Prokaryotes
Archaea
Bacteria
Eukaryotes
(microbial Protists)
Fungi
Algae
Protozoa
Viruses

• Taxanomy is the science of classifying microbes into different groups based on their phenotype or genotype characters.
• Types of classification:
• natural (introduced by Carolus Linnaeus reflecting biological nature of an organism);
• phenetic (based on similarities of biological and morphological characters);
• phylogenetic (considers differences and similarities of evolutionary processess;
• genotype (comparision of genetic similarity between organisms using newer molecular techniques.)

Prokaryotes (evolved between 3-4 billion years ago) are the original inhabitants of the planet
• Prokaryotes can be distinguished from eukaryotes in terms of their size, cell structure, and molecular make-up
• Most prokaryotes are simple cells lacking extensive, complex, internal membrane systems
• Prokaryotes are divided into: Bacteria and Archaea
• Bacteria can be classified as Gram negative or Gram positive
• Many prokaryotes are motile
• Some bacteria form resistant endospores to survive harsh environment in a dormant stage

• The Archaea are best known for growing in restricted habitats e.g. Hypersaline or high temperature
• Many have special structural, chemical, and metabolic adaptations that enable them to grow in extreme environments
• Divided into 2 phyla: Crenarchaeota (extremely thermophyllic and many acidophiles and sulfur dependent; anaerobes e.g. Thermoproteus or Gramnegative aerobes Sulfobolus
• and Euryarchaeota (diverse phylum: 5 major physiologic groups)
• Metanogenic and sulfate-reducing archae have cofactors that paticipate in methanogenesis

5 major physiologic groups:
• The Metanogens (strict anaerobes, e.g.
Methanobacterium , Methanococcus – Refer p. 507 of
Prescott);
• The Halobacteria ( gram negative or positive, chemoorganotrophs dependent on high salt content e.g.
Halobacterium salinarum ; has bacteriorhodopsin protein that can trap light energy without chlorophyll;
• The Thermoplasms ( thermoacidophiles, pleomorphic lacking cell wall e.g. Thermoplasma growing in refuse piles of coal mines);
• Extremely Thermophillic S oMetabolizers (e.g anaerobic, motile, flagellate, Thermococcus that reduces sulfur to sulfide;
• Sulfate-Reducing Euryarchaeota ( irregular gram negative coccoid anaerobic cells e.g. Archaeoglobus in marine aera.

1.2 Bacteria (Denococci and Non proteobacteria
Gram negatives, Ch.21 Prescott)
• Deeply branching very old group e.g. Aquifex,
Thermotoga
• Photosynthetic bacteria and Cyanobacteria are different distinct groups
• Chlamydiae bacteria obligate parasites
• Many have gliding motility and useful for bacteria that digest insoluble nutrients or move over the surfaces of moist, solid substrata
• Phyla in this group: 1. Aquificae and
Thermotogae; 2. Deinococcus-Thermus;
• 3. Photosynthetic bacteria; 4. Planctomycetes;
5. Chlamydiae; 6. Spirochaetes; Bactereoidetes

• Aquificae and Thermotoga bacterial thermophilles
• Aquificae oldest branch of bacteria e.g. Aquifex and Hydrogenobacter – thermophilic chemolithoautotrophs, gram negative rods.
(Chemolithoautotroph or mixotroph – a microbe that oxidizes inorganic compounds to drive both energy and electrons)
• Thermotoga e.g. Thermotoga sp.-gram negative rods with an outer sheath-like envelope (togaouter garment p.520 Prescott); hasgenes for sugar degradation

• 3 groups of gram-negative bacteria: the purple bacteria; the green bacteria; cyanobacteria, having pigments chlorophyll and bacteriophyll
• Cyanobacteria are able to carry out oxygenic photosynthesis , having photosystems I and II and use water as electron donor to release oxygen;
• dominate aerated freshwater and marine microbial communities absorbing red and blue light; e.g. Cyanobacteria sp – unicellular varying in shape and appearence;
• move by gliding motility (Refer to Prescott p. 525 for Cyanobacterial cell structure);
• can develop symbiotic relationships with other organisms like lichen, fungi, protozoa, nitrogen-fixing bacteria;
• reproduce by binary fission;
• phycobilisomes contain light –harvesting pigments phycocyanin and phycoerythrin

• Purple bacteria ( gamma proteobacteria,
Bergey’s Manual) and the green bacteria e.g.
Chlorobium sp. have only one photosystem and use anoxygenic photosynthesis .
• Because they cannot use water as electron source, they employ reduced molecules such as hydrogen sulfide, sulfur, hydrogen, and organic matter as their electron source for the reduction of NAD(P)+ to NAD(P)H

Planctomycetes – gram negative
• Have compartmentalized cells lacking peptidoglycan; role in anaerobic ammonia oxidation e.g. Candidatus Brocadia anammoxidans
Chlamydiae – gram negative
• Non motile, coccoid, gram-negative reproducing within the cytoplasmic vacoules by phagocytosing the attached elementary bodies of host cells to form reticulate bodies that can cause disease. They are energy parasites

Spirochaetes – gram neagative
• Slender, long, helical, gram-negative bacteria that are motile because of their axial filament underlying an outer membrane e.g. Myxotrichia paradoxa ; Treponema
(cause syphilus), Borrelia burgdorferi (cause Lyme disease)
Bacteroidetes e.g. Bacteroides, Cytophaga, Flexibacter spp – gram negative
• Are obligately anaerobic,gram negative, chemoheterotrophic, nonsporing, motile/nonmotile rods of various shapes;some intestinal symbiotants, others can cause disease; gliding motility; cytophagas degrade proteins and carbohydrates and active in mineralization of organic matter and produce yellow to orange colonies.

• The phylum Proteobacteria is the largest bacterial group with more than 500 genera and 2000 species
• Many species are Gram negative serving as scavengers in ecosystem or as disease agents.
Escherichia coli is a major experimental organism studied in many labs
• These bacteria are very diverse in their metabolism and life styles ranging from obligate parasites to free-living existence in soil and aquatic habitats
• Chemolithotrophic bacteria obtain energy and electrons by oxidation of inorganic compounds
• Some Proteobacteria produce specialized structures such as buds or complex fruiting bodies.

5 classesthe alpha-, beta-, gamma-, delta-, and epsilonproteobacteria
Alphaproteobacteria – aerobes, attached to hosts by cell extensions ( prosthecae ); Azospirillum and Rhizobium are nitrogen fixers
• Some members, e.g. Nitrobacter , are nitrifying bacteria that oxidize NH
3 to NO
3 by a process called nitrification
• Most purple nonsulfur phototrophs are in this group
• Pathogenic bacteria include Rickettsia (typhus), Brucella
(brucellosis), Ehrlichia (ehlichiosis)
• Beneficial bacteria include Acetobacter and Caulobacter which synthesize acetic acid; Agrobacterum is used in genetic recombination in plants

Betaproteobacteria
• Include nitrifying Nitrosomonas and pathogenic species,
Neisseria (gonorrhea), Bordetella (whooping cough),
Burkholderia (colonizes lungs)
• Thiobacillus (ecologically important), Zoogloea (sewage treatment), and Spirillum
Gammaproteobacteria – largest class
• Include purple sulfur bacteria – obligate anaerobes that oxidize hydrogen sulfide to sulfur
• intracellular pathogens ( Legionella , Coxiella ),
• methane oxodizers ( Methylococcus ),
• facultative anaerobes that utilize glycolysis and the pentose phosphate pathway ( Escherichia coli ),
• and pseudomonads (pathogenic Pseudomonas, nitrogen-fixing Azotobacter and Azomonas )

Deltaproteobacteria
• Include Desulfovibrio (important in the sulfur cycle and in corrosion of pipes); Bdellovibrio (pathogenic to bacteria);
• and myxobacteria – gram negative, soil-dwelling bacteria forming stalked fruiting bodies containing resistant, dormant myxospores; common worldwide in the soils having decaying plant material or dung
Epsilonproteobacteria
• Gram-negative rods, vibrios, or spiral
• Include important human pathogens ( Campylobacter , curved rods, causes blood poisoning; Helicobacter spirals, cause ulcers)

1.5 Low G+C Gram-positive bacteria
(Ch 11 Bauman)
• Classified within phylum Firmicutes, which include 3 groups: clostridia, mycoplasmas, other low G+C gram-positive bacilli and cocci
• Bacilli and cocci important to humans and industry
• Bacillus contain species that cause anthrax ( B.anthracis
) and food poisoning (endospores of B.cereus contaminate rice and ingestion cause nausea, vomiting, abdominal cramping), besides beneficial Bt toxin bacteria ( B.thuringiensis
- caterpillar biopesticide)
• Listeria sp.
causes meningitis in fetus and contaminate milk and meat products (L.monocytogenes does not produce endospores and continues to reproduce under refrigeration)
• Lactobacillus (non-sporing-forming rods) is used to produce yogurt and pickles; it inhibits growth of pathogens – microbial antagonism .
• Streptococcus cause strep throat and other diseases (scarlet fever, wound infections, pneumonia, & inner ear, blood, kidney diseases)
• Staphylococcus causes a number of human diseases (bacteremia, pneumonia, wound infections, food poisoning, and diseases of joints, bones, heart, and blood. S. aureus grows harmlessly on the skin in clusters.

Clostridia
• Clostridium pathogenic bacteria causing gangrene, tetanus, botulism, and diarrhea
• Epulopiscium and Veillonella found in dental plaque
Mycoplasmas
• Gram-positive (previously under gram negative category until neucleic acid sequences proved similarity with gram positive organisms) , pleomorphic, facultative anaerobes and obligate anaerobes lacking cell walls and stain pink in gram stain
• Show distinct “bull’s eye - fried egg” appearence when grown in solid media
• Usually associated with pneumonia and urinary tract infections

• Include Corynebacterium, Mycobacterium and
Actinomycetes that have a G+C ratio > 50% in the phylum Actinobacteria, which have species with rodshaped cells
• Corynebacterium store phosphates in metachromatic granules . C. diptheria causes diphtheria
• Mycobacterium cause tuberculosis and leporosy. It has unique resistant cell walls containing mycolic acids.
Hence, acid fast stain (for penetrating waxy cell walls) is used for its identification
• Actinomycetes resemble fungi as they produce spores and form filaments; important genera: Actinomyces found in human mouths; Nocardia useful in degradation of pollutants; and Streptomyces produces antibiotics

ALGAE
• Reproduce by alternation of generations (haploid and diploid thalli)
• Large algae attach to substrates by leaf-like blades or stem-like stipes
• Division Chlorophyta containd green algae that are similar to land plants and some taxanomists place them in kingdom Plantae e.g. Codium (marine used in seasoning pepper); Trebouxia (in lichens); Prototheca (colorless cauce skin rashes)
•
Rhodophyta (red algae) contain pigment phycoerythrin and agar or carrageenan cell walls, substances used as thickening agents, e.g.
Geledium, Chondrus – used as thickening agent in ice cream, toothpaste, salad, syrup, and snack foods
• Phaeophyta (brown algae) contain xanthophylls, and oils. Cell walls composed of alginic acid, another thickening agent. Spore motile having one ‘hairy’ flagellum and one whiplike flagellum
• Chrysophyta (the golden algae, yellow-green algae, and diatoms – contain chrysolaminarin, a storage product
• The silica cell walls of diatoms are arranged in nesting halves called frustules. Organic gardeners use diatomaceous earth , composed of dead diatoms, as a pesticide ageanst harmful insects and worms. It is also used in polishing compounds, detergents, paint removers, and reflective paints

• Classified into 7 groups: alveolates, cercozoa, radiolaria, amoebozoa, eglenozoa, diplomods, and parabasalids ,
• Protozoa are eukaryotic, unicelular organisms lacking cell walls;
Most are chemoautotrophs
• In the life cycle, trophozoite is the feeding stage; cyst resting stage.
A few undergo sexual stage by forming gametocytes that fuse to form zygotes
• Alveolates have small cavities (alveoli) beneath cell walls. They also have tubular mitochondrial cristae or folds; Imp. groups: Ciliates –
Vorticella (create whirlpool current during feeding); Balantidium
(human pathogen; Didinium ( Paramecium predator);
Apicomplexans – Plasmodium (cause malaria); Dinoflagellates
(freshwater and marine photoautotrophs, producing light via metabolic reactions e.g. ‘red tide’in sea) – Gymnodinium and
Gonyaulax produce ‘neurotoxins’.
• Cercozoa – amoebae, moving and feeding by pseudopodia. Major taxonforaminifera (fossil species forming thick layers of limestone
Egyptian pyramids built of such limestone)

• Radiolaria – amoebae with threadlike pseudopodia; have ornate shells composed of silica; dead bodies settle at bottom of ocean and form ooze that is dispersed hundred of meters thick
• Amoebozoa – have lobe-shaped pseudopodia; are slime molds
(lacking cell wall and are phagocytes); 2 groups : plasmodial molds
(acellular slime molds e.g. Physarium phagocytizing organic debris in the forest and bacteria; cellular slime molds e.g. haploid
Dictyostelium that phagocytize bacteria, yeasts, dung, and decaying vegetation
• Eglenozoa – share characteristics of both plants and animals; 2 groups: euglenids are photoautotrophic having chlorophyll a and b, and carotene; movement by flagella and by flowing,contracting, and expanding their cytoplasm or ‘squirming movement’ e.g. Euglena sp; kinetoplastids have a single large mitochondrion with unique mitochondrial DNA (kinetoplast); mostly intracellular and some pathogenic e.g. Trypanosoma and Leishmania cause fatal diseases in animals and humans .

Plant cell

• Dilpomonadida – lack several organelles of a cell; have 2 equal-sized nuclei and mutiple flagella; Giardia – diarrhea-causing pathogen spread by ingestion of food
• Parabasala – lack mitochondria and have a single nucleus a parabasal body (a Golgi bodylike structure); Trychonympha inhabits guts of termites assisting in didestion of wood;
Trichomonas cause sterility in raised acidic pH of human vagina

• Eukaryotes differ from prokaryote cells in having a variety of complex membranous organelles in the cytoplasm matrix and genetic material within membrane
–delimited nuclei
• Each organelle has a distintive structure directly related to specific functions
• A cytoskeleton composed of microtubles, microfilamentsa and intermediate filaments helps give eukaryotic cells shape; the cytoskeleton is also involved in cell movements, intracellular transport, and reproduction
• When eukaryotes reproduce, genetic material is distributed between cells by mitosis and meiosis
• Despite great differences between eukaryotes and prokaryotes with respect to morphology, they are similar on the biochemical level.

PREVIEW OF THE FUNGI (EUMYCOTA )
Fungi widely distributed and are both beneficial and harmful
They are mostly associated with moist environment and exist as filamentous hyphae which collectively is termed as mycelium
They digest insoluble organic matter by exoenzymes and absorb the solubilized nutrients
Their reproductive structures incluse: sporangia forming asexual spores and gametangia forming sexual gametes
Fungal systematics include 8 subdivisions:
Chytriodomycetes, Zygomycota, Ascomycota,
Basidiomycota, Urediniomycetes, Ustilaginomycetes,
Glomeromycota, and Microsporidia

The Chytriodomycetes are terrestrial and aquatic that reproduce by motile zoospores with single, posterior, whiplike flagella e.g. Pythium , Phytophthora spp.
The Zygomycota are coenocytic molds forming resting zygospores in which zygotes are formed e.g. Black bread mold Rhizopus nigricans
The Ascomycota (32,000 known species of molds and yeasts [unicellular]) form zygotes within sac-like structures called asci (singular ascus ) occuring in sexual ascocarp fruiting bodies. The ascus contains 2-8 ascospores
They reproduce asexually by coniodospores e.g.
Penicillium

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Economic importance of ascomycetes include:
Underground edible mushrooms truffles grow as mycorrhizae in association with oak trees( Tuber melanosporum priced at $500 per pound); ascocarps of common morel ( Morchella esculenta )
Claviceps purpurea growing on grains produces lysergic acid diethylamide (LSD) which causes abortions in cattle and hallucinations in humans;
Penicillium mold source of penicillin;
Saccharomyces ferments sugar to produce alcohol and
CO2 gas, used in bakery and brewery industries;
Pink bread mold Neurospora , has been important tool in genetics and biochemistry;
Many ascomycetes partner with green algae to form lichens

• Taxanomists in the middle of 20th century created the division Deuteromycota to contain collection of fungi whose sexual stages are unknown
• These fungi do not produce sexual spores or sexual spores have not been observed
• Recently, analysis of rRNA sequences revealed that most deuteromycetes in fact belong to division
Ascomycota
• Modern taxanomists have abandoned Deuteromycota as a formal taxon, but many medical lab technologists continue to refer “deuteromycetes” as a tradisional name
• Most deuteromycetes are terresterial saprobes, pathogens of plants, or pathogens of other fungi.
Trichophyton causes ringworm and Aspergillus , allergies in humans,

• Basidiomycota (22,000 known soecies) possess dikaryotic hyphae, one of each mating type. The hyphae divide uniquely, forming basidiocarps within which clubshaped basidia (sin. basidium) can be found. The basidia bear 2-4 basidiospores.
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• They are mostly cosmopolitan in nature found growing in fields and woods as visible basidiocarps of mushrooms, puffballs, stinkhorns, jelly fungi, bird’s nest fungi ( Crucibulum ). Poisonous mushrooms are sometimes as toadstools e.g Amanita muscaria
Economic importance of basidiomycetes Refer Ch 12 of Bauman’s book: edible mushrooms e.g. Agaricus and Cortinellis; Important decomposers that digest plant material and return nutrients to the soil; Many produce hallucinatory chemicals or toxins ;
Basidiomycete yeast Cryptococcus neoformans causes fungal meningitis.

Urediniomycetes (rusts in plants) and
Ustilaginomycetes (smuts)include important plant pathogens, whereas the Glomeromycota form mycorrhizae (vascular plant roots forming associations with fungi) that enhance plant nutrient uptake
Some members of Microsporidia are considered as pathogens for humans e.g Nosema and
Microsporodium . They are similar to zygomycetes and are obligatory parasites in insects e.g. Nosema infecting silkworms and honey bees, and grasshoppers

Viruses are simple, acellular entities ( obligate intracellular parasites ) reproducing only within living cells
Structurally, all viruses have a nucleocapsid composed of a nucleic acid genome surrounded by a protein capsid
Some viruses have a membranous envelope that lies outside the nucleocapsid
The nucleic acid of virus can be RNA or DNA , single stranded or double stranded, linear or circular
Capsids may hace a helical, icoshedral, or complex symmetry. They are constructed of protomers [individual subunits of a virus capsid] that self assemble through noncovalent bonds

Each virus has unique aspects to its life cycle but the generalised pattern of replication consists of 5 steps:
1. Attachment to the host cell
2. Entry into the host cell
3. Synthesis of viral nucleic acids and proteins within the host cell
4. Self assembly of virons[ sin. virion- a complete virus particlerepresenting the extracellular phase of the virus life cycle ]] within the host cell
5. Release of virions from the host cells

• Viruses are cultured by inoculating living hosts or cell cultures with a virion preparation
• Purification depends on their large size relative to cell components, high protein content and great stability
• The virus concentration may be determined from the virion count or from the number of infectious units
• Viruses are classified on the basis of their nucleic acid’s characteristics, reproductive strategy, capsid symmetry, and the presence or absence of an envelope

Types of eukaryotic viruses:
• Causing cancer viruses
• Plant viruses and plant diseases [most plant viruses have an RNA genome and may be helical or icosahedral]
• Animal viruses and diseases [e.g. Parvoviruses, retroviruses]
• Mycoviruses from higher fungi have isometric capsids and dsRNA, whereas lower fungi may have either dsRNA or dsDNA genomes
• Insect viruses produce inclusion bodies that aid in their trasmission
Baculoviruses and other viruses are finding uses in biological control of insects

• Viriods are infectious agents simpler than existing viruses. In plants they are short strands of infectious RNA
• Virusoids are infectious RNAs that encode one or more gene products and require a helper virus for replication
• Prions are small proteinaceous agents associated with degenerative nervous system disorders e.g. Fatal familial insomnia, bovine spongiform encaphalopathy. The precise nature of prions is unclear.

Give the Linneaus classification of the following microbes:
1.
That turns milk sour
2.
That ferments sugar
3.
That carries out exygenic photosynthesis
4.
That is found in the human intestine
5.
That carries out nitrification
6.
That is used in genetic recombination in plants
7.
That is a methane oxidizer
8.
That is used as diatomaceous earth
9.
That were used as limestone for building the Egyptian pyramids
10. Is an edible mushroom