SOS 4303C / 5305C - Syllabus

 

Andy Ogram

Abid Al Agely

 

avo@mail.ifas.ufl.edu

aaag@ufl.edu

 

392 1951 EXT 211

392 1951 EXT 220

 

Office Hours: Following class lecture or by appointment. There is also a web-based forum to provide a convenient mechanism for dialogue among class participants.

TEXT:

·               Robert L Tate III; editor. 2000. Soil Microbiology, 2nd Edition. John Wiley & Sons Inc, New York.  You may order this book online. 

·         Laboratory Manual (available in  University Copy & More) or download.

DESCRIPTION:

Advance studies, discussions, student oral presentations, and practical laboratories are the topics of the organisms that live in the soil and their activities in the soil ecosystem.  Sessions of these activities will cover the soil as a habitat for organisms, the taxonomy and biology of the soil organisms, the fundamentals of nutrient cycles, soil biology, symbiotic associations, and bioremediation.  Oral presentation will be the student choice of either a review of a current journal article or graduate research that related to class objective.

GOALS:

To gain knowledge of the occurrence and activities of soil microorganisms and their influence on soil productivity and environmental quality. This course is targeted at advanced undergraduate and beginning graduate students who require a comprehensive treatment of the field of soil microbiology.

FORMATS:

3-credit course taught fall semesters in two formats:

·                     On-campus: two lectures (Tues. & Thurs., 9:35-10:25 AM, 2186 McCarty) and one lab (Mon., 3:00-4:55 PM, 2186 McCarty ) per week

·         Off-campus: web-based lecture notes, readings, and threaded discussions. This option is only available to off-campus students. REGISTRATION DETAILS

REQUIREMENTS:

Payment of tuition, World Wide Web access, and the following minimum computer hardware and software—Pentium 150 MHz with 32 MB RAM and 250 MB available hard disk space, SVGA monitor, 28.8 kb modem (v3.4), Windows 95 operating system, and current version of Internet Explorer or Netscape. Off-campus students also need to identify an Exam Administrator.

Prerequisites: Introductory Soil Science, Biology, or Microbiology.

RESOURCES:

Both the on-campus and off-campus sections rely on interactive computer technologies. Registered students will use their gator link user name and password to access the course homepage located at WebCTVista 

The course web site has links to:

·                     detailed lecture and laboratory schedule with associated readings

·                     copies of all presentations and handouts used in lecture and laboratory

·                     distance education supplement for students taking the course via the web

·                     supplementary reference materials (some with PDF downloadable files)

·                     threaded discussion forum

·                     glossary of terms

·                     related on-line resources

Student Responsibilities:

Students are expected to attend lectures and laboratories, and participate in an online bulletin board.  Attendance in the laboratory is especially critical because it is difficult, if not impossible, to make up missed exercises.  Exams and assignments are due as follows.  Make-up exams will only be given to those with a valid and documented excuse

Academic Honesty:

As a result of completing the registration form at the University of Florida, every student has signed the following statement: “I understand that the University of Florida expects its students to be honest in all their academic work. I agree to adhere to this commitment to academic honesty and understand that my failure to comply with this commitment may result in disciplinary action up to and including expulsion from the University.”

Software Use:

All faculty, staff and students of the University are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against University policies and rules, disciplinary action will be taking as appropriate.

Accommodations for Students with Disabilities:

Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation.

UF Counseling Services:

Resources are available on-campus for students having personal problems or lacking clear career and academic goals, which interfere with their academic performance. These resources include:

·                     University Counseling Center, 301 Peabody Hall, 392-1575, personal and career counseling;

·                     Student Mental Health, Student Health Care Center, 392-1171, personal counseling;

·                     Sexual Assault Recovery Services, Student Health Care Center, 392-1161, sexual assault counseling; and

·                     Career Resource Center, Reitz Union, 392-1601, career development assistance and counseling.

We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity.

Course Schedule:

 

WEEK

DATE

TOPIC                                                                                                                                                                              

 

1

THU

08/25

INTRODUCTION & OVERVIEW

 

 

MON

08/29

FIELD TRIP & SAMPLING

2

TUE

08/30

Physical and Chemical Boundaries (TB Chapter 1)

 

THU

09/01

Physical and Chemical Boundaries (TB Chapter 1)

 

 

MON

09/05

HOLIDAY LABOR DAY

3

TUE

09/06

Biological Participants (TB Chapter 2)

 

THU

09/08

Biological Participants (TB Chapter 2)

 

 

MON

09/12

Exercise 1 - Initiate mycorrhizal experiment (LM P 8 -13)

4

TUE

09/13

Biological Participants (TB Chapter 2)

 

THU

09/15

Soil Enzymes as Indicators of Ecosystem Status (TB Chapter 6)

 

 

MON

09/19

Exercise 2 - Dilution plating (LM P 14 - 20), Discuss oral presentations

5

TUE

09/20

Microbial Diversity of Soil Ecosystems (TB Chapter 3) check bacterial plates!

 

THU

09/22

Exam I,   Title/Summaries Forms Due

 

 

MON

09/26

Exercise 3 - Microscopy, observe bacteria, Riddell mounts (LM P 21 -32)

6

TUE

09/27

Microbial Interactions and Community Development and Resilience (TB Chapter 7)

 

THU

09/29

Energy Transformation and Metabolic Activities (TB Chapter 4)

 

 

MON

10/03

Exercise 4 - Direct counts, observe fungi (LM P 37 - 38)

7

TUE

10/04

Energy Transformation and Metabolic Activities (TB Chapter 4)

 

THU

10/06

Process Control in Soil (Chapter 5)

 

 

MON

10/10

Exercise 5 - Initiate soil decomposition experiment (LM P 39 - 41)

8

TUE

10/11

Microbial Interactions and Community Development (TB Chapter 7)

 

THU

10/13

Microbial Interactions and Community Development and Resilience (TB Chapter 7)

 

 

MON

10/17

Exercise 6 - Initiate Rhizobium experiment (MP 42 -44) FIRST LAB REPORT DUE

9

TUE

10/18

The Rhizosphere/Mycorrhizosphere (Chapter 8)

 

THU

10/20

The Rhizosphere/Mycorrhizosphere (Chapter 8)

 

 

MON

10/24

Exercise 7 - Initiate algae MPN, phosphatase assay (LM P 37 - 49)

10

TUE

10/25

Exam ii

 

THU

10/27

Introduction to Biogeochemical Cycles (TB Chapter 9)

 

 

MON

10/31

Exercise 8 - Initiate respiration experiment (LM P 51 - 56)

11

TUE

11/01

The Carbon Cycle (TB Chapter 10)

 

THU

11/03

The Carbon Cycle (TB Chapter 10)

 

 

MON

11/07

Collect WEEK 1 Respiration data

12

TUE

11/08

Nitrogen cycle (TB Chapters11, 14)

 

THU

11/10

 

 

 

MON

11/14

Collect WEEK 2 Respiration data

13

TUE

11/15

Nitrogen Fixation (TB Chapters 12, 13)

 

THU

11/17

Principles of Bioremediation (TB Chapter 16)

 

 

MON

11/21

Exercise 9 - DNA analyses (LM P 57 - 66)

14

TUE

11/22

Sulfur, Phosphorus, and Mineral Cycles (TB Chapter 15)

 

THU

11/24

HOLIDAY THANKSGIVING

 

 

MON

11/28

Collect Mycorrhizal data, Oral Presentations

15

TUE

11/29

Oral Presentations (Continued)

 

THU

12/01

 Exam iii

 

 

MON

12/05

Exercise 10 - Soil rhizosphere (LM P 67 - 68) SECOND LAB REPORT DUE

16

TUE

12/06

Wrap up and evaluation 

 

WED

12/07

END CLASSES

 

17

MON

12/12

Optional Final Exam

 

EXAMINATIONS:

 

SOS 4303

(1st Exam + 2nd Exam + 3rd Exam + Optional Final) * 0.7 + (1st Lab Report + 2nd Lab Report) * 0.3 + Oral presentation * 0.1 (extra credit)

 

SOS 5305

(1st Exam + 2nd Exam + 3rd Exam + Optional Final) * 0.6 + (1st Lab Report + 2nd Lab Report) * 0.3 + Oral presentation * 0.1

Oral and Written ASSIGNMENTS:

·         Optional for SOS 4303 students

·         Distance education students will prepare an online presentation instead of an oral presentation

As a scientist you will be judged largely on your ability to present your research findings in an accurate and lucid manner. We all need practice to improve these skills. Your laboratory reports will provide an exercise in scientific writing (see Lab. Manual for more details). You will also be required to give a 15 minute oral presentation on a topic in Soil Microbial Ecology of particular interest to you (12 min for presentations, 3 min for discussion—typical of a scientific meeting). Please discuss your topic with me in advance. Title/Summary forms will be due toward the end of September. You will research the topic, prepare visual aids (we will discuss options in class), and practice before the actual presentation. You will be judged on the content and organization of your talk.

Grade Scale:

A

> 90

B

89 - 80

C

79 - 70

D

69 - 60

E

< 60