1. Microbial classification 140 MBIO panel (semester 2; 1437-1438H)
140MIC: Microbiology
الشعبة
Lecture-13
Microbial classification
140 MBIO panel (semester 2; H)
د. فاطمة العتيبي Dr. Fatmah Alotaibi
د. كاكاشان بروين Dr. Kahkashan Perveen
د. حميراء رضوان Dr. Humaira Rizwana
أعدت العروض التقديمية منسقة المقرر: د. أسماء الصالح
رقم المكتب 5T201
الموقع:
إيميل

2. Content Definitions Phenotypic Analysis Genotypic Analysis
Taxonomy
Systematics
Phenotypic Analysis
Genotypic Analysis
Classification and Nomenclature

3. Definitions Taxonomy Systematics
The science of identification, classification, and nomenclature
Systematics
The study of the diversity of organisms and their relationships
Links phylogeny with taxonomy

4. Definitions The polyphasic approach to taxonomy uses three methods:
1. Phenotypic analysis
2. Genotypic analysis
3. Phylogenetic analysis

5. Approaches in taxonomy
The polyphasic approach to taxonomy uses three methods:
1. Phenotypic analysis
2. Genotypic analysis
3. Phylogenetic analysis
Examines the morphological, metabolic, physiological, and chemical characters of the cell
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6. Approaches in taxonomy
The polyphasic approach to taxonomy uses three methods:
1. Phenotypic analysis
2. Genotypic analysis
3. Phylogenetic analysis
Several methods of genotypic analysis are available:
DNA–DNA hybridization
DNA profiling
Multilocus sequence typing (MLST)
GC ratio
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7. Approaches in taxonomy
The polyphasic approach to taxonomy uses three methods:
1. Phenotypic analysis
2. Genotypic analysis
3. Phylogenetic analysis
The means of estimating the relationships between microorganisms
16S rRNA gene sequences are useful in taxonomy; serve as “gold standard” for the identification and description of new species
Whole-genome sequence analyses are becoming more common
Genome structure: size and number of chromosomes, GC ratio, etc.
Gene content
Gene order
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8. 16S rRNA Gene Tree Multigene Tree ATCC 11040T ATCC 51760T BAA-1194T
Photobacterium damselae
FS-2.1
FS-4.2
50 changes
Photobacterium phosphoreum
Photobacterium leiognathi
FS-3.1
FS-5.1
FS-2.2
Photobacterium mandapamensis
ATCC 11040T
FS-5.2
Photobacterium angustum
ATCC 51761
Photobacterium phosphoreum
NCIMB 13476
Photobacterium iliopiscarium
NCIMB 13478
Photobacterium iliopiscarium
NCIMB 13481
ATCC 51760T
Photobacterium kishitanii
chubb.1.1
ckamo.3.1
Figure Multigene phylogenetic analysis.
canat.1.2
hstri.1.1
Photobacterium kishitanii
calba.1.1
BAA-1194T
apros.2.1
ckamo.1.1
vlong.3.1
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9. Classification and Nomenclature
Organization of organisms into groups on the basis of either phenotypic similarity or evolutionary relationship
Prokaryotes are given descriptive genus names and species epithets following the binomial system of nomenclature used throughout biology
Assignment of names for species and higher groups of prokaryotes is regulated by the International Code of Nomenclature of Bacteria
Major references in bacterial diversity:
Bergey’s Manual of Systematic Bacteriology
The Prokaryotes
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11. Microbial diversity and groups 140 MBIO panel (semester 2; 1437-1438H)
140MIC: Microbiology
الشعبة 24511
Lecture-14
Microbial diversity and groups
140 MBIO panel (semester 2; H)
د. فاطمة العتيبي Dr. Fatmah Alotaibi
د. كاكاشان بروين Dr. Kahkashan Perveen
د. حميراء رضوان Dr. Humaira Rizwana
أعدت العروض التقديمية منسقة المقرر: د. أسماء الصالح
رقم المكتب 5T201
الموقع:
إيميل

12. Content
Archaebacteria
Fungi
Algae
Viruses.

13. Archaebacteria

14. Definitions
Archaea share many characteristics with both Bacteria and Eukarya
Archaea are split into two major groups
Crenarchaeota
Euryarchaeota

15. Euryarchaeota
Bioenergetics and metabolism of Archaea are similar to those found in Bacteria
Except some Archaea use methanogenesis autotrophy via several different pathways is widespread in Archaea
Types of euryarchaeota:
Extremely Halophilic Archaea
Methanogenic Archaea
Thermoplasmatales
Thermococcales and Methanopyrus
Archaeoglobales
Nanoarchaeum and Aciduliprofundum
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16. Extremely Halophilic Archaea
Have a requirement for high salt concentrations. Typically require at least 1.5 M (~9%) NaCl for growth
Found in artificial saline habitats (e.g., salted foods), solar salt evaporation ponds, and salt lakes.
Haloarchaea
Key genera:
Halobacterium
Haloferax
Natronobacterium

17. Methanogenic Archaea ميثانوجينك أركيا
Microbes that produce CH4 , Obligate anaerobes, Found in many diverse environments
Methanogens
Key genera:
Methanobacterium
Methanocaldococcus
Methanosarcina

18. Thermoplasmatales ثيرموبلازماتالس
Thermophilic and/or extremely acidophilic, Chemoorganotrophs
Facultative aerobes via sulfur respiration
Evolved unique cytoplasmic membrane structure to maintain positive osmotic pressure and tolerate high temperatures and low pH levels
Key genera:
Thermoplasma
Ferroplasma
Picrophilus
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19. Thermococcales and Methanopyrus ثيرموكوكالس و ميثانوبيرَس
Indigenous to anoxic thermal waters, Highly motile
Thermococcus
Pyrococcus
Methanopyrus: Methanogenic, Contains unique membrane lipids
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20. Archaeoglobales أركيوجلوبالس
Archaeoglobales: : Hyperthermophilic, Couple oxidation of H2, lactate, pyruvate, glucose, or complex organic compounds to the reduction of SO42 to H2S
Key genera:
Archaeoglobus
Ferroglobus
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21. Nanoarchaeum and Aciduliprofundum نانوركيم و أسيدوليبروفندم
One of the smallest cellular organisms (~0.4 µm), Contains one of the smallest genomes known, Lacks genes for all but core molecular processes, Depends upon host for most of its cellular needs
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22. Definitions
Archaea share many characteristics with both Bacteria and Eukarya
Archaea are split into two major groups
Crenarchaeota
Euryarchaeota

23. Crenarchaeota Inhabit temperature extremes
Most cultured representatives are hyperthermophiles
Found in extreme heat environments Other representatives found in extreme cold environments
Crenarchaeota from Terrestrial Volcanic Habitats
Crenarchaeota from Submarine Volcanic Habitats
Crenarchaeota from Nonthermal Habitats and Nitrification in Archaea
© 2012 Pearson Education, Inc.

26. Microbial diversity and groups 140 MBIO panel (semester 2; 1437-1438H)
140MIC: Microbiology
الشعبة 24511
Lecture-15
Microbial diversity and groups
140 MBIO panel (semester 2; H)
د. فاطمة العتيبي Dr. Fatmah Alotaibi
د. كاكاشان بروين Dr. Kahkashan Perveen
د. حميراء رضوان Dr. Humaira Rizwana
أعدت العروض التقديمية منسقة المقرر: د. أسماء الصالح
رقم المكتب 5T201
الموقع:
إيميل

27. Content
Archaebacteria
Fungi
Algae
Viruses.

28. Fungi

29. Fungal Physiology and structure
Most fungi are multicellular, forming a network of hyphae
Hyphae that extend above the surface can produce asexual spores called conidia.
Conidia are often pigmented and resistant to drying
Hyphae form compact tufts called mycelia. Most fungal cell walls are made of chitin
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30. Fungal Physiology and structure
Most fungi reproduce by asexual means (three forms)
Growth and spread of hyphal filaments
Asexual production of spores
Simple cell division
Some fungi produce spores as a result of sexual reproduction
Sexual spores can originate from the fusion of two haploid cells to form a diploid cell (ascospores, basidiospores, zygospores)
Spores are resistant to drying, heating, freezing, chemicals

31. Germination Conidia (spores) Conidiophore Aerial hyphae Subsurface
Figure 20.27
Germination
Conidiophore
Conidia (spores)
Aerial hyphae
Subsurface
Hyphae
Figure Fungal structure and growth.
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32. Fungal Physiology, Structure, and Symbioses
Some fungi produce macroscopic reproductive structures called fruiting bodies (Figure 20.29)
Mushrooms and puffballs are fruiting bodies
Some benefits:
Mycorrhizae help plant roots obtain phosphorus
Nutritious rich in protein (e.g. mashroom)
Fungi can cause disease in plants and animals
Dutch elm trees were devastated by fungal infection of the ascomycete Ophiostoma ulmi
Mycoses in humans range in severity from “athlete’s foot” to histoplasmosis
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33. Basidiocarp Basidiospores Spore germination Mature mushroom
Figure 20.29
Basidiocarp
Basidiospores
Figure Mushroom life cycle.
Spore germination
Mature mushroom
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34. Figure 20.30
Figure Scanning electron micrograph of the common baker’s and brewer’s yeast Saccharomyces cerevisiae (ascomycetes).
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35. Algea

36. Red and Green Algae Red Algae Green Algae
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37. Red Algae Key genus: Cyanidioschyzon
Red algae are also called rhodophytes
Mostly marine, but some freshwater and terrestrial
Red color is from phycoerythrin, a secondary pigment.
At greater depth, more phycoerythrin is produced by cells
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38. Figure 20.39 Figure 20.39 Polysiphonia, a marine red alga.
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39. Green Algae Key genera: Chlamydomonas, Volvox
Green algae are also called chlorophytes
Closely related to plants
Most green algae inhabit freshwater, but some are marine or terrestrial
Can be unicellular to multicellular
Have sexual and asexual reproduction
Endolithic algae grow inside porous rocks
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40. Figure 20.41
Figure Light micrographs of representative green algae.
© 2012 Pearson Education, Inc.