Download Microbes Overview

Microbes Overview
Course content
 Prokaryotes
Archaea
Bacteria
 Eukaryotes
(microbial Protists)
Fungi
Algae
Protozoa
 Viruses
Introduction
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Taxonomy is the science of the
classification of organisms, with the goal of
showing relationships among organisms.
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Taxonomy also provides a means of
identifying organisms.
How would you classify?
Types of classification:
 natural (Carolus Linnaeus, members share same
characteristics)
 phenetic (based on similarities of biological and
morphological characters);
 phylogenetic (considers differences and
similarities of evolutionary processess)
 genotype (comparision of genetic similarity
between organisms, 70% homologous belong to
the same species)
Taxonomic Ranks
microbes are placed in hierarchical
taxonomic levels with each level or rank
sharing a common set of specific features
 highest rank is domain
 within domain
- phylum, class, order, family, genus,
species epithet, some microbes have
subspecies
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Binomial System of Nomenclature
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devised by Carl von Linné (Carolus Linnaeus)
each organism has two names
name – italicized and capitalized (e.g.,
Escherichia)
 species epithet – italicized but not capitalized (e.g.,
coli)
 genus
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can be abbreviated after first use (e.g., E. coli)
Techniques for Determining Microbial
Taxonomy and Phylogeny
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classical characteristics
morphological
physiological
biochemical
ecological
genetic
Ecological Characteristics
life-cycle patterns
 symbiotic relationships
 ability to cause disease
 habitat preferences
 growth requirements
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Molecular Characteristics
nucleic acid base composition
 nucleic acid hybridization
 nucleic acid sequencing
 genomic fingerprinting
 amino acid sequencing
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The prokaryotes:
Domain Archaea
and
Domain Bacteria
Bergey’s Manual of Systematic
Bacteriology
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1923,David Bergey (prof of bacteriology)
published a classification of bacteria for
identification of bacterial (and archaea) species.
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Bergey’s Manual categorizes bacteria into taxa
based on rRNA sequences.
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Bergey’s Manual lists identifying characteristics
such as Gram stain reaction, cellular
morphology, oxygen requirements, and
nutritional properties.
The Archaea
Archaea
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Scientist identified archaea as a distinct type of
prokaryotes based on its unique rRNA sequence
Reproduce by : binary fusion, budding or
fragmentation
Cells shape : cocci, bacilli, spiral, lobed, cuboidal
etc
Not causing disease to humans/animals
Cell wall contain proteins, glycoproteins,
lipoproteins, polysaccharides
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Very high/low temp/pH, concentrated salts or
completely anoxic (extreme environments)
Archae are either gram +ve or gram –ve
Classified into two phylum :
1) Crenarchaeota – most thermophyllic and many
acidophiles and sulfur dependent; anaerobes e.g.
Thermoproteus and Sulfobolus
2) Euryarchaeota – 5 major physiologic groups
(the metanogens, the halobacteria, the
thermoplasms, extremely thermophilic S°reducers and sulfate-reducing)
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The Methanogens
- strict anaerobes
- obtain energy by converting CO2, H2, methanol
to methane or methane & CO2
- eg. Methanobacterium, Methanococcus
- methanogenesis
* last step in the degradation of organic
compounds
*occurs in anaerobic environments
e.g., animal rumens
 e.g., anaerobic sludge digesters
 e.g., within anaerobic protozoa
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The Halobacteria
- extreme halophiles
- aerobic chemoorganotrophs (use organic
compound as energy sources)
- dependent on high salt content
- cell wall dependent on NaCl, they
disintegrated when [NaCl] < 1.5M
- dead sea
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The Thermoplasms
- lack cell walls
- but plasma membrane strengthen by diglycerol
tetraether, lipopolysaccharides, and glycoproteins
- grow best at 55-59°C, pH1-2
- eg. Thermoplasma
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Extremely Thermophillic So-Reducers
- strictly anaerobic
- can reduce sulfur to sulfide
- grow best at 88-100°C
- motile by flagella
- eg. Thermococcus
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Sulfate-reducing
- irregular garm –ve coccoid cells
 cell walls consist of glycoprotein subunits
- extremely thermophilic
 optimum 83°C
 isolated from marine hydrothermal vents
- obtain their energy by oxidizing organic
compounds or H2 while reducing sulfates to
sulfides. In a sense, they "breathe" sulfate rather
than oxygen
- eg. Archaeoglobus
Bacteria
Domain Bacteria
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Bacteria are essential to life on Earth.
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We should realize that without bacteria, much of
life as we know it would not be possible.
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In fact, all organisms made up of eukaryotic
cells probably evolved from bacterialike
organisms, which were some of the earlist forms
of life.
The Proteobacteria
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Largest group of bacteria. More than 500 genera
gram-negative, some motile using flagella
Most are facultative/obligate anaerobes
Share common 16s rRNA sequence
5 distinct classes of proteobacteria (α,β, ε, ɣ,δ) :
- Alphaproteobacteria
- Betaproteobacteria
- Gammaproteobacteria
- Deltaproteobacteria
- Epsilonproteobacteria
Alphaproteobacteria
 Gram -ve
 Most are oligotrophic (capable of growing at low nutrient
levels)
 Example of alphaproteobacteria ;
1) Most purple nonsulfur phototrophs are in this group
(use light energy and CO2 and do not produce O2)
2) Nitrifying bacteria e.g. Nitrobacter (oxidize NH3 to NO3
by a process called nitrification)
3) Pathogenic bacteria eg. Rickettsia (typhus), Brucella
(brucellosis), Ehrlichia (ehlichiosis)
4) Beneficial bacteria eg. Acetobacter and Caulobacter
(synthesize acetic acid); Agrobacterium (used in genetic
recombination in plants)
Acetobacter
Agrobacterium infect plant
Betaproteobacteria
 Gram –ve
 oligotrophic (capable of growing at low nutrient
levels)
 Differ with alphaproteobacteria in rRNA sequence
 Example of betaproteobacteria :
1) nitrifying bacteria eg. Nitrosomonas
2) pathogenic species, Neisseria (gonorrhea),
Bordetella (whooping cough)
3) Thiobacillus (ecologically important), Zoogloea
(sewage treatment)
Gammaproteobacteria – largest class
 purple sulfur bacteria – obligate anaerobes that
oxidize hydrogen sulfide to sulfur
 intracellular pathogens (Legionella, Coxiella),
 methane oxidizers (Methylococcus),
 facultative anaerobes that utilize glycolysis and
the pentose phosphate pathway (Escherichia
coli),
 pseudomonads –aerobes that catabolize
carbohydrates (Pseudomonas, and Azomonas)
Deltaproteobacteria
 Sulfate reducing microbes Eg. Desulfovibrio
(important in the sulfur cycle)
 Myxobacteria – gram negative, soil-dwelling
bacteria , dormant myxospores; common
worldwide in the soils having decaying plant
material or dung
Epsilonproteobacteria
 Gram-negative rods, vibrios, or spiral
 Include important human pathogens
 Eg. Campylobacter (causes blood poisoning)
The Gram Positive Bacteria
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In Bergey’s Manual, gram-positive bacteria (able to
form endospore) are divided into those that have :
- low G + C ratio (base pair in genome below 50%)
- high G + C ratio
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Low G + C gram-positive bacteria include 3 groups
clostridia, mycoplasms, Gram-positive Bacilli and
Cocci
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High G + C gram-positive bacteria include
mycobacteria, corynebacteria, and actinomycetes.
Clostridia
 Eg. Clostridium – anaerobic, form
endospores, rod shape, gram +ve
 pathogenic bacteria causing gangrene,
tetanus, botulism, and diarrhea
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Mycoplasmas
Facultative or obligate anaerobes lack cell walls
Gram +ve (previously under gram negative
category until nucleic acid sequences proved
similarity with gram positive organisms)
When culture on agar, form ‘fried egg’
appearance bcoz cell in the center of the colony
grow into the agar while those around the spread
outward
Usually associated with pneumonia and urinary
tract infections
Fried egg appearance
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Gram positive Bacilli and Cocci
Eg. Bacillus – form endospores, flagella
(B.licheniformis synthesis antibiotic. B.anthracis
cause anthrax)
Eg. Lactobacillus – nonsporing rods, nonmotile,
produce lactic acid as fermentation product.
Mostly found in human mouth, intestinal tract,
stomach. Protect body from pathogens
Streptococcus – nonmotile, cocci associated in
pairs and chain. Cause pneumonia, scarlet fever
Bacillus
Streptococcus
High G+C gram-positive bacteria
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Include Corynebacterium, Mycobacterium and
Actinomycetes that have a G+C ratio > 50% in the phylum
Actinobacteria, which have species with rod-shaped 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
THE EUKARYOTES :
FUNGI, ALGAE,
PROTOZOA
FUNGI
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Organisms in kingdom fungi include molds,
mushrooms, yeasts
Fungi are aerobic or facultatively anaerobic
(yeast), chemoheterotrophs, spore-bearing,
lack chlorophyll
Most fungi are decomposers, and a few are
parasites of plants and animals
Some fungi – cause disease (mycoses)
Some fungi – essential to many industries
(bread, wine, cheese, soy sauce)
Characteristics of Fungi
Body/vegetative struc. of fungi – Thallus
 Thalli of yeast – small, globular, single cell
 Thalli of mold – large, composed of long,
branched, threadlike filaments of cell called
hyphae that form mycelium
 Hyphae - septate
- Aseptate (coenocytic)
 Fungi grow best in the dark, moist habitats
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Acquire nutrients by absorption. Secrete
enzyme to break large organic mol. Into
simple mol.
 Reproduction of fungi – sexual & asexual
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Asexual reproduction
Several ways :
1) Transverse fission - Parent cell undergo
mitosis, divide into daughter cell by formation of
new cell wall
2) Budding – after mitosis, one daughter nucleus
is sequestered in a small bleb that is isolated
from parent cell by formation of cell wall
3) Asexual spore formation - filamentous fungi
produce asexual spores through mitosis and
subsequent cell division.
several types of asexual spores :
1) Sporangiospores form inside a sac called
sporangium
2) Chlamydospores form with a thickened cell wall
inside hyphae
3) Conidiospores (conidia) produced at the tip or
side of hyphae, not within sac
4) Blastospores produced from vegetative mother
(hyphae) cell by budding
5) Arthrospores hyphae that fragment into
individual spores
conidiospores
sporangiospores
Chlamydiospores
Arthrospores
conidiospores
chlamydospores
Blastospores
sporangiospores
4) Sexual reproduction in fungi
Fungal mating type designated as + and –.
4 basic steps :
1) Haploid (n) cells from + and – thallus fuse,
form dikaryon (cell with both +&- nuclei)
2) pair of nuclei within a dikaryon fuse to form
one diploid (2n) nucleus
3) meiosis of the diploid restores the haploid
state
4) haploid nuclei partitioned into + and - spores
Classification of fungi
1) Zygomycota
 Coenocytic molds – zygomycetes
 produce sporangiospores (asexual) and
zygospores (sexual)
 e.g. Black bread mold Rhizopus nigricans
2) Ascomycota
 Septate hyphae
 Form ascospores within sac-like structure
call asci (sexual)
 Form conidiospores in asexual
reproduction
 Eg Penicillium
3) Basidiomycota
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septate hyphae
produce basidiospores (sexual), some produce
conidiospores (asexual)
Eg mushrooms, puffballs, stinkhorns
Protozoa
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Eukaryotic, unicellular and lack of cell wall
Motile (cilia, flagella, pseudopodia)
Grow in moist habitats
Some are in group of Planktonic (floating free in
lakes, ocean and form the basis of aquatic food
chain)
Some protozoa can produce a cyst that provides
protection during adverse environmental
conditions
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Asexuall reproduction by binary fission,
schizogony/multiple fission
Sexually reproduction by conjugation
1)Nucleus undergoes mitosis
2)Cytoplasm divides by cytokinesis
Schizogony/multiple fission
Classification of protozoa
Grouping based on locomotive structure
do not reflect genetic relationship.
 7 taxa of protozoa : alveolates, cercozoa,
radiolaria, amoebozoa, eglenozoa,
diplomonads, and parabasalids
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Alveolates
 Have small membrane cavities called
alveoli beneath cell surface.
 3 groups : ciliates (have cilia),
apicomplexans (pathogen to animal),
dinoflagellates (have flagella)
Cercozoa
 Unicellular, called amoeba
 Move & feed by pseudopodia
 Have snail-like shells of calcium carbonate
Radiolaria
 Amoeba that have ornate shells composed of
silica
Amoebozoa
 Have lobe-shaped pseudopodia, no shell
 Eg Acanthamoeba, Naegleria
Eglenozoa
 move by means of flagella and lack sexual
reproduction; they include Trypanosoma
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Diplomonad
 Lack mitocondria, golgi bodie
 Have 2 nuclei and multiple flagella
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Giardia
Algae
Simple eukaryotic, phototrophic
organisms, like plants
 Carry out photosynthesis using chlorophyll
 Most live in aquatic environments
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Characteristic of Algae
Unicellular or simple multicellular (thalli)
 Thallus of seaweed (large marine algae)
are complex, with holdfast (attached to
rock), stemlike stipes and leaflike blades
 Algae reproduce sexual and asexual
(fragmentation & cell division)
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Classification of algae
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Classify according to their structure and
pigment :
- red algae
- brown algae – cell wall composed of
cellulosa & alginic acid
- green algae
- diatoms – silica cell wall composed of two
halves called frustules that fit together like
petri dishes
frustule
DIATOMS
VIRUSES
Characteristics of Viruses
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Viral disease – SARS, AIDS, influenza, herpes, common
cold
Viruses – miniscule, infectious agent with simple acellular
organization and pattern of reproduction
Viruses can exist – extracellular or intracellular
Virion (complete virus particle) consist of :
- nucleocapsid (composed of 1 or more DNA or RNA, held
within capsid)
- in some viruses – envelope (phospholipid membrane)
Capsid - build by few types of protein = protomer
- 3 types – helical, icosahedral, complex symmetry
Virus structure
Different types of virus
Helical
Icosahedral
Types of capsids
Helical
Complex symmetry
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Virus size range 10-1000nm
Most virus infect only particular host’s cells
Eg. HIV only infect T lymphocytes (a type of
white blood cell)
Some viruses infect many kinds of cells in many
different hosts
Eg. Rabies can infect most mammals
Viruses are obligatory intracellular parasites.
They multiply by using the host cell’s
synthesizing machinery to cause the synthesis
of specialized elements that can transfer the
viral nucleic acid to other cells
Viral replication
Virus cannot reproduce themselves bcoz:
- have no genes for all enzyme needed for
replication
- have no ribosomes for protein synthesis
 Viruses dependent of host’s organelles
and enzymes to replicate
 Virus replication – Lytic replication
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Lytic replication of bacteriophage
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Consist of 5 stages – attachment, entry,
synthesis, assembly, release
1) Attachment – structure responsible for
attachment to host = tail fiber. Attachment is
dependent on chemical attraction and precise fit
between T4 tail and protein receptor on E.coli
cell wall
2) Entry – T4 release lysozyme to weaken
peptidoglycan of E.coli cell wall. T4 inject
genome into E.coli, leaving T4 coat outside.
3-4) Synthesis – viral enzyme degrade the bacterial
DNA. E.coli start synthesis new viruses. T4 DNA
is transcribed, producing mRNA which is
translated to T4 protein (component of tail and
head, lysozyme)
5) Assembly – T4 components are assemble in
spontaneous manner to form mature virion
6) Release – newly assembled virions are released
from the cell as lysozyme completes its work on
the cell wall
Lytic replication takes about 25min can produce
100-200 new virions each cycle