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Classification of Bacteria
Chapter 4
Taxonomy / Systematics
• Identification
• Distinguishing features
• Organization into groups
• Engine size
• Car
• Mileage
• Truck
• Number of passengers
• SUV
• Type of transmission
• Van
• Classification
• Nomenclature
– Providing a formal name
– Genus & species
•
•
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Ford Crown Victoria
Chevy Impala
Toyota Camry
Honda Civic
Consistent rules for all scientist
Relevant
Meaningful
Make biological sense
Evolutionary context
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Five Kingdoms
Uni or multicellular
Eukaryotic
Bacteria
Archaea
Eukaryotic
Unicellular
Unicellular
Prokaryotic
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Bacteria
Archaea
Eukarya
3CarlDomain
System
Woese
Late 1970’s & early 1980’s
Woese, C. R. 2004. A New Biology for a New Century. MMBR. June 68(2):173-86.
Woese, C.R. 2002. On the evolution of cells. Proc Natl Acad Sci USA 99(13):8742-7.
Woese, C.R. 2000. Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97(15):8392-6.
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Binomial nomenclature
Genus & species
Escherichia coli
Genus name is always capitalized
Species name is never capitalized coli
Both names are always either italicized or underlined
Abbreviation: E. coli
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Domains can be Divided into Many
Sub-classifications Biological species concept
does not apply to
prokaryotes!!!
• Domain: Bacteria
• Phylum: Proteobacteria
• Class: Gamma Proteobacteria
Species – a collection of
• Order: Enterobacteriales
bacterial cells which share an
• Family: Enterobacteriaceae
overall similar pattern of
• Genus: Escherichia
traits in contrast to other
• Species: Escherichia coli
bacteria whose pattern differs
significantly
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strain or variety – a culture derived from a single
parent that differs in structure or metabolism from other cultures
of that species (biovars, morphovars)
type – a subspecies that can show differences in antigenic
makeup (serotype or serovar), susceptibility to bacterial viruses
(phage type) and in pathogenicity (pathotype)
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Classification of Bacteria
Light microscope was the
original tool.
Initial classification was based on
of the shape of the bacterial cells.
4 Main Shapes of Bacteria
Cocci
Bacilli
Spirilla
Spirochetes
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Medical Microbiologists said…
One bacterium = One disease
So to these scientists, bacteria were also
classified as to the disease they caused…
They were also named based on this…
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Four Groups Based on Cell Wall
Composition
1.
2.
3.
4.
Gram-positive cells
Gram-negative cells
Bacteria without cell walls
Bacteria with chemically unique cell walls
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N-acetylmuramic acid
(NAM)
Peptidoglycan
• Macromolecule composed of a
repeating framework of long chains
cross-linked by short peptide fragments
– Unique to Bacteria
– Composed of 2 sugars: NAG &
NAM
– Sugars alternate in the backbone
– Rows linked by polypeptides N-acetylglucosamine
(NAG)
• Provides strong, flexible support to keep
bacteria from bursting or collapsing
because of changes in osmotic pressure
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Gram Positive Cell Wall
• Consists of
– A thick, homogenous sheath of peptidoglycan
20 - 80 nm thick
– Tightly bound acidic polysaccharides, including
teichoic acid and lipoteichoic acid
– Retains crystal violet with iodine as a mordant
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Gram Negative Cell Wall
• Consists of
– An outer membrane containing lipopolysaccharide
(LPS)
– Thin shell of peptidoglycan between inner and outer
membranes
– Periplasm
– Inner membrane
– Loses crystal violet-iodine complex when cells are
exposed alcohol (decolorization step) and stains red
with safranin counterstain
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Be able to identify all the parts of
a Gram + & - cell wall for the next exam.
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Bacteria with Chemically Unique Cell Walls
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•
•
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Acid-Fast Cells
Mycobacterium species
Gram + type of cell wall
Unique lipid
– Mycolic acid – waxy substance
• Does not decolorize
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Rickettsia – Chemically Unique Cell Wall
• Stains Gram • Cell wall contains diaminopimelic acid
& lacks teichoic acid
• 0.25 m in diameter
• Obligate intracellular pathogens
– Encapsulated
– Enter cell by induced phagocytosis
– Divide rapidly once inside
• Pathogens that alternate between mammals and fleas,
lice or ticks
– Rickettsia rickettisii – Rocky Mountain spotted fever
– Rickettsia prowazekii – epidemic typhus
– Coxiella burnetti – Q fever
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Chlamydia – Chemically Unique Cell Wall
• Obligate intracellular parasites
• 0.3 and 1.0 m in diameter
• Cell wall contains an outer lipopolysaccharide membrane
but lacks peptidoglycan
– Contains cysteine-rich proteins that are assumed to be the
functional equivalent of peptidoglycan
– Stains Gram -
• Chlamydia trachomatis
– The most common sexually transmitted disease
• Chlamydia psittaci
– Ornithosis, parrot fever
• Chlamydia pneumoniae
– Lung infection
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Bacteria without Cell Walls - Mycoplasma
• Lack a rigid cell wall during their entire life cycle
• Smallest known organisms – smallest genomes
(other than viruses)
– Diameter ranges from 0.15 m to 0.30 m
• Do not stain with the Gram stain
• Pleomorphic
– Tiny pleomorphic cocci, short rods, short
spirals, and sometimes doughnut shape
• Mycoplasma pneumoniae
– Atypical pneumonia in humans
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Numerical Taxonomy
Looked at all traits of an organism… every
trait had equal importance
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rRNA Sequence
• The greatest advancement in classifying
organisms
• Differences in the nucleotide sequence are used
to classify prokaryotes
Actually look at the DNA that
• 16S rRNA sequences
codes for the rRNA
• 23S rRNA sequences
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How is this accomplished?
Extract DNA from a colony, or from
an environmental sample without
growing the organism.
PCR with primers for
rRNA sequences
Automated DNA
sequencer
Coefficient of Similarity
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Bacteria phylogenetic relationships based on rRNA sequences
Phylogenetic tree
of 16S rDNA
sequences
Coefficient of Similarity
Texas A&M
Microbiology
www-odp.tamu.edu/.../ 203/images/03_f03b.gif
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Gamma Proteobacteria
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Bergey’s Manual of Systematic Bacteriology
• Prokaryotes into 25 phyla
– Archaea
•2
– Bacteria
• 23
• Consensus of experts
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rRNA Sequence
Relevant
Meaningful
Make biological sense
Evolutionary context
• The greatest advancement in
classifying organisms
• Differences in the nucleotide
sequence are used to classify
prokaryotes
Actually look at the DNA that
codes for the rRNA
• 16S rRNA sequences
• 23S rRNA sequences
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A Selection of Biologically
Important Groups of Bacteria
These groups have been
traditionally defined by
cell shape, metabolism,
method of motility or
type of infection.
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Cyanobacteria
• Gram negative phototrophs
– Oxygenic photosynthesis 12H2O + 6CO2  C6H12O6 + 6H2O + 6O2
– Existed for  2.3 bya
– Largest and one of the most important groups of bacteria on
Earth
• Extremely diverse group
– Unicellular, colonial & filamentous form
– Some species fix N2 in heterocysts
– Some species produce akinete
• Analogous to a endospore
Most species are found in fresh water
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Marine
Damp soil
Temporarily moistened desert rocks
Endosymbionts in lichens, plants, various protists or sponges
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Some cyanobacteria can
fix nitrogen
Internal photosynthetic
membrane
Heterocysts
N2 fixation
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Oscillatoria sp.
Merismopedia sp.
Spirulina sp.
vis-pc.plantbio.ohiou.edu/algaeimage/pages/anabaena.html
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Spirochetes
Borrelia burgdorferi
www.microbeworld.org
• Long, helically coiled cells.
• Gram –
• Axial filaments
– Running lengthwise between the cell membrane and cell wall
– Most spirochetes are free-living and anaerobic, but there are
exceptions
• 3 families
• Leptospira spp.
– Leptospirosis
• Borrelia burgdorferi
– Lyme disease
• Treponema pallidum
– syphilus
www.bbc.co.uk/.../stis_syphilis.shtml
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www.surrey.ac.uk/SBMS/ACADEMICS_homepage/mcfadden_johnjoe/sbms243.html
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Enterics
• Gram – rods, facultative anaerobes
• Family Enterobacteriaceae
• Many are part of the intestinal microflora of mammalian
intestines
• Infamous pathogens
– Salmonella, Escherichia, Klebsiella, Proteus, Enterobacter,
Citrobacter
• Most ferment glucose, reduce nitrates to nitrites and oxidase
negative
• Many diagnostic tests to identify these organisms
– Page 615 & 616
– Table 20.2
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page 613
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Magnetotactic
• Magnetosome
– Crystalline particles of iron oxide or sulfide
– Magnetite Fe3O4
– Greigite Fe3S4
• All are either obligate microaerophiles or strict
anaerobes
• Motile, aquatic bacteria
• Direction of motility is affected by the Earth’s
geomagnetic field
• Strains are either north- or south-seeking
depending upon oxic conditions
– North-seekers predominate in the northern hemisphere
– South-seekers predominate the southern hemisphere
– Exist in equal numbers at the equator
• Current hypothesis states that these bacteria use
the geomagnetic field to locate lower O2 or
anaerobic habitats
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There are Two Types of Magnetoaerotaxis...
Axial Magnetoaerotaxis
e.g., Magnetospirillum magnetotacticum
Polar Magnetoaerotaxis
e.g., strain MC-1, a magnetotactic coccus
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N2 Fixation
• Archaea & Bacteria
• Nodules
– Rhizobium and Bradyrhizobium form nodules on the roots of legumes
– Frankia forms nodules on the roots of alders (Alnus), wax myrtles (Myrica)
and mountain lilacs
• “pioneer plants”
• Free-living
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Azospirillum
Azotobacter
Clostridium
Bacillus
Klebsiella
Methanosarcina
• Archaea
– Cyanobacteria
www.tari.gov.tw/ARI_E/E_image/ACD_13.jpg
• No eukaryotic organisms fix N2
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mdchoice.com/photo/img/img0110.jpg
Pyogenic cocci
• Causes many suppurative infections
• Gram + cocci
– Staphylococcus aureus, Streptococcus
pyogenes & Streptococcus pneumoniae,
• Gram - cocci
– Neisseria gonorrhoeae & N. meningitidis
• ⅓ of all human bacterial infections
– Food poisoning, strep throat, pneumonia,
various skin diseases, septic shock, gonorrhea
& meningitis
• Bacteria in this group are unrelated
nova.medicina.cz/files/gonorrhea_01.jpg
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Lactic Acid Bacteria
• Fementative bacteria that produce
lactic acid under anaerobic
conditions (can be described as
oxytolerant anaerobes)
– Convert pyruvate to lactic acid
• Also produce acetic acid & CO2
– Regenerate NAD+ for glycolysis
• Species of Streptococcus and
Lactobacillus
• Dairy industry
– Cheese, cottage cheese, yogurt
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Endospore-forming Bacteria
• Gram +
– Bacillus, Clostridium and
Sporosarcina
• Survival structure
– Resistant to heat, UV,
desiccation
• Pathogen
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Bacillus anthracis
Clostridium tetani
C. perfringens
C. botulinum
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Purple and Green Bacteria
• Anoxygenic photosynthesis
– 12H2S + 6CO2  C6H12O6 + 12S°
• Colors due to color of
slightly different
bacteriochlorophylls
– Green - deposit S° outside
– Purple - S° is inside the cell
• Anaerobic H2S-containing
mud and water
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Vibrios
• Gram -, slightly curved rods, polar flagellum
• Estuarine & marine environments
• Pathogenic and cooperative interactions with
eukaryotic host
• Vibrio cholerae
– Cholera
• Extreme watery diarrhea
– Only species that can survive in both fresh and
www.nature.com/.../020603/full/020603-2.html
salt water
– Potent toxin
• Vibrio fischeri
– Bacterial bioluminescence
– Lives planktonically in seawater but can also
colonizes organs of squids and marine fish
– Autoinducer
– Quorum sensing
ergo.integratedgenomics.com46
Myxobacteria
• Glide over surface
– No flagella
• Vegetative cells swarm
during nutrient
depletion
• Fruiting body
• Dormant myxospores
• Spores “germinate”
under favorable
conditions
www.textbookofbacteriology.net
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Actinomycetes
• Filamentous, Gram + soil bacteria
• Aerobic decomposition of organic
compounds
– Biodegradation
– Carbon cycle
• Geosmins
– Earth odor
• Antibiotics
– Streptomyces
– Tetracyclines, macrolides and aminoglycosides
• Pathogens
– Mycobacterium tuberculosis
– Corynebacterium diphtheriae
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Radioresistant
• Deinococcus radiodurans
– Gram +
• Survive a dosage of radiation that is
3,000 times greater than what would
kill a human
• Survive DNA damaging chemicals, and
high levels of ionizing and ultraviolet
radiation, and dehydration
• Able to repair chromosome fragments
within 12-24 hours
science.nasa.gov
– Repair chromosomes that have been
broken into 100 fragments
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