Microbial classification 140 MBIO panel (semester 2; 1437-1438H) 140MIC: Microbiology الشعبة Lecture-13 Microbial classification 140 MBIO panel (semester 2; 1437-1438H) 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: http://fac.ksu.edu.sa/asmalsaleh إيميل asmalsaleh@KSU.EDU.SA

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

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

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

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 © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

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 16.24 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 © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

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; 1437-1438H) 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: http://fac.ksu.edu.sa/asmalsaleh إيميل asmalsaleh@KSU.EDU.SA

Content Archaebacteria Fungi Algae Viruses.

Archaebacteria

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

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 © 2012 Pearson Education, Inc.

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

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

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 © 2012 Pearson Education, Inc.

Thermococcales and Methanopyrus ثيرموكوكالس و ميثانوبيرَس Indigenous to anoxic thermal waters, Highly motile Thermococcus Pyrococcus Methanopyrus: Methanogenic, Contains unique membrane lipids © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

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

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.

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; 1437-1438H) 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: http://fac.ksu.edu.sa/asmalsaleh إيميل asmalsaleh@KSU.EDU.SA

Content Archaebacteria Fungi Algae Viruses.

Fungi

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 © 2012 Pearson Education, Inc.

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

Germination Conidia (spores) Conidiophore Aerial hyphae Subsurface Figure 20.27 Germination Conidiophore Conidia (spores) Aerial hyphae Subsurface Hyphae Figure 20.27 Fungal structure and growth. © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

Basidiocarp Basidiospores Spore germination Mature mushroom Figure 20.29 Basidiocarp Basidiospores Figure 20.29 Mushroom life cycle. Spore germination Mature mushroom © 2012 Pearson Education, Inc.

Figure 20.30 Figure 20.30 Scanning electron micrograph of the common baker’s and brewer’s yeast Saccharomyces cerevisiae (ascomycetes). © 2012 Pearson Education, Inc.

Algea

Red and Green Algae Red Algae Green Algae © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

Figure 20.39 Figure 20.39 Polysiphonia, a marine red alga. © 2012 Pearson Education, Inc.

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 © 2012 Pearson Education, Inc.

Figure 20.41 Figure 20.41 Light micrographs of representative green algae. © 2012 Pearson Education, Inc.