation:
The grade of each student is based on evaluations of multiple
individual lab reports (60%) and a synthetic final report (40%) (See detailed
information about the writing of these reports later). The overall grade will
be given based on the overall weighed score percentage of each student using
the following table:
|
Grade |
Total % range |
|
Pass (A+) |
97-100% |
|
Pass (A) |
93-96.9% |
|
Pass (A-) |
89-92.9% |
|
Pass (B+) |
85-88.9% |
|
Pass (B) |
81-84.9% |
|
Pass (B-) |
77-80.9% |
|
Pass (C+) |
73-76.9% |
|
Pass (C) |
69-72.9% |
|
NP (D) |
60-68.9% |
|
NP (F) |
0-59.9% |
Expected
Work Time:
4 hours per week for lab/field demonstrations with
lectures; 4 hours per week for independent field/lab/literature work; 4 hours
per week for preparing preliminary reports; 30 hours for developing and writing
the final synthetic report.
Learning
Outcomes: Through experiential learning projects,
students will learn: (1) how to design a project, (2) how to use both
field-based and lab-based methods in soil ecology, (3) how to evaluate and
synthesize data, and (4) how to write a synthetic report.
Rules
and Notes:
Striving for excellence and maintaining a positive
attitude and cooperative spirit are fundamental to learning and success in the
class. The course schedule (dates, times and the locations) are 100%
fixed. If you anticipate any kind of
conflict or problem, contact Professor Cheng as soon as possible. All students are expected to perform the
required tasks in a timely manner. Late submission of any report will result in
score deduction based on the table below:
Amount of time overdue vs. % score deduction
<2
hours overdue: 5%
2-24.0 hours overdue: 25% score deduction
24.1-48.0
hours 50%
>48 hours overdue: 100% score deduction (zero score)
A request for an incomplete (I) grade will not be
considered except for readily verifiable direct personal emergencies. All class
work that you do has to be your own original work. Cheating and academic
dishonesty of any kind will not be tolerated (see UCSC Academic Integrity
webpage).
Schedule
and outline:
Week 1:
Tuesday lecture—
Introduction (UCSC Campus reserves; Structures and functions of soil biotic and
abiotic components; Start to think about your own project)
Thursday field practice
or lab—Soil samples, sampling, experimental design, and power analysis
Home work—Outlines of
potential project ideas
Readings:
1. Jess Davies. 2017.
The business case for soil. Nature 543: 309-311. https://www.nature.com/news/the-business-case-for-soil-1.21623
2.
G.P. Quinn and M. J. Keough. 2002. Chapter 7 Design and Power Analysis
Week 2:
Tuesday lecture with
field trip—Why and how to measure soil physical properties
Thursday field practice
or lab—Texture, structure and bulk density
Home work—Design of
your project
Readings: Chapters 13,
15, 17 in A Klute edited: Methods of Soil Analysis Part 1
Week 3:
Tuesday lecture with
field trip—Why and how to measure soil temperature and moisture
Thursday field practice
or lab—Data logging, TDR probes and thermal couples
Home work—Summary of
soil abiotic components
Readings:
1. Chapters 21, 37 in A
Klute edited: Methods of Soil Analysis Part 1
2. R.L. Ray et al.
2017. Evaluation and Inter-Comparison of Satellite Soil Moisture Products Using
In Situ Observations over Texas, U.S. Water 9(6): 372; doi:10.3390/w9060372
http://www.mdpi.com/2073-4441/9/6/372
Week 4:
Tuesday lecture with
field trip—Primary sources of soil organic matter (roots, litter, etc)
Thursday field practice
or lab—Field glass rhizotrons and litter baskets
Home work—Why roots
build more SOM than aboveground litter?
Readings:
1.
Rasse, D. P. et al. 2005. Is soil carbon
mostly root carbon? Mechanisms for a specific stabilisation. Plant Soil 269,
341–356.
2.
Kong, A. Y. Y. and Six, J. 2010. Tracing root vs. residue carbon into soils
from conventional and alternative cropping systems. Soil Sci. Soc. Am. J. 74,
1201–1210.
3.
Jackson, Robert B. and Lajtha, Kate and Crow, Susan E. and Hugelius, Gustaf and
Kramer, Marc G. and Piñeiro, Gervasio. 2017. The Ecology of Soil Carbon: Pools,
Vulnerabilities, and Biotic and Abiotic Controls. Annual Review of Ecology,
Evolution, and Systematics 48: 419-445.
Week 5:
Tuesday lecture with short
lab—Soil microbes: the unseen majority in biodiversity
Thursday field practice
or lab—Measuring soil microbial biomass (fumigation and SIR)
Home work—Relate microbes
to soil processes and ecosystem functions (a mini-review)
Readings:
1. Chapter 36 in R.W.
Weaver et al. edited: Methods of Soil Analysis Part 2
2.
Graham, E.B. et al. 2017. Microbes as Engines of Ecosystem Function: When Does
Community Structure Enhance Predictions of Ecosystem Processes? Frontiers in
Microbiology, https://www.frontiersin.org/articles/10.3389/fmicb.2016.00214/full
Week 6:
Tuesday lecture with
field trip—Soil fauna and their functional roles
Thursday field practice
or lab—Methods of quantifying soil fauna
Home work—Mid-quarter
project report
Readings:
1. Chapters 22, 23, 24
in R.W. Weaver et al. edited: Methods of Soil Analysis Part 2
2. Lavelle, P. et al.
1997. Soil function in a changing world: the role of invertebrate ecosystem
engineers. http://agris.fao.org/agris-search/search.do?recordID=FR1999003405
Week 7: Respiration
Tuesday lecture with
field trip—Methods for soil respiration: a personal narrative
Thursday field practice
or lab—IRGA for CO2, CO2 traps, field chambers and mesh
cores
Home work—Quantitative
relationship between soil CO2 and the global carbon cycle
Readings:
1. Chapters 38 in R.W.
Weaver et al. edited: Methods of Soil Analysis Part 2
2. Lou, Y and Zhou X.
2006. Chapter 2: Importance and roles of soil respiration
Week 8:
Tuesday lecture with
field trip—Litter and SOM decomposition
Thursday field practice
or lab—litter bags and mesh cores (put out at the start of the quarter)
Home work—Write final
report
Readings:
1. Parton et al 2007. Global-scale
similarities in nitrogen release patterns during long-term decomposition.
Science 315: 361-364. http://science.sciencemag.org/content/315/5810/361
Week 9:
Tuesday lecture with
field trip—C:N ratio and the balance act of soil N dynamics
Thursday field practice
or lab—N responses to compost and cover crop incorporation
Home work—Write final
report
Readings:
1. Chapters 42 in R.W.
Weaver et al. edited: Methods of Soil Analysis Part 2
2. Schimel JP and
Bennett J. 2004. Nitrogen mineralization: Challenges of a changing paradigm.
Ecology, 85: 591–602.
http://onlinelibrary.wiley.com/doi/10.1890/03-8002/abstract
Week 10: Quality and Sustainability
Tuesday lecture with
field trip—Soil Quality and Sustainability
Thursday field practice
or lab—Presentation and discussion of project results
Home work—Finish
project report
Readings:
NATURE collection--
Soil and its sustainability, https://www.nature.com/collections/fyyphcfxjb
Writing
Reports:
Students
will individually write their own reports.
The reports should provide a critical analysis of a specific issue. Each
report should include extensive research, be well-organized, and be proof-read,
and should include the following sections:
1. A 1-2 pages general introduction
to the problem being addressed to provide a context for your paper.
2. A paragraph that clearly states
the goal of this paper and lays out your “roadmap” for the paper. In other words, what question are you
addressing and how is your paper structured to address this question?
3. A Materials & Methods section
(sites, samplings, measurements, statistical analysis, etc)
4. 5-10 pages presenting the
research you have done on your topic in an organized manner.
5. 1-2 page conclusion section in
which you summarize the 3-4 specific conclusions that stem directly from the
research you present
The
report should have page numbers and should be double spaced. Be sure to spell-check and proofread your
paper, and include a list of references cited.
The final report: The final report is due at 5:00 pm on the last day of class for the
quarter, and should be 15-20 pages double spaced. The final report will be graded on
thoroughness of research, organization, writing style, and critical analysis.
Some notes about writing the reports:
The
final report may have the following characteristics:
Process - Developing research papers in Environmental Studies
follows an iterative process.
Critical
Analysis – The final project report requires
interpreting data from a range of sources collected using differing
methodologies. The information must be
compared, weighed and interpreted. Just because a book or article is published
does not mean that its conclusions are well supported. Any conclusions drawn in the paper must be
substantiated by the material presented whether it is primary data or a review
paper. It is always important to
distinguish between the opinions of others, your conclusions based on the
information presented, and your speculations and opinions.
Style - Good
organization and writing style is essential to help the reader understand your
main points. Start with an outline and
use it to organize your ideas. Once you
have done most of your research, you may write it in reverse sequence. In other words, first think about your
conclusions; then consider the information needed to support those conclusions;
then write an introduction that gives your reader only the relevant background
information to the rest of your report.
In short, make sure there is coherence between the different sections of
your paper. Do not introduce new topics
in the conclusion.
Citing and Plagiarism - Identifying ideas or quoting passages to
strengthen arguments and to acknowledge sources is essential and is the
hallmark of scholarly work. Any writing which is directly copied or any idea
not your own must be identified and cited. Not to do this is plagiarism, and
is unethical. Essentially this is how scientific and scholarly writing
differs from journalism: sources must always be disclosed for the purpose of
verification. Acknowledgments must also be made for maps, tables, figures, and
text, if they are copied. See final page
of this handout for citation format guidelines.
SOURCES
FOR INFORMATION:
Scholarly
(peer-reviewed) journal articles
– Most researchers publish their work in journals where the articles are
reviewed by their peers. This review
provides a certain degree of quality control for their work. Nonetheless, readers still need to review the
work thoughtfully to determine if they agree with conclusions and supporting
evidence. A wide range of journal
databases available to UC faculty and students are listed at http://guides.library.ucsc.edu/az.php. Many journal
articles are now available electronically, making access even easier (http://library.ucsc.edu/find/online-journals ).
Popular
articles – Popular magazines publish
articles written by professional writers (rather than experts in a particular
field) and are written for the lay reader.
They are not generally used as references for research papers.
Books – Books are published by many publishing companies for a
wide range of audiences. They vary a
great deal in the degree and type of review.
Most books for academic audiences are peer reviewed. The UCSC book holdings (cruzcat) and the
University of California holdings (melvyl) are accessible through the UCSC
library web site http://library.ucsc.edu/. Books at other UC
campuses can be requested through Interlibrary loan, but this requires allowing
sufficient time (at least a week) to get these sources. It can be harder to find books on a specific
topic as the search engines only search words in titles rather than in
abstracts.
Government
documents – All government documents owned by
UCSC can be found using Cruzcat. For
some regional issues you may need to contact specific government agencies to
determine where you can access specific documents, such as Environmental Impact
Statements.
Internet – The internet may be the only source of
information, but should not be the primary source of support for papers. Be critical of sources found on the
Internet. Think about who produced the information, their credentials, and
their agenda. Since there is no overall quality control it is up to you to
check the reliability of the information and whether or not it is refereed. The
internet is also problematic because it is constantly changing, so a source you
cite may not be there if a reader wants to corroborate your source. If you end up using material from the
Internet it needs to be cited in your bibliography, including the url, title,
author, date posted, and date accessed. Give preference to refereed
publications such as books and journal articles rather than those found on the
Web.
Personal
interviews – Personal interviews may provide
key information on some environmental issues, but should be used judiciously to
answer questions that cannot be answered by published material. Also, as discussed earlier in the quarter,
when approaching individuals be well organized, polite, and respectful of their
time and the favor they are doing for you.
Citing
References – a refresher
Why
cite references?
1.
You need to give credit to people for ideas and information.
2.
Your points are much stronger if you back them up with studies illustrating or
expert opinion supporting them.
In
text citations
Ex.: Low seed dispersal commonly limits tropical forest recovery
(Cubiña and Aide 1994, Holl et al. 2000).
Ex.: Holl and Howarth (2000) report that restoration costs are
often underestimated.
Ex:
Development projects at UCSC often poorly mitigate for cumulative impacts (K.
Holl, UCSC professor, pers. comm.).
Ex: Efforts
to control pike in Lake Davis have been unsuccessful (SLDTF 2000).
Format
for citing references
Peer-reviewed
journal article
Holl, K. D., M. E. Loik, E. H. V. Lin, and I. A. Samuels.
2000. Restoration of tropical rain forest in
abandoned pastures in Costa Rica. Restoration Ecology
8:339-349.
Book
Gauch, H. G. Jr. 1982. Multivariate analysis in community ecology.
Cambridge University Press, Cambridge.
Book chapter
Bradshaw, A. D. 1987. Restoration: an acid test for ecology.
Pages 23-29 in W. R. I. Jordan, M. Gilpin, and J. D. Aber (eds)
Restoration Ecology. Cambridge University Press, Cambridge.
Edited book
Pennington, T. D. and E. C. M. Fernandes (eds). 1998. The
genus Inga. Continental Printing, Belgium.
Newspaper article
Knox,
R. 1997. Please don’t dial and drive, study suggests. Boston Globe, 13 February
1997: A1, A17.
Web
pages
Save
Lake Davis Task Force (SLDTF[1]
2000.[2]
Managing northern pike at Lake Davis: a plan for Y2000.
Retrieved January 5, 2004 [3]
from the California Department of Fish and Game web site
<www.dfg.ca.gov/northernpike/mgpike.htm >.
Acknowledgement:
Most of the instructions about writing papers given above are taken from
Professor Karen Holl’s ENVS 190 syllabus previously provided to students in her
class.
[1]If there is no author you can list a document as anonymous, but, in general, if there is no author listed with a document then the credibility of the web site should be considered. If possible, find a more reliable reference.
[2]If there is no date indicating when the web page was posted then put n.d. where the date should go. But, be careful that the information is not outdated.
[3]It is standard practice to include the access date for web pages since they may change.