Classification of Bacteria
Chapter 4
Taxonomy / Systematics
• Identification
• Classification
• Distinguishing features
• Organization into groups
• Engine size
• Car
• Mileage
• Truck
• Number of passengers
• SUV
• Type of transmission
• Van
• Nomenclature Consistent rules for all scientist
– Providing a formal name
– Genus & species Relevant
• Ford Crown Victoria Meaningful
• Chevy Impala Make biological sense
• Toyota Camry Evolutionary context
• Honda Civic
2
Five Kingdoms
Uni or multicellular
Eukaryotic

Eukaryotic
Unicellular
Bacteria
Archaea
Unicellular Prokaryotic
3
 Bacteria Archaea Eukarya

3CarlDomain
Woese
System
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.
4
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

5
 Domains can be Divided into Many
Sub-classifications Biological species concept
does not apply to
• Domain: Bacteria
prokaryotes!!!
• Phylum: Proteobacteria
• Class: Gamma Proteobacteria
• Order: Enterobacteriales Species – a collection of
• Family: Enterobacteriaceae bacterial cells which share an
overall similar pattern of
• Genus: Escherichia
traits in contrast to other
• Species: Escherichia coli bacteria whose pattern differs
significantly

6
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

9
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…

10
Four Groups Based on Cell Wall
Composition
1. Gram-positive cells
2. Gram-negative cells
3. Bacteria without cell walls
4. Bacteria with chemically unique cell walls

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 N-acetylmuramic acid
Peptidoglycan (NAM)

• 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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13
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

15
Be able to identify all the parts of
a Gram + & - cell wall for the next exam.

16
Bacteria with Chemically Unique Cell Walls
• 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 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  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  to 0.30 
• 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

21
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

24
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

28
rRNA Sequence Relevant
• The greatest advancement in Meaningful
classifying organisms Make biological sense
Evolutionary context
• 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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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.
31
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
• Marine
• Damp soil
• Temporarily moistened desert rocks
• Endosymbionts in lichens, plants, various protists or sponges

32
 Some cyanobacteria can
fix nitrogen

Internal photosynthetic
membrane Heterocysts
N2 fixation 33
 Oscillatoria sp.

Merismopedia sp. Spirulina sp.

vis-pc.plantbio.ohiou.edu/algaeimage/pages/anabaena.html 34
 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 35
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

37
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 O 2 or anaerobic habitats

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There are Two Types of Magneto-
aerotaxis...

Axial Magneto- Polar Magneto-

aerotaxis aerotaxis
e.g., Magnetospirillum magnetotacticum 40
e.g., strain MC-1, a magnetotactic coccus
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
– 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.jp
g

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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
– 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
salt water www.nature.com/.../020603/full/020603-2.html
– 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 science.nasa.gov
high levels of ionizing and ultraviolet
radiation, and dehydration
• Able to repair chromosome fragments
within 12-24 hours
– Repair chromosomes that have been
broken into 100 fragments

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