Dept. Name Land, Water, and Environment

Soil Microbiology

University of Jordan Faculty of Agriculture Dept. Name Land, Water, and Environment Semester Second Semester 2012/2013 Course Title Soil Microbiology Course Code 0644324 Prerequisite Course Coordinator Badarneh Instructor

Name Office Number Office Phone E-mail Dr. Deifallah Badarneh 108 22444 [email protected]

Course Objectives:

The course aims to introduce to the students one of the most important residents of the soil with regarding to the following topics:

1) History and development of soil microbiology 2) Cell structure, composition, requirement for growth 3) Modes of ATP generating metabolism 4) Classification of based on their requirement to carbon and energy source, temperature, and oxygen 5) Ecology of the major groups of micro-flora and their functions in soils: a-bacteria b-actinomycetes c-fungi d-algae 6) Growth curve of bacteria and population development 7) Biogeochemical cycle of: a-carbon b-nitrogen

Learning outcomes:

Successful completion of this module should lead to the following outcomes: A-Knowledge and Understanding :

Student should be able to:

1- Know how the microbial world was discovered and it has been developed 2- Understand the microbial cell requirement and its growth 3- Understand how the microorganisms generate energy for their survival 4- Describe the environmental factors influencing the abundance, activities and functions of microorganisms in soils 5- Describe the role of microorganisms in the biogeochemical cycles of carbon and nitrogen 6- Understand the contribution of these microorganisms in causing or correcting the environmental problems

B-Intellectual skills-with ability to:

1- Properly utilizing the microscope to identify microorganisms in soil 2- Learn the different methods of sterilizing, glassware, media,…etc 3- Carry out series of dilution 4- Learn technique of staining bacteria 5- Enumerate the heterotrophic, bacteria, fungi and actinomycetes 6- Enumerate the autotrophic bacteria (Nitrosomonas) 7- Measuring the microbial activities through repiration and mineralization

Laboratory

Lab attendance is mandatory. Lab work will be performed in teams, but write-ups and assignments are to be done INDEPENDTLY. If there is “shared work” your grade will be based SOLELY on your exams. You MUST ATTEND and PARTICIPATE in lab if you wish to pass the class. Most lab assignments are due at the beginning of the next lab except some which are due later. Lab cleanliness is essential. You are responsible for cleaning your lab equipment and work area, Anyone leaving them dirty or untidy will lose some mark from the final lab mark. Absence from a quiz or mid-term test will be excused only with a valid medical certificate. Sworn affidavits will not be accepted.

Teaching Methods:

Duration: 16 weeks in a semester, equivalent to 32 hours in total. Lecture : 2 lectures per week (50 min ea.) Lab : 3 hours per week (equivalent to 1 hour lecture)

Grading: Midterm exam = 30% Lectures = 25 Lab = 05% Quizzes = 05 Lab reports = 05% 2nd exam = 10% Final (comprehensive) = 40% Final (lab) = 10%

SYLLABUS TOPICS

Week Topic

1+2 Introduction: a) discovery of the microbial world. b) development of soil microbiology.

3+6 Microbial cell growth: a) nutrients demand and functions in the microbial cell. b) generation of ATP in the organisms. - substrate level phosphorylation - electron transport phosphorylation. - photophosphorylation. c) modes of ATP generating metabolism. - fermentation. - respiration. - photosynthesis. -enzyme 4/4 Midterm Exam 7/4/2013

7+8 Diversity of soil microorganisms: a) Introduction. b) Bacteria. - distribution & abundance in soils. - environmental influences. 9+10 c) Actinomycetes: - interrelation with fungi and bacteria. - environmental influences. - activities & functions. 11+12 d) Fungi: - distribution and abundance. - environmental influences. - persistence in soils. - function and activities.

13+14 f) Algae: - groups. - ecology. - environmental influences. - function and activities.

15+16 Transformation of organic nitrogen in the soil: a) nitrogen cycle b) nitrogenous compounds of organic material c) nitrogen mineralization d) nitrogen immobilization e) nitrification. - environmental influences. - microorganisms involved. - nitrate pollution. f) denitrification. .

REFERENCES:

1-Alexander,M.1977. Introduction to soil microbiology. John Wiley and Sons. New York. 2-Mclaren, A.D.,and G.H.Peterson.1967. Soil biochemistry Edward Arnold (Publishers) LTD., London. 3-Stevenson, F.J. (ed.) .1982. Nitrogen in soils . Agronomy 22: Am. Soc. Of Agron, Madison, Wis. 4-Sylvia, D.M., Peter G.H., Jeffry J.F. and David A.Z. 2005. Principles and applications of soil microbiology. Pearson Pritce Hall. Upper Saddle River, New Jersey. 5-Madigan, T.M., John M.M. and Jack P. 2005. Brock biology of microorganisms.(10 th. ed.). Printice Hall. Pearson Education International. 6-Tortora, G.J Berdell R.F. and Christine L.C.1992. Microbiology an Introduction. `4th (ed.) The Benjamin Cummings Publishing Company INC.