SOIL MICROBIOLOGY – SOIL 476

COURSE SYLLABUS
SPRING SEMESTER 2017

Instructor: Dr. Nicole Pietrasiak Office-hours:

Office: Room N328, Skeen Hall Mo and Fr 1.00 pm -2.00 pm (Email first
Tel: (575) 646-1910 if you’re making a special trip to campus)
Email: npietras@nmsu.edu or by appointment

CLASS SCHEDULE:
When: M, W, F, Jan 18 - May 12 at 11:30 - 12:20 am Where: Skeen Hall W122

PREREQUISITE:
The prerequisite for this class is SOIL 252. To be completely prepared for this class a course taken in
Microbiology is also useful but not required.

COURSE OVERVIEW AND OBJECTIVES:

Microbes are the hidden players in the environment. They are numerous and encompass highly diverse
lineages. Microbes play crucial roles in biogeochemical cycling, soil gas exchange, nutrient status, and
food web interactions. The goal of SOIL 476 is to present a broad overview of the microbial diversity,
physiology, and ecosystem services in soils. The course content will mainly be geared towards general
ecological phenomena and processes of soil microbes rather than targeting specific aspects of
microbiology in agronomy or plant pathology (if you are interested in those topics then see classes in the
EPPWS Department such as Fungal Biology, Diagnosing Plant Disorders, Plant Pathology).

Specific learning goals:

1) Distinguish major groups of microbial organisms.
2) Gain a basic understanding of the current methodology used for surveying soil microbial
diversity.
3) Understand the environmental factors influencing microbial distribution and abundance.
4) Describe intra-specific interactions of microbes as well as interspecific relationships with other
organismal groups.
5) Gain knowledge of the microbial roles in elemental cycling and transformation, with a particular
focus on carbon, nitrogen, and phosphorus cycling.
6) Obtain, read, understand, and critically evaluate primary literature on diverse topics related to
Soil Microbiology.
7) Develop skills in oral and written communication.

REQUIRED TEXT BOOK:

Soil Microbiology, Ecology, and Biochemistry, Paul, E.A., 4th ed. New and used textbooks are available at
the NMSU Bookstore, online, or in Zuhl Library.

SUPPLEMENTAL RESOURCES:
The following text books are useful to understand basic concepts of soil science or microbiology.
• Introduction to Soil Science: Elements of the Nature and Properties of Soils. Brady, N.C. and R.R. Weil
(3rd edition preferred but accept any edition) Prentice Hall.
• Introduction to Microbiology: Brock Biology of Microorganisms. Madigan, M.T. et al. (14th edition
preferred) Prentice Hall.
You are responsible for regularly checking CANVAS for course material. I will post lectures, additional
reading assignments, assignment guidelines, links to useful sites and tutorials, as well as other material.
There are computer labs around campus with printers for your use. If computer access and printing is a
problem, let me know immediately so that other arrangements can be made to facilitate your learning. For
technical help and locating resources, see http://studenttech.nmsu.edu/computer-labs/

ATTENDANCE:
Attendance in lecture is vital if you want a good grade. When class attendance is noticeably low, I will
start administering “pop” quizzes or in-class exercises. My goal is to keep you engaged and learning, not
just passively sitting through lectures; but in order to accomplish this, everyone has to come to class
prepared by having read and reviewed the material in advance. I also encourage you ask questions
pertaining to the content especially when something is unclear. I may not always have an answer but will
try my best to point you in the right direction or refer you to pertinent resources.

QUIZZES AND EXAMINATIONS:

Scheduled quizzes will be given roughly every other week. Missed quizzes cannot be made up.
Quizzes will usually be given at the beginning of class. They will include questions pertaining to the
lecture material (lecture slides) but can also include a few questions about assigned readings/viewings
(from the textbook and/or posted on Canvas). The lowest quiz grade will be dropped. If you arrive after a
quiz has been collected for the day, you may not take it. The final exam is comprehensive and will cover
the entire course, but will emphasize the latter half of the class. Make-up exams are only given if you
prove that your absence had a valid reason (see Attendance section above). Also, I must be able to read
your writing, so please be neat and write legibly.
The midterm exam will be on March 8 and the final will be on May 10. If you will be out of town for
an approved University activity on that day, please notify me in advance of the exam. Absence during an
exam will only entitle you to a make-up opportunity if you provide a written verification of a valid reason
(medical, traffic accident or a major family emergency) within one week of your absence.

ASSIGNMENTS:
Class assignments will focus on strengthening oral and written communication skills in science.
Specifically, assignments will involve 1) reading and assessing primary literature of current topics in Soil
Microbiology, and 2) presenting a poster on a chosen subject in Soil Microbiology.
Assignment 1) Students are required to read 6 assigned research articles obtained from the scientific
literature and actively participate in the paper discussions. For each paper two students will be assigned to
be the discussion leaders. One student will present positive aspects of the research paper and the other
student will discuss drawbacks. The other students are required to submit a list of comments and
questions pertaining to the research article. Thus, for the total of 6 discussions held in this course each
students will be an engaging discussion leader twice, will participate in discussion when not the
moderator, plus will submit 4 high level comments and question papers to receive full credit. Remember,
a portion of your grade will be based on how well you keep the discussion going, as well as on your
participation in discussions you are not leading.
Assignment 2) Each student will be assigned to a team. Each team is responsible to collect background
information and case studies related to a chosen subject in Soil Microbiology. The team then is required
to design and present a poster at the end of the semester. The poster presentations will be peer-reviewed.
If you cannot turn in your assignment in class on the day it is due, you may leave it in my
department office mailbox in Skeen Hall 127N by 5 pm. Do not put your assignments under my office
door – they can easily get lost.

LATE ASSIGNMENT POLICY:

My late assignment policy only applies to assignment 2. My goal is to give you adequate time and
instruction to complete your assignments. Unlike the “real world” I may accept late assignments up to 5
days after the due date unless other arrangements are made. However, ten percent will be deducted
for each day any assignment is handed in late; no credit will be given to assignments handed in
after 5 days. If you fail to submit the papers required for assignment 1 you will receive zero points.

EXTRA CREDIT:
Occasionally there will be additional opportunities to present fun facts on a topic in class, attend seminars,
films, help with outreach activities, etc., that may provide some learning opportunities and “extra credit”.
These will be announced in class and if necessary posted on Canvas along with the requirements needed
to receive credit. If you have ideas for such activities, please let me know via email and include any
details. Cumulative extra credit can comprise up to 5% of your total points.

POINT BREAKDOWN:
Midterm Examination 100 pts
Bi-Weekly Quizzes (Best 5 of 6) 5 @ 20 pts
Reviewing journal article and leading paper discussions 2 @ 25 pts
Submitting comments and questions about journal article s 4 @ 10 pts
Poster Presentation 60 pts
In-Class activities, participation during lecture and discussions 50 pts
Final Examination (Comprehensive) 150 pts
Total 550 pts
Extra credit 30 pts

GRADING:

A+ >99% C 73-76.95%
A 93-98.95% C- 70-72.95%
A- 90-92.95% D+ 67-69.95%
B+ 87-89.95% D 63-66.95%
B 83-86.95% D- 60-62.95%
B- 80-82.95% F <60%
C+ 77-79.95%

You will be responsible for keeping a record of your grades earned in the class. Your final grade will be
posted through BANNER. However, I also will keep records of your points earned in an excel
spreadsheet. I will not post your grades in a public location. Other students will not be able to see your
grades unless you give them your login and password identification. To comply with FERPA laws, all
students are required to use their NMSU email accounts for contact and information about grades or other
sensitive information. Faculty are not supposed to send email to non-NMSU accounts of students.
If you feel that graded material (exam, assignment, or quiz) has been incorrectly tallied, please bring it to
my attention immediately. If you have a disagreement with the amount of partial credit you receive on an
exam question or assignment, explain your case in writing and submit for a response within one week
of the return of your exam or assignment. Include your original assignment or exam as well. You will
only get full credit if you answer the entire question.

SOIL 476L:
The lab is a separate 1 credit course. It’s a fun lab course with hands-on experience that helps explain
many of the lecture concepts, so I encourage you to enroll if you have the time and interest.

GENERAL INFORMATION:
My goal is that everyone in the class, including myself, will be treated with respect and dignity. I will try
my best to make the class an enjoyable and worthwhile investment of your time and energy and I expect
you to do your part by studying, coming to class prepared, and actively participating in class. Please
silence your cell phones while in class. No texting or taking calls is permitted during lectures or
exams; you cannot use your phone as a calculator in exams.

DISCRIMINATION AND DISABILITY ACCOMMODATION:

Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act Amendments Act
(ADAAA) covers issues relating to disability and accommodations. If a student has questions or needs
accommodation made in the classroom (all medical information is treated confidentially), contact:
Trudy Luken, Director, Student Accessibility Services (SAS), Corbett Center Student Union, Rm. 208
Phone: (575) 646-6840, E-mail: sas@nmsu.edu, Website: http://sas.nmsu.edu/

Student Responsibilities: Register with SAS and obtain accommodation documents early in the
semester; Deliver the completed accommodation and testing form(s) to the instructor(s) within the first
two weeks of beginning of classes (or within one week of the date services are to commence); Retrieve
the signed form(s) from faculty and return these to SAS within (5) days of the receipt from faculty and at
least one week before any scheduled exam; and, Contact the SAS Office if the services/accommodations
requested are not being provided, not meeting your needs, or if additional accommodations are needed.
Do not wait until you receive a failing grade. Retroactive accommodations cannot be considered.

NMSU policy prohibits discrimination on the basis of age, ancestry, color, disability, gender identity,
genetic information, national origin, race, religion, retaliation, serious medical condition, sex, sexual
orientation, spousal affiliation and protected veterans status. Furthermore, Title IX prohibits sex
discrimination to include sexual misconduct: sexual violence (sexual assault, rape), sexual harassment and
retaliation. For more information on discrimination issues, Title IX, Campus SaVE Act, NMSU Policy
Chapter 3.25, NMSU’s complaint process, or to file a complaint contact:
Lauri Millot, Title IX Coordinator or Agustin Diaz Title IX Deputy Coordinator, Office of Institutional
Equity (OIE), O’Loughlin House, 1130 University Avenue, Phone: (575) 646-3635, E-
mail: equity@nmsu.edu, Website: http://eeo.nmsu.edu/

Other NMSU Resources:

NMSU Police Department: (575) 646-3311 www.nmsupolice.com
NMSU Police Victim Services: (575) 646-3424
NMSU Counseling Center: (575) 646-2731
NMSU Dean of Students: (575) 646-1722
For Any On-campus Emergencies: 911
OTHER HELP:
The Center for Academic Success is a valuable resource center for help in note taking, test taking, time-
management and other useful academic skills. The website is very informative (http://ssc.nmsu.edu/) or
you can visit in person at Corbett Center, Room 148 (Aggie Underground). Also, I am happy to see you
during office hours and provide whatever help I can. I look forward to working with all of you!
ACADEMIC AND NON-ACADEMIC MISCONDUCT:
The Student Code of Conduct defines academic misconduct, non-academic misconduct and the
consequences or penalties for each. The Student Code of Conduct is available in the NMSU Student
Handbook online: http://studenthandbook.nmsu.edu/. Academic misconduct will not be tolerated and
will result in severe penalties including an F in the class. This means not copying your classmates’
answers and no plagiarism. Academic misconduct is explained here:
http://studenthandbook.nmsu.edu/student-code-of-conduct/academic-misconduct/.
ANTICIPATED LECTURE SCHEDULE*
Date Topic
18 January Introduction to course
20 January History
23 January Dirt the Movie
25 January Soil as Habitat
27 January Soil as Habitat
30 January Microbial Metabolism & Physiology
1 February Microbial Metabolism & Physiology
3 February Microbial Metabolism & Physiology
6 February Research Paper Discussion # 1
8 February Microbial Genetics
10 February Microbial Diversity: Bacteria
13 February Microbial Diversity: Bacteria
15 February Microbial Diversity: Cyanobacteria – Guest Lecturer: Truc Mai
17 February Research Paper Discussion # 2 *** PROPOSED POSTER TOPIC DUE***
20 February Microbial Diversity: Archaea
22 February Microbial Diversity: Eukaryotic Algae
24 February Microbial Diversity: Fungi – Guest Lecturer: Dr. Soumaila Sanogo
27 February Microbial Diversity: Fungi
1 March Microbial Diversity: Fauna - Guest Lecturer: Dr. Paul De Ley
3 March Research Paper Discussion # 3 ***PROPOSED POSTER TITLE DUE***
6 March Microbial Ecology – Basics, Communities
8 March MIDTERM EXAM
10 March Microbial Ecology –Intraspecific Interactions
13 March Microbial Ecology –Interspecific Interactions
15 March Microbial Ecology – Interspecific Interactions
17 March Research Paper Discussion # 4 **ANNOTATED BIBLIOGRAPHY DUE**
20-24 March Spring Break
27 March Elemental transformation and cycling: Carbon
29 March Elemental transformation and cycling: Carbon
31 March Elemental transformation and cycling: Carbon
3 April Elemental transformation and cycling: Carbon
5 April Research Paper Discussion # 5 *** POSTER ABSTRACT DUE***
7 April Elemental transformation & cycling: Nitrogen
10 April Elemental transformation & cycling: Nitrogen
12 April Elemental transformation & cycling: Nitrogen **POSTER DRAFT #1 due**
14 April Spring Holiday
17 April Elemental transformation and cycling: Nitrogen
19 April Research Paper Discussion # 6
21 April Elemental transformation and cycling: other elements
24 April Elemental transformation and cycling: other elements
26 April Management of Soil Microbes ***FINAL POSTER DRAFT DUE***
28 April Management of Soil Microbes
1 May Additional topics of relevance
3 ***POSTER PRESENTATION AND PEER REVIEW***
5 Class synthesis and review
10 FINAL EXAM
* Lecture schedule is subject to change.