Description of Individual Course Units
Course Unit CodeCourse Unit TitleType of Course UnitYear of StudySemesterNumber of ECTS Credits
402023112006PROKARYOTIC DIVERSITY-IICompulsory365
Level of Course Unit
First Cycle
Objectives of the Course
In order to make sense of the diversity of organism, it is necessary to group similar organisms together and organize these groups in a non-overlapping hierarchical arrangement. Taxonomy is the science of biological classification. Bacterial taxonomy is rapidly changing due to the acquisition of new data, particularly the use of molecular techniques such as the comparison of rRNA structure and chromosome sequences. This is leading to new phylogenetic classifications. The current edition of Bergey’s Manuel of Systematic Bacteriology is phylogenetically organized and distributes the Bacteria and Archaea among 25 phyla. The aim of this course is to provide detailed description of phyla.
Name of Lecturer(s)
Prof.Dr. Füsun B. UÇAR
Learning Outcomes
1To gain skills in order to understand the systematic categories of Bacteria and Archaea Domains by using genotypic and phenotypic methods during the evolution and to adapt these data to life
2To gain skills in order to establish the relationship between phylogeny and the physiology and reproduction of prokaryotic cells and to categorize them
3To recognize the relationship between the understanding of basic mechanisms of prokaryotic cells and the evolutionary process
4To understand the decomposition process of natural wastes resulting from the use of organic and inorganic compounds by prokaryotic cells as an energy source and to adapt this to life
5To understand the contribution of the members of the Archeae domain living in extreme environments to the nature and humankind
6To recognize the relationship between the understanding of basic mechanisms of prokaryotic cells and the evolutionary process
7To understand how to make use of the members of the Archeae domain in biotechnology and to adapt these data to life
8To understand how to make use of the members of the Archeae domain in biotechnology and to adapt these data to life
Mode of Delivery
Face to Face
Prerequisites and co-requisities
None
Recommended Optional Programme Components
None
Course Contents
A classis of Phototrophic, chemolithotrophic and methanotrophic Proteobacteria; aerobic and facultative aerobic chemoorganotrophic Proteobacteria, morphologically unusual Proteobacteria classis (α, β, γ,) and classis of Δ, ε Proteobacteria physiology, morphology and ecology; Non-Proteobacteria groups: Phylum Aquaficea and Thermotogae, Phylum Deinococcus-Thermus, Phylum Chlamydia, Phylum Planctomyces, Phylum Spirochaetes, Phylum Bacterioides; Low G+C gram-positive bacteria; High G+C gram-positive bacteria; Cyanobacteria; Phylum Chloroflexi, Phylum Chlorobi; hyperthermophilic bacteria; Archaeal cell walls and membranes, genetics and molecular biology, taxonomy, Phylum Crenarchaeota; Phylum: Euryarchaeota, Metanogenes, mechanism of metanogenesis; Halobacteria, physiology, bacteriorhodopsin and rhodopsin-based phototrophy, extreme termophilic S0 metabolizers and sulphate reducing Euryarchaeota.
Weekly Detailed Course Contents
WeekTheoreticalPracticeLaboratory
1A classis of Phototrophic, Proteobacteria, Cyanobacteria, Heliobacteria, Green-sulphure and green-nonsulphure bacteriaMethods of spread plate, pour plate, streak plate
2Members of chemolithotrophic and methanotrophicEnumeration of cell with microscope
3Members of anaerobic ProteobacteriaCultural enumeration in broth media (EMS, tube dilution, filtration)
4Members of Chemoorganotrophic ProteobacteriaAnaerobic enumeration methods
5Non-Proteobacteria phylum: members of Aquaficea ve Thermotogae phylumThe enzymatic activity of microorganisms (Hydrolysis of polysaccharide, protein and virulence factors)
6Members of Deinococcus-Thermus phylum, Chlamidia phylum, Planctomyces phylumBiochemical tests used in the identification of microorganisms
7Members of Spirochaeta phylum, Bacterioides phylumMidterm exam
8Midterm examProtein and aminoacid metabolism
9Low G+C gram (+) bacteria Isolation of actinomycetes
10Low G+C gram (+) bacteriaIsolation of liminouous bacteria
11Low G+C gram (+) bacteriaIsolation of extramophile bacteria
12High G+C gram (+) bacteria Isolation of sheeted bacteria
13High G+C gram (+) bacteriaIsolation of enteric bacteria
14Archeal cell wall and membranes, genetics, metabolisms, systematics, Phylum: Crenarchaeota; Phylum: Euryarchaeota. Methanogens, metanogenesis mechanism. Isolation of halophilic archaea
15Physiology of Halobacteria, bacteriorhodopsine, rhodopsine based photothrophy ekstreme thermophilic S metabolizer and sulphate redusing members of Euryarchaeota.Final exam
16Final exam
Recommended or Required Reading
•Willey, J.M., Sherwood, L.M. and Woolverton, C.J. Prescott, Harley, and Klein’s Microbiology, 7th Ed, Mc Graw Hill Higher Education, 2008. •Madigan, M.T., Martinko, J.M., Dunlap, P.V. and Clark, D. P., Biology of Microorganisms 12th Ed, Pearson. USA. 2009. •Brenner, D.J., Krieg, N.R and Staley, J.T., Bergey’s Manuel of Systematic Bacteriology, Volume 2: Proteobacteria Part B: Gammaproteobacteria, Springer, 2005. •Kim, B.H. and Gadd, G.M., Bacterial Physiology and Metabolism,1th Ed, Cambridge University Press, 2008. Withman, W.B., Parte, A.C., Bergey’s Manuel of Systematic Bacteriology, Volume 3: The Firmicutes, Springer, 2009
Planned Learning Activities and Teaching Methods
Activities are given in detail in the section of "Assessment Methods and Criteria" and "Workload Calculation"
Assessment Methods and Criteria
Term (or Year) Learning ActivitiesQuantityWeight
SUM0
End Of Term (or Year) Learning ActivitiesQuantityWeight
SUM0
SUM0
Language of Instruction
Turkish
Work Placement(s)
None
Workload Calculation
ActivitiesNumberTime (hours)Total Work Load (hours)
Midterm Examination166
Final Examination166
Report Preparation5525
Report Presentation5525
Criticising Paper8648
Individual Study for Homework Problems4312
Individual Study for Mid term Examination166
Individual Study for Final Examination166
Reading8216
TOTAL WORKLOAD (hours)150
Contribution of Learning Outcomes to Programme Outcomes
PO
1
PO
2
PO
3
PO
4
PO
5
PO
6
PO
7
PO
8
PO
9
PO
10
PO
11
PO
12
PO
13
PO
14
LO1555      44 55
LO25453 4   55 55
LO3555      44555
LO4555      44555
LO5555 5    5 555
LO65555     5  55
LO75555    45  55
LO855544454   555
* Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High
 
Ege University, Bornova - İzmir / TURKEY • Phone: +90 232 311 10 10 • e-mail: intrec@mail.ege.edu.tr