Bth 103 general microbiology

PROF. BALASUBRAMANIAN SATHYAMURTHY 2014 EDITION BTH – 103: GENERAL MICROBIOLOGY
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BTH – 103 GENERAL MICROBIOLOGY
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M.SC BIOCHEMISTRY BANGALORE UNIVERSITY SYLLABUS
I SEMESTER M.Sc. BIOTECHNOLOGY
BTP -103: GENERAL MICROBIOLOGY
Unit – 1: MICROBIAL CLASSIFICATION: 12 hrs
Three domain system of classification, Phylogenetic Relationships, Code for bacterial
nomenclature and taxonomy, Criteria for microbial classification – morphological,
staining techniques, biochemical methods, serological techniques, phage typing, fatty
acid profiles, Flow cytometry, DNA base composition, DNA fingerprinting, rRNA
sequences, Nucleic acid hybridization, Numerical Taxonomy, Chemotaxonomy,
Classification of bacteria according to Bergey’s Manual of systemic Bacteriology,
Dichotomous keys, Cladograms, dendrograms, universal phylogenetic tree.
Unit – 2: PROKARYOTIC MICROORGANISM: 10 hrs
General properties, Structure, and reproduction: Domain Bacteria: Proteobacteria
(Alpha, Beta, Gamma, Delta and Epsilon Proteobacteria), Cyanobacteria, Chlorobium,
Firmicutes, Actinobacteria, Chlamydiae, Spirochaetes, Bacteroidetes, Fusobacteria.
Domain Archea: Crenarchaeota, Euryarchaeota.
Unit – 3: EUKARYOTIC MICROORGANISM: 8 hrs
General characters, Structure, and reproduction: Fungi (Saccharomyces), Algae
(Spirulina), Protozoa (Plasmodium), Slime molds (Physarum).
Unit – 4: VIRUSES, VIRIOIDS AND PRIONS (ACELLULAR ENTITIES): 10 hrs
General characters, Structure, Criteria for classification of Viruses, Viruses that affect
humans, animals and plants, Isolation, Cultivation and identification of Viruses
(Growing in Bacteria, Living Animals, embryonated eggs, Cell cultures). Viral
Multiplication (Lytic and lysogenic life cycle), Virioids and Prions – General properties
and diseases caused by virioids and prions.
Unit – 5: MICROBIAL GROWTH AND CONTROL: 6 hrs
Physical parameters (Temperature, pH, Osmotic pressure), Chemical parameters
(Carbon, Nitroge, Phosphorous, Sulphur, Trace elements, Oxygen), Growth factors,

Culture Media, Phases of Growth, Growth Measurements, Microbial growth control –
Physical methods ( Heat, Pasteurization, Filteration, Radiation, Dessication, Low
Temperature, High Pressure, Osmotic Pressure) and Chemical Methods ( Phenols,
Halogens, Alcohols, quaternary ammonium compounds).
Unit – 6: MICROBIOLOGICAL METHODS: 6 hrs
Isolation ans cultivation of microorganisms from Water, Soil, Air, Rhizoshere,
Phyllosphere and Mycorrhiza, Biochemical cycle.
References:
1. Microbiology by MJ Pelczar Jr, ECS Chan, NR Krieg 5th Edition, Pub: Tata Mcgra-Hill
Publishing Co Ltd.
2. Introductory Microbiology by Heritage Pub Heritage
3. General Microbiology by Stainer Pub; Ingraham and Wheeler (McMillan)
4. Alexander M (1977) Introduction to soil microbiology, John Wiley and Sons Inc.N.Y.
5. Atlas R.M. (1998) Microbiology, Fundamentals and applications 2nd Edition, Milan
Publishing Co.
6. Brock T.D. and Madigan M.T (1992) Biology of Microorganisms 6th Edn. Prentice Hall,
Eagle wood cliffs N.j.
7. Holt J.S. Kreig N.R., Sneath P.H.A and Williams S.T (1994) Bergey’s Manual of Systemic
Bacteriology 9th Edn. William and Wilkins, Baltimore.
8. Prescott L.M, Harley T.P and Klein D.A. (1996) Microbiology WMC. Brown publishers

UNIT – 1: MICROBIAL CLASSIFICATION
Three domain system of classification, Phylogenetic Relationships, Code for
bacterial nomenclature and taxonomy, Criteria for microbial classification –
morphological, staining techniques, biochemical methods, serological techniques,
phage typing, fatty acid profiles, Flow cytometry, DNA base composition, DNA
fingerprinting, rRNA sequences, Nucleic acid hybridization, Numerical Taxonomy,
Chemotaxonomy, Classification of bacteria according to Bergey’s Manual of
systemic Bacteriology, Dichotomous keys, Cladograms, dendrograms, universal
phylogenetic tree.
THREE DOMAIN SYSTEM OF CLASSIFICATION, PHYLOGENETIC RELATIONSHIPS
It has been estimated that our planet is about 4.6 billion years old. Fossilized remains
of procaryotic cells around 3.5 to 3.8 billion years old have been discovered in
stromatolites and sedimentary rocks.
Fossilized Bacteria.
Several microfossils resembling cyanobacteria are shown, some with interpretive
drawings. (a) Thin sections of Archean Apex chert from Western
Australia; the fossils are about 3.5 billion years old. (b) Gloeodiniopsis, about 1.5
billion years old, from carbonaceous chert in the Satka Formation of the southern
Ural Mountains. The arrow points to the enclosing sheath. (c) Palaeolyngbya,
about 950 million years old, from carbonaceous shale of the Lakhanda Formation
of the Khabarovsk region in eastern Siberia.
Stromatolites are layered or stratified rocks, often domed, that are formed by
incorporation of mineral sediments into microbial mats.

Stromatolites.
These are stromatolites at Shark Bay, Western Australia. Modern stromatolites are
layered or stratified rocks formed by the incorporation of calcium sulfates,
calcium carbonates, and other minerals into microbial mats. The mats are formed
by cyanobacteria and other microorganisms.
Modern stromatolites are formed by cyanobacteria; presumably at least some fossilized
stromatolites were formed in the same way. Thus procaryotic life arose very shortly after
the earth cooled. Very likely the earliest procaryotes were anaerobic. Cyanobacteria and
oxygen-producing photosynthesis probably developed 2.5 to 3.0 billion or more years
ago. Microbial diversity increased greatly as oxygen became more plentiful.
According to the more popular endosymbiotic hypothesis, the first event was nucleus
formation in the pro-eucaryotic cell. The ancestral eucaryotic cell may have developed
from a fusion of ancient bacteria and archaea. Possibly a gram-negative bacterial host
cell that had lost its cell wall engulfed an archaeon to form an endosymbiotic
association. The archaeon subsequently lost its wall and plasma membrane, while the
host bacterium developed membrane infolds. Eventually the host genome was
transferred to the original archaeon, and a nucleus and the endoplasmic reticulum was
formed. Both bacterial and archaeal genes could be lost during formation of the
eucaryotic genome. It should be noted that many believe that the Archaea and Eucarya
are more closely related than this hypothetical scenario implies.
They propose that the eucaryotic line diverged from the Archaea and then the nucleus
formed, possibly from the Golgi apparatus. Mitochondria and chloroplasts appear to
have developed later. The free-living, fermenting ancestral eucaryote with its nucleus
established a permanent symbiotic relationship with photosynthetic bacteria, which
then evolved into chloroplasts. Cyanobacteria have been considered the most likely

ancestors of chloroplasts. More recently Prochloron has become the favorite candidate.
Prochloron lives within marine invertebrates and resembles chloroplasts in containing
both chlorophyll a and b, but not phycobilins. The existence of this bacterium suggests
that chloroplasts arose from a common ancestor of prochlorophytes and cyanobacteria.
Mitochondria arose from an endosymbiotic relationship between the free-living primitive
eucaryote and bacteria with aerobic respiration (possibly an ancestor of three modern
groups: Agrobacterium, Rhizobium, and Rickettsia). Some have proposed that aerobic
respiration actually arose before oxygenic (oxygen-producing) photosynthesis and made
use of small amounts of oxygen available at this early stage of planetary development.
The exact sequence of development is still unclear.
The endosymbiotic hypothesis has received support from the discovery of an
endosymbiotic cyanobacterium that inhabits the biflagellate protist Cyanophora
paradoxa and acts as its chloroplast. This endosymbiont, called a cyanelle, resembles
the cyanobacteria in its photosynthetic pigment system and fine structure and it is
surrounded by a peptidoglycan layer. It differs from cyanobacteria in lacking the
lipopolysaccharide outer membrane characteristic of gram-negative bacteria. The
cyanelle may be a recently established endosymbiont that is evolving into a chloroplast.
Further support is provided by rRNA trees, which locate chloroplast RNA within the
cyanobacteria. At present both hypotheses have supporters. It is possible that new data
may help resolve the issue to everyone’s satisfaction.
However, these hypotheses concern processes that occurred in the distant past and
cannot be directly observed. Thus a complete consensus on the matter may never be
reached.
CODE FOR BACTERIAL NOMENCLATURE AND TAXONOMY
In preparing a classification scheme, one places the microorganism within a small,
homogeneous group that is itself a member of larger groups in a nonoverlapping
hierarchical arrangement. A category in any rank unites groups in the level below it
based on shared properties.
Hierarchical Arrangement in Taxonomy

In this example, members of the genus Shigella are placed within higher
taxonomic ranks. Not all classification possibilies are given for each rank to
simplify the diagram.
In procaryotic taxonomy the most commonly used levels or ranks (in ascending order)
are species, genera, families, orders, classes, and phyla. Microbial groups at each level
or rank have names with endings or suffixes characteristic of that level.
An Example of Taxonomic Ranks and Names
Microbiologists often use informal names in place of formal hierarchical ones. Typical
examples of such names are purple bacteria, spirochetes, methane-oxidizing bacteria,
sulfate-reducing bacteria, and lactic acid bacteria. The basic taxonomic group in
microbial taxonomy is the species. Taxonomists working with higher organisms define
the term species differently than do microbiologists. Species of higher organisms are
groups of interbreeding or potentially interbreeding natural populations that are
reproductively isolated from other groups. This is a satisfactory definition for organisms
capable of sexual reproduction but fails with many microorganisms because they do not
reproduce sexually. Procaryotic species are characterized by phenotypic and genotypic

differences. A prokaryotic species is a collection of strains that share many stable
properties and differ significantly from other groups of strains. This definition is very
subjective and can be interpreted in many ways. The following more precise definition
has been proposed by some bacterial taxonomists. A species (genomospecies) is a
collection of strains that have a similar G +C composition and 70% or greater similarity
as judged by DNA hybridization experiments.
Ideally a species also should be phenotypically distinguishable from other similar
species. A strain is a population of organisms that is distinguishable from at least some
other populations within a particular taxonomic category. It is considered to have
descended from a single organism or pure culture isolate. Strains within a species may
differ slightly from one another in many ways. Biovars are variant procaryotic strains
characterized by biochemical or physiological differences, morphovars differ
morphologically, and serovars have distinctive antigenic properties. One strain of a
species is designated as the type strain. It is usually one of the first strains studied
and often is more fully characterized than other strains; however, it does not have to be
the most representative member. The type strain for the species is called the type
species and is the nomenclatural type or the holder of the species name. A
nomenclatural type is a device to ensure fixity of names when taxonomic
rearrangements take place.
For example, the type species must remain within the genus of which it is the
nomenclatural type. Only those strains very similar to the type strain or type species
are included in a species. Each species is assigned to a genus, the next rank in the
taxonomic hierarchy. A genus is a well-defined group of one or more species that is
clearly separate from other genera. In practice there is considerable subjectivity in
assigning species to a genus, and taxonomists may disagree about the composition of
genera.
Microbiologists name microorganisms by using the binomial system of the Swedish
botanist Carl von Linné, or Carolus Linnaeus as he often is called. The Latinized,
italicized name consists of two parts. The first part, which is capitalized, is the generic
name, and the second is the uncapitalized specific epithet (e.g., Escherichia coli). The
specific epithet is stable; the oldest epithet for a particular organism takes precedence
and must be used. In contrast, a generic name can change if the organism is assigned
to another genus because of new information. For example, the genus Streptococcus has

been divided to form two new genera, Enterococcus and Lactococcus based on rRNA
analysis and other characteristics. Thus Streptococcus faecalis is now Enterococcus
faecalis. Often the name will be shortened by abbreviating the genus name with a single
capital letter, for example E. coli. Approved lists of bacterial names were published in
1980 in the International Journal of Systematic Bacteriology, and new valid names are
published periodically.
Classification Systems
Once taxonomically relevant characteristics of microorganisms have been collected,
they may be used to construct a classification system. The most desirable classification
system, called a natural classification, arranges organisms into groups whose
members share many characteristics and reflects as much as possible the biological
nature of organisms. Linnaeus developed the first natural classification, based largely
on anatomical characteristics, in the middle of the eighteenth century. It was a great
improvement over previously employed artificial systems because knowledge of an
organism’s position in the scheme provided information about many of its properties.
For example, classification of humans as mammals denotes that they have hair, self-
regulating body temperature, and milk-producing mammary glands in the female.
There are two general ways in which classification systems can be constructed.
Organisms can be grouped together based on overall similarity to form a phenetic
system or they can be grouped based on probable evolutionary relationships to produce
a phylogenetic system. Computers may be used to analyze data for the production of
phenetic classifications. The process is called numerical taxonomy. This section briefly
discusses phenetic and phylogenetic classifications, and describes numerical taxonomy.
CRITERIA FOR MICROBIAL CLASSIFICATION – MORPHOLOGICAL
Morphological features are important in microbial taxonomy for many reasons.
Morphology is easy to study and analyze, particularly in eucaryotic microorganisms and
the more complex procaryotes. In addition, morphological comparisons are valuable
because structural features depend on the expression of many genes, are usually
genetically stable, and normally (at least in eucaryotes) these do not vary greatly with
environmental changes. Thus morphological similarity often is a good indication of
phylogenetic relatedness. Many different morphological features are employed in the
classification and identification of microorganisms.

Some Morphological Features Used in Classification and Identification
Although the light microscope has always been a very important tool, its resolution limit
of about 0.2 μm reduces its usefulness in viewing smaller microorganisms and
structures. The transmission and scanning electron microscopes, with their greater
resolution, have immensely aided the study of all microbial groups.
STAINING TECHNIQUES
Introduction:
The Gram stain, a differential stain was developed by Dr. Hans Christian gram, a
Danish physician in 1884. It is very useful staining for identifying bacteria into two
major groups. The gram positive, and gram negative by applying four different reagents
like
-- Crystal violet (primary stain)
-- Iodine solution (mordant)
-- 95% Ethanol (decolorized agent)
-- Safranin (counter stain)
Definition:
Which retain the primary stain appear in dark – blue – violet not be decolourized when
stained with Gram’s method are called Gram positive whereas incase those loose the
violet coloured and stained by safranin (appear in red) are referred to as ram negative.
The staining procedure is called gram negative.
Principle:
The gram negative bacterial cell wall is thin, complex, multilayered structured and
contain relatively a high lipid contents, in addition to protein and mucopeptides.

The higher amount of lipids is easily dissolved by alcohol resulting in the formation of
large pores in the cell wall, thus facilitating the leakage of crystal violet iodine complex
(cv-1) and resulting in the decolorization of the bacterium, which later takes counter
stain and appears red, in contrast gram positive cell walls are thick and four chemically
simple composed mainly of protein and treated with alcohol it causes dehydration of
cell wall pores there by not allowing loss of complex.
Method:-
Make thin smear of the given organism on a clean glass slide.
↓
Let the smear air – dry.
↓
Heat fixes the smear.
↓
Hold the smear rising sliding rack.
↓
Flood the smear with crystal violet and let stand for one minute.
↓
Wash with slow running tap water.
↓
Flood the smear with gram’s iodine mordant and let stand for one minute.
↓
Wash with tap water.
↓
Decolorized with 95% ethanol. Add reagent drop by drop until no more colur flows from
the smear.
↓
Wash the slide with slow running tap water.
↓
Counter stain with safranin for 45 sec.
↓
Wash with the tap water.
↓

Air dry and examine the smear under slow running tap water.
Inference:
Gram positive purple coloured and rod shaped bacteria.
Gram positive purple coloured and chain in shaped, cocci bacteria.
Gram negative pink coloured and rod shaped bacteria.
Gram negative
Staining-pink color
Peptidoglycan layer is thin hence low% of peptidoglycans lipid content
It has outer cell membrane
Importance:
Cell wall is a the layer fairly rigid, that lies just outside the plasma membrane
It helps in determine the shape of the cell
It protect the cell from asmotic laysis
It can contribute to pathogencity
The important of cell wall is flecked in the fact that relatively few prokaryotes cell wall
Major component of cell wall is peptidoglycan
Composition:

PEPTIDOGLYCAN substance present in most gram positive and gram negative
organism.
It has two parts
Glycan: It is made up of N-acetyl glucosomine and N-acetyl muramic acid linked by β-
1,4 glycosidic linkage.
NAG.............NAM [Lactyl ester of NAG]
Peptide: It consists of two parts:
Tetra peptide: It consists of various D and L form of amino acid connected to carboxyl
group of N-acetyl mumaric acid. They are:
Gram negative - L-alanine,D-glutamic acid,diamino pimelic acid,D-alanine.
Peptide linkage:
Peptide linkage is formed between D-alanine and L-lysine (in case of gram +ve) and
diamino primalic acid (in case of gram –ve)
The peptide chain (containing &amino acids) are linked to “NAM” and a peptide chain in
the two side chains.
In gram negative cell wall inter chain peptide linkage is a CO-NH linkage
In the lactyl group because of the free C=0 group (in NAM peptide) chain is attached to
it for example in gram negative cell wall
Peptidoglycan substance present in most gram positive and gram negative organism.
It has two parts
Glycan: It is made up of N-acetyl glucosomine and N-acetyl muramic acid linked by β-
1, 4 glycosidic linkages.
NAG.............NAM [Lactyl ester of NAG]
Peptide: It consists of two parts:
Tetra peptide: It consists of various D and L form of amino acid connected to carboxyl
group of N-acetyl mumaric acid. They are:-
Gram negative - L-alanine, D-glutamic acid, diamino pimelic acid,D-alanine.
Peptide linkage:
Peptide linkage is formed between D-alanine and L-lysine (in case of gram +ve) and
diamino primalic acid (in case of gram –ve)
The peptide chain (containing &amino acids) are linked to “NAM” and a peptide chain in
the two side chains.
In gram negative cell wall inter chain peptide linkage is a CO-NH linkage

In the lactyl group because of the free C=0 group (in NAM peptide) chain is attached to
it for example in gram negative cell wall
GRAM NAGATIVE CELL WALL: It has 3 major components.
Outer membrane:
BROWN’S LIPOPROTEIN
It acts as a connective line between peptidoglycan layer and the outermost layer and the
outermost layer.
It is most aboundent protein in outer membrane.
Lipo polysaccharides:
Large and complex molecules containing both lipid and carbohydrate.
It consists of three parts.
Lipid (A): It is an endotoxin because it is attached to the micro organisms.
It is glucosomes sugar with fatty acids and phosphate(or0 pyrophasphate attached.
Core polysaccharide:
Joined to lipid A
Made up of 10 different saccharide units depending on the species of bacteria.
o-polysaccharides:
Size is 600-700 Dalton
Helps information or poles for exchange or passage of small molecule like glucose and
other mono sacharides.
It is called ‘o’ antigen because it elicits an immenoresponse.
PORINS:
Size is 600-700Dalt.
Helps in formation of poles for exchange or passage of small molecules like glucose and
other monosaccharides.
Porin protein cluster together to form a trimer in outer membrane.
PERIPLASMIC SPACE:
Contain peptidoglcan in case of gram negative.
Contains periplasm having absorption, protein hydrolytic enzyme etc.
STRUCTURE OF GRAM POSITIVE CELL WALL
Gram positive bacteria usually have a much greater amount of peptidoglycan in their
cell wall than do gram negative bacteria.
Cell wall made up of 95% peptidoglycan and 10% techoic acid.

Peptidoglycan: It is made up of alternating chains of N-acetylglucosamine and N-acetyl
muramic acid molecule. These chains are cross linked by peptide chains. 80nm thick.
The space between peptidoglycan and cytoplasmic membrane is called perilasmic space.
Teichoic acid: It consists of two acids. They are lipotechoic acids and poltechoic acid.
Lipotechoic acid- polymer of glycerol phosphate
Poltechoic acid- polymer of ribitol phosphate
The cell wall of streptococcus aureus contain techoic acid (glycerol phosphate, ribitol
phosphate) covalently linked with peptidoglycan which can be extracted with cold dilute
acid.
Teichoic acid bind magnesium ions and there is some evidence that they help to protect
bacteria from thermal injury.
Lipid: The cell wall of most gram positive bacteria contain very amount of lipid.
Functions of Teichoic acid:-
Helps in attachment of bacteria to host cell.
Prevent phagocytosis.
It is highly antigenic in nature.
Function of peptidoglycan:-
Maintain osmotic balance.
Act as a barrier.
BIOCHEMICAL METHODS & SEROLOGICAL TECHNIQUES
Typically microorganisms have been identified by their particular growth patterns and
biochemical characteristics.
Some Biochemical Tests Used by Clinical Microbiologists in the Diagnosis of Bacteria
from the Patient’s Specimen.

a. Methyl Red Test
This is a qualitative test of the acidity produced by bacteria grown in MR-VP broth. After
the addition of several drops of methyl red solution, a bright red color (left tube) is a

positive test; a yellow or orange color (right tube) is a negative test. Used to separate
enterics, for example E. coli is MR positive and Enterobacter aerogenes is MR negative.
b. Voges-Proskauer Reaction
VP-positive bacteria produce acetylmethylcarbinol or acetoin, which reacts with the
reagents to produce a red color (left tube); a VP-negative tube is shown on the right.
Used to differentiate Bacillus species and enterics. For example, E. coli is VP negative
and Enterobacter aerogenes is VP positive.
c. Starch Hydrolysis
After incubation on starch agar, plates are flooded with iodine solution. A positive test is
indicated by the colorless area around the growth (left); a negative test is shown on the
right. Used to detect the production of α-amylase by certain bacteria.
d. Tube Catalase Test
After incubation of slant cultures, 1 ml of 3% hydrogen peroxide is trickled down the
slants. Catalase converts hydrogen peroxide to water and oxygen bubbles (left tube); a
negative catalase test is shown in the right tube. Used to differentiate Streptococcus
(catalase negative) from Staphylococcus (catalase positive).
e. Slide Catalase Test

A wooden applicator stick (or nichrome wire loop) is used to pick up a colony from a
culture plate and place it in a drop of hydrogen peroxide on a glass slide. A positive
catalase reaction (left slide) shows gas bubbles; a negative catalase reaction reveals an
absence of gas bubbles (right slide). Used to differentiate Streptococcus (catalase
negative) from Staphylococcus (catalase positive).
f. Nitrate Reduction
After 24–48 hours of incubation, nitrate reagents are added to culture tubes. The tube
on the left illustrates gas formation (a positive reaction for nitrate reduction); the tube
in the middle is a positive reaction for nitrate reduction to nitrite as indicated by the red
color; the tube on the right is a negative broth control. Used to test for miscellaneous
gram-negative bacteria.
g. Test for Amino Acid Decarboxylase
The tube on the left is an uninoculated control; the second tube from the left is lysine
decarboxylase negative; the third tube is lysine decarboxylase positive; and the tube on
the right is lysine deaminase positive. Used to classify enteric bacteria. Recommended
for detection of arginine dihydrolase and lysine and ornithine decarboxylase activities.

h. Test for Indole
Tryptophan can be broken down to indole by some bacteria. The presence of indole is
detected by adding Kovacs’ reagent. A red color on the surface is a positive test for
indole (left tube) and an orange-yellow color is a negative test for indole (right tube).
Used to separate enterics such as E. coli (indole positive) and Enterobacter (indole
negative).
i. Gelatin Hydrolysis or Liquefaction
If gelatin is hydrolyzed by the enzyme gelatinase, it does not gel when cooled but
remains a liquid. Thus it flows when the culture is tilted backward (right tube). A
negative control is on the left. Note that the solid gelatin does not flow when the tube is
tilted. Used to differentiate a variety of heterotrophic bacteria, such as clostridia.
j. Phenylalanine Deamination Test
When 10% ferric chloride is added to a phenylalanine deaminase agar slant culture, a
dark green color (tube on the right) is a positive test for the enzyme. The tube on the left
is an uninoculated control, and the tube in the middle is a negative test. Used to

differentiate members of the Proteus group (Proteus vulgaris, positive, from E. coli,
negative).
k. Bile Solubility for Pneumococcus
The tube on the left and the one in the middle contain cultures of pneumococcus
(Streptococcus pneumoniae). The tube on the right contains α-streptococcus. One-tenth
ml of deoxycholate was added to the middle and right tubes, and 0.1 ml of distilled
water was added to the left tube. The pneumococci in the center are bile soluble, as
indicated by the clear suspension. The bacteria in the right tube are not bile soluble, as
indicated by the turbidity.
l. Stormy Fermentation of Litmus Milk
The tube on the left shows fermentation; the tube on the right is negative for stormy
fermentation. Used for the identification of Clostridium species.
m. Fermentation Reactions
The tube on the left shows acid (yellow color) and gas in the Durham tube. The center
tube shows no carbohydrate utilization to produce acid or gas. The tube on the right
has less acid formation than that on the left. Used to separate enterics.
n. Oxidase Test

Filter paper is moistened with a few drops of 1% tetramethyl-p-phenylenediamine
dihydrochloride. With a wooden applicator, growth from an agar medium is smeared on
the paper. A positive test is the development of a purple color within 10 seconds. Used
to separate enterics from pseudomonads. For example, Pseudomonas aeruginosa is
positive and E. coli is negative.
o. Bacitracin Sensitivity Test
The bacteria on the left are presumptively identified as group A streptococci because of
inhibition by the antibiotic bacitracin. The bacteria on the right (Enterococcus faecalis)
are bacitracin resistant.
p. Identification of Neisseria gonorrhoeae
Oxidase-positive test on filter paper is shown on the left. Identicult reaction for N.
gonorrhoeae (center). The plate on the right shows characteristic growth on modified
Thayer-Martin medium.
q. Optochin Sensitivity

An optochin disk on blood agar specifically inhibits pneumococci. The optochin test for
Streptococcus pneumonia is based on the zone of inhibition.
r. Urease Production
Christensen urea agar slants. Urease-positive bacteria hydrolyze urea to ammonia,
which turns the phenol red indicator red-violet. From left to right: uninoculated control,
delayed positive (>24 hrs), rapidly positive (<4 hrs), negative reaction.
Used to separate enterics.
s. Triple Sugar Iron Agar Reactions
Left to right: left tube is an uninoculated control, second tube is K/K (nonfermenter),
third tube is A/A with gas indicating lactose or sucrose fermentation, and the right tube
is K/A plus H2S production. A stands for acid production, and K indicates that the
medium becomes alkaline. Used for the differentiation of members of the

Enterobacteriaceae based on the fermentation of lactose, sucrose, glucose, and the
production of H2S.
t. Lowenstein-Jensen Medium
Growth of Mycobacterium tuberculosis showing nodular and nonpigmented growth.
PHAGE TYPING
Bacteriophages (phages) are viruses that attack members of a particular bacterial
species, or strains within a species. Bacteriophage (phage) typing is based on the
specificity of phage surface receptors for cell surface receptors. Only those
bacteriophages that can attach to these surface receptors can infect bacteria and cause
lysis. On a petri dish culture, lytic bacteriophages cause plaques on lawns of sensitive
bacteria. These plaques represent infection by the virus.
In bacteriophage typing the clinical microbiologist inoculates the bacterium to be tested
onto a petri plate. The plate is heavily and uniformly inoculated with a cotton swab so
that the bacteria will grow to form a solid sheet or lawn of cells. No uninoculated areas
should be left. The plate is then marked off into squares (15 to 20 mm per side), and
each square is inoculated with a drop of suspension from the different phages available
for typing. After the plate is incubated for 24 hours, it is observed for plaques. The
phage type is reported as a specific genus and species followed by the types that can
infect the bacterium. For example, the series 10/16/24 indicates that this bacterium is
sensitive to phages 10, 16, and 24, and belongs to a collection of strains, called a
phagovar, that have this particular phage sensitivity. Bacteriophage typing remains a
tool of the research and reference laboratory.
FATTY ACID PROFILES
Gram-negative cell walls are much more complex than gram-positive walls. The thin
peptidoglycan layer next to the plasma membrane may constitute not more than 5 to
10% of the wall weight. In E. coli it is about 2 nm thick and contains only one or two

layers or sheets of peptidoglycan. The outer membrane lies outside the thin
peptidoglycan layer.
The most abundant membrane protein is Braun’s lipoprotein, a small lipoprotein
covalently joined to the underlying peptidoglycan and embedded in the outer membrane
by its hydrophobic end. The outer membrane and peptidoglycan are so firmly linked by
this lipoprotein that they can be isolated as one unit.
Another structure that may strengthen the gram-negative wall and hold the outer
membrane in place is the adhesion site. The outer membrane and plasma membrane
appear to be in direct contact at many locations in the gram-negative wall. In E. coli 20
to 100 nm areas of contact between the two membranes are seen in plasmolyzed cells.
Adhesion sites may be regions of direct contact or possibly true membrane fusions. It
has been proposed that substances can move into the cell through these adhesion sites
rather than traveling through the periplasm.
Possibly the most unusual constituents of the outer membrane are its
lipopolysaccharides (LPSs).
The Gram-Negative Envelope.
A Chemical Model of the E. coli Outer Membrane and Associated Structures.

This crosssection is to-scale. The porin OmpF has two channels in the front (solid
arrows) and one channel in the back (open arrow) of the trimeric protein complex.
LPS molecules can be longer than the ones shown here.
These large, complex molecules contain both lipid and carbohydrate, and consist of
three parts: (1) lipid A, (2) the core polysaccharide, and (3) the O side chain. The LPS
from Salmonella typhimurium has been studied most, and its general structure is
described here.
Lipopolysaccharide Structure.
(a) The lipopolysaccharide from Salmonella. This slightly simplified diagram
illustrates one form of the LPS. Abbreviations: Abe, abequose; Gal, galactose; Glc,
glucose; GlcN, glucosamine; Hep, heptulose; KDO, 2-keto-3-deoxyoctonate; Man,
mannose; NAG, N-acetylglucosamine; P, phosphate; Rha, L-rhamnose. Lipid A is
buried in the outer membrane. (b) Molecular model of an Escherichia coli

lipopolysaccharide. The lipid A and core polysaccharide are straight; the O side
chain is bent at an angle in this model.
The lipid A region contains two glucosamine sugar derivatives, each with three fatty
acids and phosphate or pyrophosphate attached. It is buried in the outer membrane
and the remainder of the LPS molecule projects from the surface. The core
polysaccharide is joined to lipid A. In Salmonella it is constructed of 10 sugars, many
of them unusual in structure. The O side chain or O antigen is a polysaccharide chain
extending outward from the core. It has several peculiar sugars and varies in
composition between bacterial strains. Although O side chains are readily recognized by
host antibodies, gramnegative bacteria may thwart host defenses by rapidly changing
the nature of their O side chains to avoid detection. Antibody interaction with the LPS
before reaching the outer membrane proper may also protect the cell wall from direct
attack. The LPS is important for several reasons other than the avoidance of host
defenses. Since the core polysaccharide usually contains charged sugars and
phosphate, LPS contributes to the negative charge on the bacterial surface. Lipid A is a
major constituent of the outer membrane, and the LPS helps stabilize membrane
structure. Furthermore, lipid A often is toxic; as a result the LPS can act as an
endotoxin and cause some of the symptoms that arise in gram-negative bacterial
infections.
A most important outer membrane function is to serve as a protective barrier. It
prevents or slows the entry of bile salts, antibiotics, and other toxic substances that
might kill or injure the bacterium. Even so, the outer membrane is more permeable
than the plasma membrane and permits the passage of small molecules like glucose
and other monosaccharides. This is due to the presence of special porin proteins.
Three porin molecules cluster together and span the outer membrane to form a narrow
channel through which molecules smaller than about 600 to 700 daltons can pass.
Larger molecules such as vitamin B12 must be transported across the outer membrane
by specific carriers. The outer membrane also prevents the loss of constituents like
periplasmic enzymes.
FLOW CYTOMETRY
Classical microbiological techniques are relatively slow in comparison to analytical
techniques, in many cases due to the need to culture microorganisms. Furthermore,
classical techniques are not useful in identifying those microorganisms that can’t be

cultured. The recent emergence of molecular biological techniques, particularly those
using antibodies and nucleic acid probes combined with amplification techniques, has
provided the clinical laboratory with rapid and very specific techniques for
microbiological diagnosis. One such new technique is flow cytometry and fluorescence.
Flow cytometry allows single- or multiple-microorganism detection in clinical samples
in an easy, reliable, fast way. In flow cytometry, microorganisms are identified on the
basis of their peculiar cytometric parameters or by means of fluorochromes that can be
used either independently or bound to specific antibodies or oligonucleotides. The flow
cytometer forces a suspension of cells through a laser beam and measures the light
they scatter or the fluorescence the cells emit as they pass through the beam. For
example, cells can be tagged with a fluorescent antibody directed against a specific
surface antigen. As the stream of cells flows past the laser beam, the fluorescent cells
can be detected, counted, and even separated from the other cells in the suspension.
The cytometer also can measure a cell’s shape, size, and content of DNA and RNA. This
technique has permitted the development of quantitative methods to access
antimicrobial susceptibility and drug cytotoxicity in a rapid, accurate, and highly
reproducible way. The most outstanding contribution of this technique is the ability to
detect the presence of heterogenous microbial populations with different responses to
antimicrobial treatments.
DNA BASE COMPOSITION
Microbial genomes can be directly compared, and taxonomic similarity can be estimated
in many ways. The first, and possibly the simplest, technique to be employed is the
determination of DNA base composition. DNA contains four purine and pyrimidine
bases: adenine (A), guanine (G), cytosine (C), and thymine (T).
In double-stranded DNA, A pairs with T, and G pairs with C. Thus the (G + C)/ (A+T)
ratio or G + C content, the percent of G + C in DNA, reflects the base sequence and
varies with sequence changes as follows:
The base composition of DNA can be determined in several ways. Although the G + C
content can be ascertained after hydrolysis of DNA and analysis of its bases with high-
performance liquid chromatography (HPLC), physical methods are easier and more
often used. The G +C content often is determined from the melting temperature (Tm)
of DNA. In double-stranded DNA three hydrogen bonds join GC base pairs, and two
bonds connect AT base pairs.

As a result DNA with a greater G + C content will have more hydrogen bonds, and its
strands will separate only at higher temperatures—that is, it will have a higher melting
point. DNA melting can be easily followed spectrophotometrically because the
absorbance of 260 nm UV light by DNA increases during strand separation. When a
DNA sample is slowly heated, the absorbance increases as hydrogen bonds are broken
and reaches a plateau when all the DNA has become single stranded.
A DNA Melting Curve.
The Tm is indicated.
The midpoint of the rising curve gives the melting temperature, a direct measure of the
G + C content. Since the density of DNA also increases linearly with G +C content, the
percent G + C can be obtained by centrifuging DNA in a CsCl density gradient.
The G + C content of many microorganisms has been determined.
Representative G + C Contents of Microorganisms
The G +C content of DNA from animals and higher plants averages around 40% and
ranges between 30 and 50%. In contrast, the DNA of both eucaryotic and procaryotic
microorganisms varies greatly in G +C content; procaryotic G +C content is the most
variable, ranging from around 25 to almost 80%. Despite such a wide range of variation,
the G + C content of strains within a particular species is constant. If two organisms
differ in their G + C content by more than about 10%, their genomes have quite
different base sequences. On the other hand, it is not safe to assume that organisms
with very similar G + C contents also have similar DNA base sequences because two
very different base sequences can be constructed from the same proportions of AT and
GC base pairs. Only if two microorganisms also are alike phenotypically do their similar
G + C content suggest close relatedness.

G +C content data are taxonomically valuable in at least two ways. First, they can
confirm a taxonomic scheme developed using other data. If organisms in the same
taxon are too dissimilar in G + C content, the taxon probably should be divided.
Second, G + C content appears to be useful in characterizing prokaryotic genera since
the variation within a genus is usually less than 10% even though the content may vary
greatly between genera. For example, Staphylococcus has a G +C content of 30 to 38%,
whereas Micrococcus DNA has 64 to 75% G + C; yet these two genera of gram-positive
cocci have many other features in common.
DNA FINGERPRINTING
Plasmid fingerprinting identifies microbial isolates of the same or similar strains;
related strains often contain the same number of plasmids with the same molecular
weights and similar phenotypes. In contrast, microbial isolates that are phenotypically
distinct have different plasmid fingerprints. Plasmid fingerprinting of many E. coli,
Salmonella, Campylobacter, and Pseudomonas strains and species has demonstrated
that this method often is more accurate than other phenotyping methods such as
biotyping, antibiotic resistance patterns, phage typing, and serotyping.
The technique of plasmid fingerprinting involves five steps:

1. The bacterial strains are grown in broth or on agar plates.
2. The cells are harvested and lysed with a detergent.
3. The plasmid DNA is separated from the chromosomal DNA.
4. The plasmid DNA is applied to agarose gels and electrophoretically separated.
5. The gel is stained with ethidium bromide, which binds to DNA, causing it to fluoresce
under UV light. The plasmid DNA bands are then located.
Because the migration rate of plasmid DNA in agarose is inversely proportional to the
molecular weight, plasmids of a different size appear as distinct bands in the stained
gel. The molecular weight of each plasmid species can then be determined from a plot of
the distance that each species has migrated versus the log of the molecular weights of
plasmid markers of known size that have been electrophoresed simultaneously in the
same gel.
Plasmid Fingerprinting: Agarose gel electrophoresis of plasmid DNA.
rRNA SEQUENCES
Although a variety of molecular techniques are used in estimating the phylogenetic
relatedness of procaryotes, the comparison of 16S rRNAs isolated from thousands of
strains is of particular importance.
Small Ribosomal Subunit RNA

Representative examples of rRNA secondary structures from the three primary
domains: bacteria (Escherichia coli), archaea (Methanococcus vannielii), and
eucarya (Saccharomyces cerevisiae). The red dots mark positions where bacteria
and archaea normally differ.
The association coefficients or Sab values from rRNA studies are assumed to be a true
measure of relatedness; the higher the Sab values obtained from comparing two
organisms, the more closely the organisms are related to each other. If the sequences of
the 16S rRNAs of two organisms are identical, the Sab value is 1.0. Sab values also are a
measure of evolutionary time. A group of procaryotes that branched off from other
prokaryotes long ago will exhibit a large range of Sab values because it has had more
time to diversify than a group that developed more recently.
Examples of Phylogenetic Trees.
(a) Unrooted tree joining four taxonomic units. (b)Rooted tree
That is, the narrower the range of Sab values in a group of procaryotes, the more
modern it is. After Sab values have been determined, a computer calculates the

relatedness of the organisms and summarizes their relationships in a tree or
dendrogram.
Oligonucleotide signature sequences are specific oligonucleotide sequences that
occur in most or all members of a particular phylogenetic group. They are rarely or
never present in other groups, even closely related ones. Thus signature sequences can
be used to place microorganisms in the proper group. Signature sequences have been
identified for bacteria, archaea, eucaryotes, and many major prokaryotic Groups.
Selected 16S rRNA Signature Sequences for Some Bacterial Groupsa
Although rRNA comparisons are useful above the species level, DNA similarity studies
sometimes are more effective in categorizing individual species and genera. These
comparisons can be carried out using G + C content or hybridization studies, as already
discussed. Techniques such as direct sequence analysis and analysis of DNA restriction
fragment pat terns also can be used. There are advantages to DNA comparisons.
As with rRNA, the DNA composition of a cell does not change with growth conditions.
DNA comparisons also are based on the complete genomes rather than a fraction, and
make it easier to precisely define a species based on the 70% relatedness criterion.
Many protein sequences are currently used to develop phylogenetic trees. This approach
does have some advantages over rRNA comparisons. A sequence of 20 amino acids has
more information per site than a sequence of four nucleotides. Protein sequences are

less affected by organism-specific differences in G+ C content than are DNA and RNA
sequences. Finally, protein sequence alignment is easier because it is not dependent on
secondary structure as is an rRNA sequence. Proteins evolve at different rates, as might
be expected. Indispensable proteins with constant functions do not change as rapidly
(e.g., histones and heat-shock proteins), whereas proteins such as immunoglobulins
evolve quite rapidly. Thus not all proteins are suitable for studying large-scale changes
that occur over long periods. As mentioned earlier, there is a question about the
adequacy of protein based clocks.
It is clear that sequences of all three macromolecules can provide valuable phylogenetic
information. However, different sequences sometimes produce different trees, and it
may be difficult to decide which result is most accurate. Presumably more molecular
data plus further study of phenotypic properties will help resolve uncertainties.
NUCLEIC ACID HYBRIDIZATION
The similarity between genomes can be compared more directly by use of nucleic acid
hybridization studies. If a mixture of singlestranded DNA formed by heating dsDNA is
cooled and held at a temperature about 25°C below the Tm, strands with
complementary base sequences will reassociate to form stable dsDNA, whereas
noncomplementary strands will remain single.
Because strands with similar, but not identical, sequences associate to form less
temperature stable dsDNA hybrids, incubation of the mixture at 30 to 50°C below the
Tm will allow hybrids of more diverse ssDNAs to form. Incubation at 10 to 15°C below
the Tm permits hybrid formation only with almost identical strands. In one of the more
widely used hybridization techniques, nitrocellulose filters with bound nonradioactive
DNA strands are incubated at the appropriate temperature with single-stranded DNA
fragments made radioactive with 32P, 3H, or 14C. After radioactive fragments are
allowed to hybridize with the membrane-bound ss- DNA, the membrane is washed to
remove any nonhybridized ssDNA and its radioactivity is measured. The quantity of
radioactivity bound to the filter reflects the amount of hybridization and thus the
similarity of the DNA sequences. The degree of similarity or homology is expressed as
the percent of experimental DNA radioactivity retained on the filter compared with the
percent of homologous DNA radioactivity bound under the same conditions. (Table
provides examples).

Two strains whose DNAs show at least 70% relatedness under optimal hybridization
conditions and less than a 5% difference in Tm often are considered members of the
same species. If DNA molecules are very different in sequence, they will not form a
stable, detectable hybrid. Therefore DNA-DNA hybridization is used to study only
closely related microorganisms. More distantly related organisms are compared by
carrying out DNARNA hybridization experiments using radioactive ribosomal or transfer
RNA. Distant relationships can be detected because Rrna and tRNA genes represent
only a small portion of the total DNA genome and have not evolved as rapidly as most
other microbial genes. The technique is similar to that employed for DNA-DNA
hybridization: membrane-bound DNA is incubated with radioactive rRNA, washed, and
counted. An even more accurate measurement of homology is obtained by finding the
temperature required to dissociate and remove half the radioactive rRNA from the
membrane; the higher this temperature, the stronger the rRNA-DNA complex and the
more similar the sequences.
Comparison of Neisseria Species by DNA Hybridization Experiments
Nucleic Acid Melting and Hybridization

Complementary strands are shown in different colors.
NUMERICAL TAXONOMY
The development of computers has made possible the quantitative approach known as
numerical taxonomy. Peter H. A. Sneath and Robert Sokal have defined numerical
taxonomy as “the grouping by numerical methods of taxonomic units into taxa on the
basis of their character states.” Information about the properties of organisms is
converted into a form suitable for numerical analysis and then compared by means of a
computer. The resulting classification is based on general similarity as judged by
comparison of many characteristics, each given equal weight. This approach was not
feasible before the advent of computers because of the large number of calculations
involved. The process begins with a determination of the presence or absence of selected
characters in the group of organisms under study. A character usually is defined as an
attribute about which a single statement can be made. Many characters, at least 50
and preferably several hundred, should be compared for an accurate and reliable
classification. It is best to include many different kinds of data: morphological,
biochemical, and physiological.
After character analysis, an association coefficient, a function that measures the
agreement between characters possessed by two organisms, is calculated for each pair
of organisms in the group.
The simple matching coefficient (SSM), the most commonly used coefficient in
bacteriology, is the proportion of characters that match regardless of whether the
attribute is present or absent.
Sometimes the Jaccard coefficient (SJ) is calculated by ignoring any characters that
both organisms lack. Both coefficients increase linearly in value from 0.0 (no matches)
to 1.0 (100% matches). The simple matching coefficients, or other association
coefficients, are then arranged to form a similarity matrix. This is a matrix in which
the rows and columns represent organisms, and each value is an association coefficient
measuring the similarity of two different organisms so that each organism is compared
to every other one in the table.
The Calculation of Association Coefficients for Two Organisms

Clustering in Numerical Taxonomy.
(a) A small similarity matrix that compares six strains of bacteria. The degree of
similarity ranges from none (0.0) to complete similarity (1.0).
(b) The bacteria have been rearranged and joined to form clusters of similar
strains. For example, strains 1 and 2 are the most similar. The cluster of 1 plus 2
is fairly similar to strain 3, but not at all to strain 4
Organisms with great similarity are grouped together and separated from dissimilar
organisms; such groups of organisms are called phenons (sometimes called phenoms).
Numerical taxonomy has already proved to be a powerful tool in microbial taxonomy.
Although it often has simply reconfirmed already existing classification schemes,
sometimes accepted classifications are found wanting. Numerical taxonomic methods
also can be used to compare sequences of macromolecules such as RNA and proteins.

CHEMOTAXONOMY
Chemotaxonomy is the systematic study of chemical variation between plant taxa.
Evidence of chemical variation has essentially been used for classification purpose serve
since ' folk taxonomies’, based on certain obvious plant characteristics were
instinctively employed by mankind centuries ago. These categories, such as edibility,
taste, colour, smell and medicinal value were founded, however unknowingly, on
chemical properties. As long ago as the first century after Christ the aromatic mints had
been recognized and grouped together by Dioscorides.
Awareness of the chemical complexity of plants grew from the desires of Europeans for
exotic spices and condiments as well as investigations into their medicinal properties.
Early knowledge about the subject was summarized in herbals, and concentrated on
information about physiologically active secondary metabolite such as alkaloids and
saponins.
Dur ing the eighteenth and nineteenth century’s knowledge in the field increased, and
some taxonomists made use of several chemical characteristics in attempts to classify
plants and to demonstrate their phylogeny. However, although the chemical characters
they used were recognized, they were manifestations of processes or compounds not yet
completely identified and so their use was based on inadequate knowledge and
evidence.
Gradually the number of recognized natural plant products increased, extending to
include proteins, nucleicacids and the major polysaccharide categories. At the same
time research into plant metabolism revealed similarities and uniformities in the
chemical functioning of plants, while simultaneously highlighting biochemical peculiar
ities which might be taxonomically or phylogenetically significant.
Successful attempts were made to correlatet his variation with known classifications,
and many claims were made as to the taxonomic merit of various chemical character.
However it is only in recent decades that reasonably rapid surveys of plant extracts
have become feasible, due to improved techniques of chemical analysis and the
elucidation of the structures of many organic compounds. Technological advances,
particularly electrophoresis and chromatography, have simplified and speeded up
analyses, and also often made analysis of smaller amounts of material viable. This is
Particularly valuable when rare herbarium material must be used.

It is now generally accepted that certain compounds and related substances may be
characteristic of certain taxonomic groups, and certainly chemotaxonomic
investigations have been employed a tall levels of the taxonomic hierarchy, from sub
variety to division.
It is thought that when the groups in question differentiated, the ability to form a
chemical substance was retained by virtue of metabolic processes retained by the group
or its ancestors. By implication we see that if the pathway of chemical evolution were
established then this might of fer insight to the evolutionary history of the group, as
well as to the understanding of the present –day relationships within and between
groups.
Research has shown that there is generally an inverse relationship between the
taxonomic distribution of a compound or class of compounds and its biogenetic
complexity such that if it is biosynthetically simple and wide spread it may be assumed
to be primitive, while those more limited in their distribution and more complex to
biosynthesise may be assumed more advanced.
However these assumptions prove simplistic when phylogenetic inferences are to be
made from chemical data. Davisand Heywood indicates the following general
complications: -
Chemical compounds and/or biosynthetic pathways are not always environmentally
stable, and so their presence ma y be affected quantitatively or qualitatively by factors
such as temperature or mineral deficiencies.
Biosynthetic knowledge is inadequate about a great many of the chemical characters
used in taxonomy, so that parallelism or convergence might confuse perception of
phylogeny. A compound might arise via two or more entirely distinct biosynthetic
pathways (convergence) and its presence would thus not necessarily imply a
relationship between taxain which it occurs. Quote the case of napthoquinone which
may arise in higher plants via four different pathways).P arallelism may cause similar
end products to arise in related groups, particularly when they are derived from
ubiquitous metabolic intermediates.
In many cases it is not known whether metabolic pathways are reversible or not, and
reversal of a pathway confuses the issue of whether a character is primitive or derived
in a specific taxon.

Large and/or complex molecules are not necessarily the most advanced. Chemical
reduction may occur in plants due to metabolic changes.
Chemical and morphological features may have evolved at different speeds due to
differing selection pressures, and thus on emight find primitive chemical characters
together with advanced morphology in a taxon.
Chemical variability occurs- for example, over a geographic range, or via, chemical
mutants within species. Chemistry may also vary between ontogenetic stages of organs
analysed.
CLASSIFICATION OF BACTERIA ACCORDING TO BERGEY’S MANUAL OF
SYSTEMIC BACTERIOLOGY
Bergey’s Manual of Systematic Bacteriology
In 1923, David Bergey, professor of bacteriology at the University of Pennsylvania, and
four colleagues published a classification of bacteria that could be used for
identification of bacterial species, the Bergey’s Manual of Determinative Bacteriology.
This manual is now in its ninth edition. The first edition of Bergey’s Manual of
Systematic Bacteriology, a more detailed work that contains descriptions of all
procaryotic species currently identified, also is available.
The first volume of the second edition has been published recently. This section briefly
describes the current edition of Bergey’s Manual of Systematic Bacteriology (or Bergey’s
Manual) and then discusses at more length the new second edition.
Because it has not been possible in the past to classify procaryotes satisfactorily based
on phylogenetic relationships, the system given in the first edition of Bergey’s Manual of
Systematic Bacteriology is primarily phenetic. Each of the 33 sections in the four
volumes contains procaryotes that share a few easily determined characteristics and
bears a title that either describes these properties or provides the vernacular names of
the procaryotes included. The characteristics used to define sections are normally
features such as general shape and morphology, Gram-staining properties, oxygen
relationship, motility, the presence of endospores, the mode of energy production, and
so forth. Procaryotic groups are divided among the four volumes in the following
manner: (1) gramnegative bacteria of general, medical, or industrial importance; (2)
gram-positive bacteria other than actinomycetes; (3) gramnegative bacteria with
distinctive properties, cyanobacteria, and archaea; and (4) actinomycetes (gram-positive
filamentous bacteria).

The First Edition of Bergey’s Manual of Systematic Bacteriology
Some Characteristic Differences between Gram-Negative and Gram-Positive
Bacteria.
Gram-staining properties play a singularly important role in this phenetic classification;
they even determine the volume into which a species is placed. There are good reasons
for this significance. Gram staining usually reflects fundamental differences in bacterial
wall structure. Gram-staining properties also are correlated with many other properties
of bacteria.
Typical gram-negative bacteria, gram-positive bacteria, and mycoplasmas (bacteria
lacking walls) differ in many characteristics, as can be seen in table.
For these and other reasons, bacteria traditionally have been classified as gram positive
or gram negative. This approach is retained to some extent in more phylogenetic
classifications and is a useful way to think about bacterial diversity.
The Second Edition of Bergey’s Manual of Systematic Bacteriology
There has been enormous progress in procaryotic taxonomy since 1984, the year the
first volume of Bergey’s Manual of Systematic Bacteriology was published. In particular,
the sequencing of rRNA, DNA, and proteins has made phylogenetic analysis of
procaryotes feasible. As a consequence, the second edition of Bergey’s Manual will be
largely phylogenetic rather than phenetic and thus quite different from the first edition.
Although the new edition will not be completed for some time, it is so important that its
general features will be described here. Undoubtedly the details will change as work
progresses, but the general organization of the new Bergey’s Manual can be
summarized.

The second edition will be published in five volumes. It will have more ecological
information about individual taxa. The second edition will not group all the clinically
important procaryotes together as the first edition did. Instead, pathogenic species will
be placed phylogenetically and thus scattered throughout the following five volumes.
Volume 1—The Archaea, and the Deeply Branching and Phototrophic Bacteria
Volume 2—The Proteobacteria
Volume 3—The Low G + C Gram-Positive Bacteria
Volume 4—The High G + C Gram-Positive Bacteria
Volume 5—The Planctomycetes, Spirochaetes, Fibrobacteres, Bacteroidetes, and
Fusobacteria (Volume 5 also will contain a section that updates descriptions and
phylogenetic arrangements that have been revised since publication of volume 1.)
Organization of Bergey’s Manual of Systematic Bacteriology

The second edition’s five volumes will have a different organization than the first
edition. The greatest change in organization of the volumes will be with respect to the
gram-negative bacteria. The first edition describes all gram-negative bacteria in two
volumes.
Volume 1 contains the gram-negative bacteria of general, medical or industrial
importance; volume 3 describes the archaea, cyanobacteria, and remaining gram-
negative groups. The second edition describes the gram-negative bacteria in three
volumes, with volume 2 reserved for the proteobacteria. The two editions treat the
gram-positive bacteria more similarly. Although volume 2 of the first edition does have
some high G + C bacteria, much of its coverage is equivalent to the new volume 3.
Volume 4 of the first edition describes the actinomycetes and is similar to volume 4 of
the second edition (high G + C gram-positive bacteria), although the new volume 4 will
have broader coverage.

Major Procaryotic Groups and Their Relatedness
Disk size is roughly proportional to the relative number of sequenced procaryotes
in each group. Closely related procaryotic groups are clustered together. Note that
the two procaryotic domains (Bacteria and Archaea) are clearly separate. The
cylinders fade out to indicate that the antiquity of these groups is uncertain.
For example, Micrococcus and Corynebacterium are in volume 2 of the first edition and
will be in volume 4 of the second edition.
Figure depicts the major groups and their relatedness to each other.
Survey of Procaryotic Phylogeny and Diversity
The second edition places procaryotes into 25 phyla, only some of which will be
mentioned here. Recall that all organisms may be placed in one of three domains or
empires as depicted in the universal phylogenetic tree.
We are concerned only with the procaryotic domains, Archaea and Bacteria, in this
survey.
Volume 1 contains a wide diversity of procaryotes in two domains: the Archaea and the
Bacteria. The Archaea differ from Bacteria in many ways as summarized in table
At present, they are divided into two phyla based on rRNA sequences.
The phylum Crenarchaeota contains thermophilic and hyperthermophylic sulfur-
metabolizing organisms of the orders Thermoproteales, Desulfurococcales, and
Sulfolobales. However, recently many other Crenarchaeota have been discovered. Some
are inhibited by sulfur; others grow in the oceans at low temperatures as picoplankton.

The phylum clearly is more diverse than first thought. The second phylum, the
Euryarchaeota, contains primarily methanogenic procaryotes and halophilic
procaryotes; thermophilic, sulfur-reducing organisms (the thermoplasmas and
thermococci) also are in this phylum.
The two phyla are divided into eight classes and 12 orders. The bacteria are an
extraordinarily diverse assemblage of procaryotes that have been divided into 23 phyla.
In volume 1 are placed deeply branching bacterial groups and phototrophic bacteria.
The more important phyla are described in the following sections.
1. Phylum Aquificae. The phylum Aquificae contains autotrophic bacteria such as Aquifex
and Hydrogenobacter that can use hydrogen for energy production. Aquifex (meaning
“water maker”) actually produces water by using hydrogen to reduce oxygen. This group
contains some of the most thermophilic organisms known and is the deepest or earliest
branch of the bacteria.
2. Phylum Thermotogae. This phylum is composed of one class and five genera.
Thermotoga and other members of the class Thermotogae are anaerobic, thermophilic,
fermentative, gram-negative bacteria that have unusual fatty acids and resemble
Aquifex with respect to their etherlinked lipids.
3. Phylum “Deinococcus Thermus.” The order Deinococcales contains bacteria that are
extraordinarily radiation resistant. The genus Deinococcus is gram positive. It has high
concentrations of carotenoid pigments, which may protect it from radiation, and unique
lipids.
4. Phylum Chloroflexi: The phylum Chloroflexi has one class and two orders. Many
members of this gram-negative group are called green nonsulfur bacteria. Chloroflexus
carries out anoxygenic photosynthesis and is a gliding bacterium; in contrast,
Herpetosiphon is a nonphotosynthetic, respiratory gliding bacterium. Both genera have
unusual peptidoglycans and lack lipopolysaccharides in their outer membranes.
5. Phylum Cyanobacteria. The oxygenic photosynthetic bacteria are placed in the phylum
Cyanobacteria, which contains the class Cyanobacteria and five subsections.
Cyanobacteria have chlorophyll a and almost all species possess phycobilins. These
bacteria can be unicellular or filamentous, either branched or unbranched. The
cyanobacteria in the subsections differ from each other in general morphological
characteristics and reproduction. Cyanobacteria incorporate CO2 photosynthetically

through use of the Calvin cycle just like plants and many purple photosynthetic
bacteria.
6. Phylum Chlorobi. The phylum Chlorobi contains anoxygenic photosynthetic bacteria
known as the green sulfur bacteria. They can incorporate CO2 through the reductive
tricarboxylic acid cycle rather than the Calvin cycle and oxidize sulfide to sulfur
granules, which accumulate outside the cell.
Volume 2 of the second edition is devoted completely to the gram-negative
proteobacteria, often called the purple bacteria. The phylum Proteobacteria is a large
and extremely complex group that currently contains over 1,300 species in 384 genera.
Even though they are all related, the group is quite diverse in morphology, physiology,
and life-style. All major nutritional types are represented: phototrophy, heterotrophy,
and chemolithotrophy of several varieties. Many species important in medicine,
industry, and biological research are proteobacteria. Obvious examples are the genera
Escherichia, Neisseria, Pseudomonas, Rhizobium, Rickettsia, Salmonella, and Vibrio. The
phylum is divided into five classes based on rRNA data. Because photosynthetic
bacteria are found in the α, β, and γ classes of the proteobacteria, many believe that the
whole phylum arose from a photosynthetic ancestor. Presumably many strains lost
photosynthesis when adapting metabolically to new ecological niches.
1. Class I—Alphaproteobacteria. The α proteobacteria includes most of the oligotrophic
forms (those capable of growing at low nutrient levels). Rhodospirillum and other purple
nonsulfur bacteria are photosynthetic. Some genera have unusual metabolic modes:
methylotrophy (e.g., Methylobacterium), chemolithotrophy (Nitrobacter), and nitrogen
fixation (Rhizobium). Rickettsia and Brucella are important pathogens. About half of the
microbes in this group have distinctive morphology such as prosthecae (Caulobacter,
Hyphomicrobium).
2. Class II—Betaproteobacteria. The β-proteobacteria overlap the α subdivision
metabolically. However the β- proteobacteria tend to use substances that diffuse from
organic decomposition in the anaerobic zone of habitats. Some of these bacteria use
such substances as hydrogen (Alcaligenes), ammonia (Nitrosomonas), methane
(Methylobacillus), or volatile fatty acids (Burkholderia).
3. Class III—Gammaproteobacteria. The γ-proteobacteria compose a large and complex
group of thirteen orders and 20 families. They often are chemoorganotrophic,
facultatively anaerobic, and fermentative. However, there is considerable diversity

among the γ-proteobacteria with respect to energy metabolism. Some important families
such as Enterobacteriaceae, Vibrionaceae, and Pasteurellaceae use the Embden-
Meyerhof pathway and the pentose phosphate pathway. Others such as the
Pseudomonadaceae and Azotobacteriaceae are aerobes and have the Entner-Doudoroff
and pentose phosphate pathways. A few are photosynthetic (e.g., Chromatium and
Ectothiorhodospira), methylotrophic (Methylococcus), or sulfur-oxidizing (Beggiatoa).
4. Class IV—Deltaproteobacteria. The -proteobacteria contain seven orders, and 17
families. Many of these bacteria can be placed in one of three groups. Some are
predators on other bacteria as the class name implies (e.g., Bdellovibrio). The order
Myxococcales contains the fruiting myxobacteria such as Myxococcus, Stigmatella, and
Polyangium. The myxobacteria often also prey on other bacteria. Finally, the class has a
variety of anaerobes that generate sulfide from sulfate and sulfur while oxidizing
organic nutrients (Desulfovibrio).
5. Class V—Epsilonproteobacteria. This section is composed of only one order,
Campylobacterales, and two families. Despite its small size two important pathogenic
genera are €-proteobacteria: Campylobacter and Helicobacter.
Volume 3 of Bergey’s Manual surveys the gram-positive bacteria with low G + C content
in their DNA, which are members of the phylum Firmicutes. The dividing line is about
50% G +C; bacteria with a mol% lower than this value are in volume 3. Most of these
bacteria are gram positive and heterotrophic. However because of their close
relationship to low G + C gram-positive bacteria, the mycoplasmas are placed here even
though they lack cell walls and stain gram negative. There is considerable variation in
morphology: some are rods, others are cocci, and mycoplasmas are pleomorphic.
Endospores may be present. The phylum contains three classes.
1. Class I—Clostridia. This class contains three orders and 11 families. Although they vary
in morphology and size, the members tend to be anaerobic. Genera such as Clostridium,
Desulfotomaculum, and Sporohalobacter form true bacterial endospores; many others do
not. Clostridium is one of the largest bacterial genera.
2. Class II—Mollicutes. The class Mollicutes contains five orders and six families. Members
of the class often are called mycoplasmas. These bacteria lack cell walls and cannot
make peptidoglycan or its precursors. Because mycoplasmas are bounded by the
plasma membrane, they are pleomorphic and vary in shape from cocci to helical or
branched filaments. They are normally nonmotile and stain gram negative because of

the absence of a cell wall. In contrast with almost all other bacteria, most species
require sterols for growth. The genera Mycoplasma and Spiroplasma contain several
important animal and plant pathogens.
3. Class III—Bacilli. This large class comprises a wide variety of gram positive, aerobic or
facultatively anaerobic, rods and cocci. The class Bacilli has two orders, Bacillales and
Lactobacillales, and 16 families. As with the members of the class Clostridia, some
genera (e.g., Bacillus, Sporosarcina, Paenibacillus, and Sporolactobacillus) form true
endospores.
The section contains many medically and industrially important genera: Bacillus,
Lactobacillus, Streptococcus, Lactococcus, Enterococcus, Listeria, and Staphylococcus.
Volume 4 is devoted to the high G +C gram positives, those bacteria with mol% values
above 50 to 55%. All bacteria in this volume are placed in the phylum Actinobacteria
and class Actinobacteria. There is enormous morphological variety among these
procaryotes. Some are cocci, others are regular or irregular rods. High G + C gram
positives called actinomycetes often form complex branching hyphae. Although none of
these bacteria produce true endospores, many genera do form a variety of asexual
spores and some have complex life cycles. There is considerable variety in cell wall
chemistry among the high G+ C gram positives.
For example, the composition of peptidoglycan varies greatly. Mycobacteria produce
large mycolic acids that distinguish their walls from those of other bacteria.
The taxonomy of these bacteria is very complex. There are five subclasses, six orders,
14 suborders, and 40 families. Genera such as Actinomyces, Arthrobacter,
Corynebacterium, Micrococcus, Mycobacterium, and Propionibacterium were placed in
volume 2 of the first edition.
They are now in the new volume 4 within the suborders Actinomycineae, Micrococcineae,
Corynebacterineae, and Propionibacterineae because rRNA studies have shown them to
be actinobacteria. The largest and most complex genus is Streptomyces, which contains
over 500 species. Volume 5 describes an assortment of nine phyla that are located here
for convenience. The inclusion of these groups in volume 5 does not imply that they are
directly related. Although they are all gram-negative bacteria, there is considerable
variation in morphology, physiology, and life cycle pattern. Several genera are of
considerable biological or medical importance. We will briefly consider four of the nine
phyla.

1. Phylum Planctomycetes. The planctomycetes are related to the chlamydias according to
their rRNA sequences. The phylum contains only one order, one family, and four
genera. Planctomycetes are coccoid to ovoid or pearshaped cells that lack
peptidoglycan. Some have a membrane-enclosed nucleoid. Although they are normally
unicellular, the genus Isosphaera will form chains. They divide by budding and may
produce nonprosthecate appendages called stalks. Planctomycetes grow in aquatic
habitats, and many move by flagella or gliding motility.
2. Phylum Chlamydiae. This small phylum contains one class, one order, and four
families. The genus Chlamydia is by far the most important genus. Chlamydia is an
obligately intracellular parasite with a unique life cycle involving two distinctive stages:
elementary bodies and reticulate bodies. These bacteria do resemble planctomycetes in
lacking peptidoglycan. They are small coccoid organisms with no appendages.
Chlamydias are important pathogens and cause many human diseases.
3. Phylum Spirochaetes. This phylum contains helically shaped, motile, gram-negative
bacteria characterized by a unique morphology and motility mechanism. The exterior
boundary is a special outer membrane that surrounds the protoplasmic cylinder, which
contains the cytoplasm and nucleoid. Periplasmic flagella lie between the protoplasmic
cylinder and the outer membrane. The flagella rotate and move the cell even though
they do not directly contact the external environment. These chemoheterotrophs can be
free living, symbiotic, or parasitic. For example, the genera Treponema and Borrelia
contain several important human pathogens. The phylum has one class, Spirochaetes,
three families, and 13 genera.
4. Phylum Bacteroidetes. This phylum has three classes (Bacteroides, Flavobacteria, and
Sphingobacteria), three orders, and 12 families. Some of the better-known genera are
Bacteroides, Flavobacterium, Flexibacter, and Cytophaga. The gliding bacteria
Flexibacter and Cytophaga are ecologically significant and will be discussed later.
Because Bergey’s Manual is the principal resource in prokaryotic taxonomy and is used
by microbiologists around the world, we will follow Bergey’s Manual in organizing the
survey of prokaryotic diversity.
In so far as possible, the organization of the second edition of Bergey’s Manual will be
employed.
Phylogenetic and organizational details may well change somewhat before publication of
each volume, but the general picture should adequately reflect the second edition.

The classification in the first and second editions of Bergey’s Manual are so different
that two appendixes are provided to help in the transition. Appendix III gives the
classification of prokaryotes according to the first edition. Appendix IV describes the
classification system the second edition of Bergey’s Manual will employ. Finally, it must
be emphasized that procaryotic nomenclature is as much in flux as classification. The
names of families and genera are fairly well established and stable in the new system (at
least in the absence of future discoveries); in fact, many family and genus names
remain unchanged in the second edition of Bergey’s Manual. In contrast, the names of
orders and higher taxa are not always completely settled in the second edition.
An excellent way of keeping up to date is through the use of the Bergey’s Manual Trust
web page (www.cme.msu.edu/Bergeys/). The web page has a variety of information
about such topics as Bergey’s Manual, microbial databases, and culture collections.
The web site also contains Bergey’s revision of the Ribosomal Database Project (RDP)
phylogenetic tree and lists of validly named procaryotic species. The phylogenetic tree
and prokaryotic species lists provide a current view of Bergey’s phylogenetic procaryotic
classification. Because the names of kingdoms, classes, and orders are still changing,
their use will be kept to the minimum necessary for consistency with the use of taxa by
the first edition, ease of communication, and student comprehension. Some higher
taxonomic names may well change in the next few years, but we will still employ them
here for the above reasons.

DICHOTOMOUS KEYS
Classic Dichotomous Keys for Clinically Important Genera.
Schematic outline for the identification of gram-positive bacteria.

Schematic outline for the identification of gram-negative bacteria.
CLADOGRAMS
Cladistics is the study of the pathway of evolution, in which the ancestor–descendant
relationship is always discussed with the topology of a rooted phylogenetic tree, called a
“cladogram”
Cladistics is a method of hypothesizing evolutionary relationships among organisms (i.e.
their phylogeny)
Cladistics was developed in 1950 by the German zoologist, Willi Hennig, but has only
become popular in the last 20-25 years.
Cladistics is based upon the analysis of traits (characters) shared by organisms
The result of a cladistic analysis is a branching tree (cladogram) that represents a
hypothesis about evolutionary relationships.
Assumptions of cladistics
Assumption 1: The characteristics of organisms change over time
Assumption 2: All organisms are related by descent from a common ancestor
Assumption 3: There is a bifurcating or branching pattern of lineage-splitting
The principle of parsimony

Cladistics is based upon the principle of parsimony
The principle of parsimony reasons that given several solutions to a problem, the
simplest one should be accepted
In cladisitics, the cladogram that requires the fewest number of evolutionary changes to
explain the distribution of inheritbale traits (characters) is the most parsimonious
The principle of parsimony does not:
– provide absolute truth
– Necessarily reveal the true phylogeny
The principle of parsimony does:
– reduce conjecture
– indicates those cladistic groupings best supported by the available data
Understanding cladograms
The root of the cladogram represents the ancestral lineage and the tips the
descendants.
Branching points in cladograms are called nodes and represent speciation events.

Part of each lineage’s history is unique to it alone and another part is shared with other
lineages.
Each lineage has ancestors that are unique and ancestors that are shared with other
lineages.
DENDROGRAMS
The results of numerical taxonomic analysis are often summarized with a treelike
diagram called a dendrogram.
A dendrogram showing the results of the analysis in part b. Strains 1 and 2 are
members of a 90-phenon, and strains 1–3 form an 80-phenon. While strains 1–3
may be members of a single species, it is quite unlikely that strains 4–6 belong to
the same species as 1–3.
The diagram usually is placed on its side with the X-axis or abscissa graduated in units
of similarity. Each branch point is at the similarity value relating the two branches. The
organisms in the two branches share so many characteristics that the two groups are
seen to be separate only after examination of association coefficients greater than the
magnitude of the branch point value. Below the branch point value, the two groups

appear to be one. The ordinate in such a dendrogram has no special significance, and
the clusters may be arranged in any convenient order.
The significance of these clusters or phenons in traditional taxonomic terms is not
always evident, and the similarity levels at which clusters are labeled species, genera,
and so on, are a matter of judgment. Sometimes groups are simply called phenons and
preceded by a number showing the similarity level above which they appear (e.g., a 70-
phenon is a phenon with 70% or greater similarity among its constituents). Phenons
formed at about 80% similarity often are equivalent to species.
UNIVERSAL PHYLOGENETIC TREE
Following the publication in 1859 of Darwin’s On the Origin of Species, biologists began
trying to develop phylogenetic or phyletic classification systems. These are systems
based on evolutionary relationships rather than general resemblance (the term
phylogeny [Greek phylon, tribe or race, and genesis, generation or origin] refers to the
evolutionary development of a species). This has proven difficult for procaryotes and
other microorganisms, primarily because of the lack of a good fossil record. The direct
comparison of genetic material and gene products such as RNA and proteins overcomes
many of these problems.
The studies of Carl Woese and his collaborators on rRNA sequences in procaryotic cells
suggest that procaryotes divided into two distinct groups very early on.
Figure depicts a universal phylogenetic tree that reflects these views. The tree is divided
into three major branches representing the three primary groups: Bacteria, Archaea,
and Eucarya. The archaea and bacteria first diverged, and then the eucaryotes
developed. These three primary groups are called domains and placed above the
phylum and kingdom levels (the traditional kingdoms are distributed among these three
domains). The domains differ markedly from one another.
Eucaryotic organisms with primarily glycerol fatty acyl diester membrane lipids and
eucaryotic rRNA belong to the Eucarya. The domain Bacteria contains procaryotic
cells with bacterial rRNA and membrane lipids that are primarily diacyl glycerol
diesters. Procaryotes having isoprenoid glycerol diether or diglycerol tetraether lipids in
their membranes and archaeal rRNA compose the third domain, Archaea.
It appears likely that modern eucaryotic cells arose from procaryotes about 1.4 billion
years ago. There has been considerable speculation about how eucaryotes might have

developed from procaryotic ancestors. It is not certain how this process occurred, and
two hypotheses have been proposed.
According to the first, nuclei, mitochondria, and chloroplasts arose by invagination of
the plasma membrane to form double-membrane structures containing genetic material
and capable of further development and specialization. The similarities between
chloroplasts, mitochondria, and modern bacteria are due to conservation of primitive
procaryotic features by the slowly changing organelles.
Universal Phylogenetic Tree
These relationships were determined from rRNA sequence comparisons.

UNIT – 2: PROKARYOTIC MICROORGANISM
General properties, Structure, and reproduction: Domain Bacteria: Proteobacteria
(Alpha, Beta, Gamma, Delta and Epsilon Proteobacteria), Cyanobacteria,
Chlorobium, Firmicutes, Actinobacteria, Chlamydiae, Spirochaetes, Bacteroidetes,
Fusobacteria. Domain Archea: Crenarchaeota, Euryarchaeota.
GENERAL PROPERTIES, STRUCTURE, AND REPRODUCTION:
DOMAIN BACTERIA: PROTEOBACTERIA - ALPHA
The α-proteobacteria includes most of the oligotrophic proteobacteria (those capable of
growing at low nutrient levels). Some have unusual metabolic modes such as
methylotrophy (Methylobacterium), chemolithotrophy (Nitrobacter), and the ability to fix
nitrogen (Rhizobium). Members of genera such as Rickettsia and Brucella are important
pathogens; in fact, Rickettsia has become an obligately intracellular parasite. Many
genera are characterized by distinctive morphology such as prosthecae. The class
Alphaproteobacteria has six orders and 18 families.
Phylogenetic Relationships Among Selected α - Proteobacteria.
The relationships of a few species based on 16S rRNA sequence data are shown
Figure illustrates the phylogenetic relationships between some typical α-proteobacteria,
and table summarizes the general characteristics of many of the bacteria.
Characteristics of Selected α – Proteobacteria

PROTEOBACTERIA –BETA
The β-proteobacteria overlaps the β-proteobacteria metabolically but tend to use
substances that diffuse from organic decomposition in the anaerobic zone of habitats.
Some of these bacteria use hydrogen, ammonia, methane, volatile fatty acids, and
similar substances. As with the β-proteobacteria, there is considerable metabolic
diversity; the β-proteobacteria may be chemoheterotrophs, photolithotrophs,
methylotrophs, and chemolithotrophs. The subgroup contains two genera with
important human pathogens: Neisseria and Bordetella.
The class Betaproteobacteria has six orders and 12 families.
Figure shows the phylogenetic relationships between some species of β-proteobacteria,
and table summarizes the general characteristics of many of the bacteria.
Phylogenetic Relationships among Selected β-Proteobacteria.

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