The Domain Bacteria

Hierarchy of Classification
• 1. Kingdom
• 2. Domain
• 3. Phylum
• 4. Class
• 5. Order
• 6. Family
• 7. Genus
• 8. Species
 Terms
• Domain: highest taxonomic rank (3 domains: Archaea, Bacteria, Eucarya), used to
distinguish between cell types
• Kingdom: a taxonomic rank composed of smaller groups (phyla or divisions), six
kingdoms: Eubacteria, Archaebacteria, Plantae, Animalia, Fungi, and Protista
• Phylum: 3rd in the hierarchy of classification. Organisms share a set of characteristics
that distinguishes them from organisms in another phylum, organisms grouped
together accdg to their body plan.
• Class-a taxonomic rank, grouping accdg to how differentiated their organ systems
are.
• Order: USE OF SUFFIXES TO DENOTE RANK
• Family: grouped within order, a group of one or more genera, grouped by
their common attributes
• Genus:can include more than one species that are closely related to each
other (similar traits, features, qualities
• Species: with genus and specific epithet (species identifier)
Kingdom Procaryotae Procaryotae
Domain Bacteria Bacteria
Phylum Firmicutes Proteobacteria
Class Bacilli Gammaproteobacteria
Order Bacillales Enterobacterales
Family Staphylococcaceae Enterobacteriaceae
Genus Staphylococcus Escherichia
Species Staphylococcus aureus Escherichia coli
 Domains of Prokaryotic organisms

• 1. Domain Bacteria
• 2. Domain Archaea
• According to Bergey’s Manual, Domain Bacteria contains 23 phyla,32
classes, 5 subclasses, 77 orders, 14 suborders, 182 families, 871 genera
and 5007 species
• Organisms in this domain are broadly divided into three phenotypic
categories (i.e. categories based on their physical characteristics: a. those
that are Gram-negative and have a cell wall b. those that are Gram-
positive and have a cell wall c. those that lack cell wall
• A bacterium’s Gram reaction (Gram-positive or Gram-negative), basic cell shape,
and morphological arrangement of the cells are very important clues to the
organism’s identification
• Many characteristics of bacteria are examined to provide data for identification and
classification
• These characteristics include cell shape and morphological arrangement,staining
reactions, motility, colony morphology, atmospheric requirements, biochemical
and metabolic activities, specific enzymes that the organism produces,
pathogenicity (the ability to cause disease, and genetic composition.
 Cell Morphology
• With the compound microscope, the SIZE,SHAPE AND MORPHOLOGIC
ARRANGEMENT of various bacteria are easily observed.
• The sizes of bacteria vary in size usually ranging from spheres measuring
about 0.2 um (micrometer) in diameter to 10.0-μm-long spiral-shaped
bacteria, to even longer filamentous bacteria
• The average coccus is about 1 μm in diameter, and the average bacillus is
about 1 μm wide X 3 μm long. Some unusually large bacteria
and unusually small bacteria have been discovered.
 Three basic shapes of bacteria
• Round or spherical bacteria-the cocci (sing; )
• Rectangular or rod-shaped bacteria –the (sing;bacillus)
• Curved and spiral-shaped bacteria sometimes referred to as spirilla
• Bacteria divide by BINARY FISSION ---once cell splits in half to become
two daughter cells.
• The time it takes for one cell to split into two cells is referred to as that
organism’s generation time
• After binary fission, the daughter cells may separate completely from each
other or may remain connected forming various morphologic
arrangements
• Bacterial names sometime provide a clue to their shape
• If “coccus” appears in the name of a bacterium, one knows the bacteria is spherical in
shape examples: Enterococcus, Peptococcus, Peptostreptococcus, Staphylococcus,
and Streptococcus. However, not all cocci have “coccus “ in their names (e.g.
Neisseria spp.
• If bacillus appears in the name of a bacterium, the organism is rod-shaped or
rectangular.
Examples: Actinobacillus, Bacillus, Lactobacillus and Streptobacilus. However , NOT
ALL BACILLI have “bacillus” in their names (e.g. E. coli)
• Examples of medically important cocci include: Enterococcus spp, Neisseria spp.,
Staphylococcus spp.,and Streptococcus spp.
• Bacilli (rod-shaped) may be short or long, thick or thin, and pointed or with curved or
blunt ends (diplobacilli-in pairs, streptobacilli-in chains, in long filaments or branched.
Some rods are quite short, resembling elongated cocci ; they are called coccobacilli.
Listeria monocytogenes and Haemophilus influenzae are examples of coccobacilli
• Some bacilli stack up next to each other, side by side in a palisade
arrangement,Corynebacterium diphtheriae (cause of diphtheria)and organisms that
resemble it in appearance (diphtheroids)
• Examples of medically important bacilli : members of the family
Enterobacteriaceae (example: Enterobacter, Klebsiella,
Proteus,Salmonella, and Shigella spp.
Pseudomonas aeruginosa, Bacillus spp., and Clostridium spp.
• Cocci may be seen singly or in pairs (diplococci), chains (streptococci),
clusters (staphylococci), packets of four (tetrads) or packets of eight
(octads) depending on the particular species and the manner in which the
cells divide
• NOTE: BEWARE THE WORD “BACILLUS” When Bacillus is
capitalized and underlined or italicized, it is a PARTICULAR GENUS OR
ROD-SHAPED BACTERIA, however, if it is not capitalized, underlined
or italicized, it refers to any rod-shaped bacterium
• Curved and spiral-shaped bacilli are placed into a third morphologic grouping. For
example Vibrio spp., such as V. cholera (causative agent of cholera) and
V. Parahaemolyticus (causative agent of diarrhea), are curved (comma-shaped) bacilli
Curved bacteria usually occur singly, but some species may form in pairs. A pair of
curved bacilli resembles a bird and is described as having a gull-wing morphology
Campylobacter spp. (a common cause of diarrhea) have a gull-wing morphology
• Spiral- shaped bacteria are referred to as SPIROCHETES. Different species of
spirochetes vary in size, length, rigidity and the number and amplitude of their
coils. Some are tightly coiled such as Treponema pallidum, the cause of syphilis
with a flexible cell wall that enables them to move readily through tissues. Its
morphology and characteristic motility—spinning around its long axis—make T.
pallidum easy to recognize in wet preparations of clinical specimens obtained
from patients with primary syphilis
• Borrelia spp., the causative agents of Lyme disease and relapsing fever are
examples of less tightly coiled spirochetes
• Some bacteria may lose their characteristic shape because adverse growth conditions
( eg. the presence of certain antibiotics) prevent the production of normal cell walls.
They are referred to as cell-wall deficient bacteria (CWD bacteria) or L-forms. Some
CWD bacteria revert (back) to their original shape when placed in favorable growth
conditions, whereas others do not.
• Bacteria in the genus Mycoplasma do not have cell walls, thus when examined
microscopically, they appear in various shapes. Bacteria that exist in a variety of shapes
are described as being pleomorphic (the ability to exist in a variety of shapes-
pleomorphism) BECAUSE THEY HAVE NO CELL WALLS, MYCOPLASMAS ARE
RESISTANT TO ANTIBIOTICS THAT INHIBIT CELL WALL SYNTHESIS.
 Motility

• If the bacterium is able to “swim”, it is said to be motile. Bacteria unable

to swim are said to be NONMOTILE
• Bacterial motility is most often associated with the presence of flagella or
axial filaments, although some bacteria exhibit a type of gliding motility
on secreted slime. BACTERIA NEVER POSSESS CILIA. Most spiral-
shaped bacteria and about one-half of the bacilli are motile by means of
flagella, but cocci are generally nonmotile.
 Colony Morphology
• A single bacterial cell that lands on the surface of a solid culture medium cannot be seen, but
after it divides over and over again, it produces a mound or pile of bacteria known as
BACTERIAL COLONY. A colony contains millions of organisms.The colony morphology
(appearance of colonies) of bacteria varies from one species to another. Colony morphology
includes the SIZE, COLOR, OVERALL SHAPE, ELEVATION AND THE APPEARANCE
OF THE EDGE OR MARGIN OF THE COLONY
• The size of the colonies is determined by the organism’s rate of growth (generation time)
and is an important characteristic of a particular bacterial species
• Colony morphology also includes the results of enzymatic activity on various types of
culture media.
 Atmospheric requirements

• In microbiology laboratory, it is useful to classify bacteria on the basis of

their relationship to oxygen and carbon dioxide.
• With respect to oxygen, a bacterial isolate can be classified into one of
five major groups: obligate aerobes, microaerophilic aerobes
(microaerophiles), facultative anaerobes, and obligate anaerobes
 Aerobes

• Obligate aerobes and microaerophiles require oxygen. Obligate aerobes require an

atmosphere containing about 20% to 21% oxygen, whereas microaerophiles require
reduced oxygen concentrations (usually around 5% oxygen)
• Mycobacteria and certain fungi are examples of microorganisms that are obligate aerobes
• Microaerophiles (microaerophilic aerobes) also require oxygen for multiplication but in
concentrations lower than that found in room air. Neisseria gonorrhoeae (causative agent
of gonorrhea) and Campylobacter spp.(which are the major causes of bacterial diarrhea)
are examples of microaerophilic bacteria that prefer an atmosphere containing about 5%
of oxygen
 Anaerobes
• Anaerobes are defined as organisms that do not require oxygen for life and reproduction.However,
they vary in their sensitivity to oxygen.
• OBLIGATE ANAEROBE: an anaerobe that can grow only in an anaerobic environment
(environment containing no oxygen)
• AEROTOLERANT ANAEROBE: does not require oxygen, grows better in the absence of oxygen
but can survive in atmospheres containing molecular oxygen (such as air and CO2 incubator)
• FACULTATIVE ANAEROBE: are capable of surviving in either the presence or absence of
oxygen anywhere from 0% Oxygen to 20% oxygen. Many of the bacteria routinely isolated from
clinical specimens are facultative anaerobes (e.g. members of the family Enterobacteriaceae, most
streptococci and most staphylococci).
• Room air contains less than 1% CO2. Some bacteria, referred to as
capnophiles (capnophiic organisms) grow better in the laboratory in the presence
of increased concentrations of CO2.
• Some anaerobes (e.g Bacteroides and Fusobacterium species)are
capnophiles, as are some aerobes ( certain Neisseria, Campylobacter,
Haemophilus species)
 Nutritional requirements

• All bacteria need some form of the elements carbon, hydrogen, oxygen, sulfur, phosphorus
and nitrogen for growth.
• Special elements such as potassium, calcium, iron, manganese, magnesium,cobalt, copper, zinc
and uranium are required by some bacteria
• Certain microbes have specific vitamin requirements and some need organic substances
secreted by other living microorganisms during their growth
• Organisms with especially demanding nutritional requirements are said to fastidious (“fussy”).
The nutritional needs of a particular organism are usually characteristic for that species of
bacteria and sometimes serve as important clues when attempting to identify the organism.
 Biochemical and Metabolic activities
• As bacteria grow, they produce many waste products and secretions some
of which are enzymes that enable them to invade their host and cause
disease.
• The pathogenic strains of many bacteria such as staphylococci and
streptococci can be tentatively identified by the enzymes they secrete.
• Also in particular environments, some bacteria are characterized by the
production of certain gases such as carbon dioxide, hydrogen sulfide,
oxygen, or methane.
 Pathogenicity
• Many pathogens are able to cause disease because they possess capsules,
pili or endotoxins (biochemical components of the cell walls of Gram-
negative bacteria), or because they secrete exotoxins and exoenzymes that
damage cells and tissues.
 Unique bacteria
• Rickettsias, chlamydias and mycoplasmas are bacteriabut they DO NOT
POSSES ALL THE ATTRIBUTES OF TYPICAL BACTERIAL CELLS,
thus they are often referred to as “UNIQUE”or “RUDIMENTARY”
bacteria. Bacause they are so small and difficult to isolate, they were
formerly thought to be viruses
 Rickettsias, Chlamydias and closely related
bacteria
• Rickettsias and chlamydias are bacteria with a Gram-negative type cell
wall. The are obligate intracellular pathogens that cause diseases in
humans and other animals. As the name implies, an obligate pathogen , a
pathogen that must live within a host cell
• To grow such organisms in the laboratory, they must be inoculated into
embryonated chicken eggs, laboratory animals or cell cultures. They will
not grow on artificial (synthetic) culture media
• The genus Rickettsia was named for Howard T. Ricketts, a US
pathologist; these organisms have no connection to the disease called
rickets which is the result of Vit. D deficiency
• Most rickettsias must live inside another cell (they have leaky cell
membranes) to retain all necessary cellular substances. ALL DISEASES
CAUSED BY RICKETTSIA species are arthropod-borne meaning they are
transmitted by arthropod vectors (carriers)
• Arthropods (lice, fleas, and ticks) transmit the rickettsias from one host to another
by their bites or waste products. Diseases caused by Rickettsia spp include
typhus and typhus-like diseases (e.g. spotted fever rickettsiosis). All these
diseases involve production of a rash. Medically important bacteria that are
closely related to rickettsias include Coxiella burnetii, Bartonella Quintana,
Ehrlichia spp.,and Anaplasma spp. cause human tick-borne diseases such as
human monocytic ehrlichiosis (HME) and human granulocytic anaplasmosis)
• Ehrlichia and Anaplasma are intraleukocytic pathogens, meaning that they live
within certain types of WBC
• The term “chlamydias” refers to Chlamydia spp. and closely related
organisms (such as Chlamydophila spp.)
• Rickettsias and chlamydias are examples of obligate intracellular
organisms-organisms that can exists only within host cells)
• Chlamydias are referred to as “energy parasites” . Although they can
produce ATP molecules, they preferentially use ATP molecules produced
by their host cells. ATP molecules are the major energy-storing or energy
carrying molecules of cells
• Chlamydias are are obligate intracellular pathogens that are transferred by
inhalation of aerosols (suspension of fine solid particles or liquid droplet
in air or another gas) or by direct contact between hosts----not by
arthropods
 Strains and serotypes
• Serotype: is serologically and antigenically distinct variety of microorganism,
like a subgroup of a species of bacteria (serotypes are also called serovars).
Serotypes of an organism differ from each other as a result of differences in
their surface molecules (surface antigens). DIFFERENT SEROTYPES OF A
GIVEN SPECIES CAUSE DIFFERENT DISEASES
• Strain is an organism or a population of such organisms, which can be
distinguished from other organisms within a taxon (e.g. species) based on
certain characteristics (E. coli has many strains , some strains of the microbe
may be producing enzymes different from another strain of the said microbe.)
 Medically important chlamydias
• Chlamydia trachomatis, Chlamydophila pneumonia, and Chlamydophila
psittaci
• Different serotypes of C. trachomatis cause different diseases including
trachoma (the leading cause of blindness in the world), inclusion
conjunctivitis (another type of eye disease), and non gonococcal urethritis
(NGU; not caused by Neisseria gonorrhoeae
• C. pneumonia cause a type of pneumonia
• C. psittaci causes a respiratory disease called psittacosis
 Mycoplasmas
• Mycoplasmas are the SMALLEST CELLULAR MICROBES.
• They lack cell walls so they assume many shapes from coccoid to filamentous;
thus they appear pleomorphic when examined microscopically
• Mycoplasmas were formerly called pleuropneumonia-like organisms
(PPLOs)first isolated from cattle with lung infections
• Mycoplasmas may be free-living or parasitic and are pathogenic to many
animals and some plants. In humans, pathogenic mycoplasmas cause primary
atypical pneumonia pneumonia and genitourinary infections
• Mycoplasmas have no cell walls so they are resistant to treatment with
penicillin and other antibiotics that work by inhibiting cell wall synthesis
• Mycoplasmas can be cultured on artificial media in the laboratory where
they produce tiny colonies (called “fried egg colonies”) that resemble
sunny-side-up fried eggs
Especially large and especially small bacteria

• The size of the typical coccus (e.g. Staphylococcus aureus cell) is 1 μm in

diameter. A typical bacillus (e.g. an E.coli cell) is about 1.0 μm wide x 3.0
μm long, although some bacilli are long thin filaments—up to about 12
μm in length or even longer—but still only about 1 μm wide.
• MOST BACTERIA ARE MICROSCOPIC,requiring the use of a microscope to
be seen
• The largest of all bacteria—large enough to be seen by the unaided human
eye– is Thiomargarita namibiensis, a colorless, marine, sulfide-oxidizing
bacterium, they do not form filaments
• Single spherical cells of T. namibiensis are 100-300 μm but may be as
large as 750 μm (0.75 mm)
• Beggiatoa and Thioploca with diameters from 10 um to
more than 100 um (they form filaments)
• Epulopscium fishelsonii, has been isolated from the intestines of the reef
surgeonfish (tang); this bacillus is about 80 um wide x 600 um(micrometer) or
0.6 mm long. Epulopscium cells are about five times longer than eukaryotic
Paramecium cells. Epulopscium cell is about a million times greater than the
volume of a typical bacterial cell.
• Spore forming bacteria called metabacteria, found in the intestines of
herbivorous rodents, are closely related to Epulopiscium but they reach lengths
of only 20 to 30 um. Metabacteria although shorter than Epulopiscium is longer
than most bacteria
• Tiny bacteria are called nanobacteria
• They are less than 1 um in diameter, in some cases they are as small as 20nm in
diameter
• They are found in soil, minerals, ocean water, human and animal blood, human dental
calculus (plaque), arterial plaque and even rocks (meteorites) of extraterrestrial origin
• Scientists believe that these tiny structures are formed by geological rather biological
processes. They feel that nanobacteria are smaller than the minimum possible size for
a living cell.
 Photosynthetic bacteria
• Include: purple bacteria, green bacteria and cyanobacteria
(erroneously referred to in the past as blue-green algae
• All three groups use light as an energy source but they do not carry out
photosynthesis in the same way. For example: purple and green bacteria
do not produce oxygen, whereas cyanobacteria do. Photosynthesis that
produces oxygen is called oxygenic photosynthesis whereas
photosynthesis that does not produce oxygen is called anoxygenic
photosynthesis
• In photosynthetic eukaryotes (algae and plants), photosynthesis takes
place in plastids.
• In cyanobacteria, photosynthesis takes place on intracellular membranes
known as thylakoids. Thylakoids are attached to the cell membranes at
various points and are thought to represent invagination of the cell
membrane. Attached to the thylakoids in orderly rows are numerous
phycobilisomes—complex protein pigment aggregates where light
harvesting occurs.
• Scientists claim that cyanobacteria were the first organisms capable of
carrying out oxygenic photosynthesis and thus, played a major role in the
oxygenation of the atmosphere
• Fossil records reveal that cyanobacteria were already in existence 3.3 to
3.5 billion years ago
• Cyanobacteria may be cocci, bacilli or may form long filaments
• When appropriate conditions exist, cyanobacteria in pond or lake water will
overgrow, creating water bloom – a “pond scum” that resembles a thick layer of
bluish green (turquoise) oil paint.
• The conditions include a mild or balmy water temperature (15 deg to 30 deg C ), a
water pH of 6 to 9, and an abundance of the nutrients nitrogen and phosphorus in
the water.
• Many cyanobacteria are able to convert nitrogen gas (N2) from the air into
ammonium ions (NH4+) in the soil or water, this process is known as nitrogen
fixation
• Some cyanobacteria produce toxins such as neurotoxins (which affect the
central nervous system), hepatotoxins (affect the liver) and cytotoxins
( affect other types of cells). These cyanotoxins can cause disease and
death in wildlife species and humans that consume contaminated water.
• Many scientists are concerned that global temperatures
(“global warming” will lead to increases in
cyanobacterial populations and concurrent increases in
cyanotxins
 Domain Archaea
• Prokaryotic organisms in Domain Archaea were discovered in 1977.
• Archae means “ancient” and the name archaea was originally assigned when
it was thought that these prokaryotes evolved earlier than bacteria.
• Genetically, even though they are prokaryotes archaea are more closely related
to eukaryotes than they are to bacteria; some possess genes otherwise found
only in eukaryotes. Many scientists believe that bacteria and archaea diverged
from a common ancestor relatively soon after life began on this planet.
• Later, eukaryotes split off from archaea.
• According to Bergey’s Manual of Systematic Bacteriology, the Domain
Archaea contains 1 phyla, 8 classes, 12 orders, 21 families, 69 genera and
217 species
• Archaea vary widely in shape,some are cocci, some are bacilli, and others
form long filaments.
• Many archaea are “extremophiles”, in the sense that they live in extreme
environments, such as extremely acidic, alkaline, hot, cold or salty
environments, or environments where there is extremely high pressure.
• Some live at the bottom of the ocean in and near thermal vents, where in
addition to heat and salinity, there is extreme pressure. Other archaea,
called methanogens, produce methane, which is a flammable gas.
• End of lecture
• Study well!