SEMESTER -II
CORE PAPER II: MICROBIAL DIVERSITY
UNIT – I
Introduction & Detailed classification of Eubacteria - Bergey’s Manual and its importance.
UNIT – II
General classification & Characteristics of Archaebacteria and Actinomycetes.
UNIT – III
Taxanomy & General Characteristics of Fungi - Life Cycle of Aspergillus, Mucor, Rhizopus
and Penicillium - Modes of reproduction & its economic importance .
UNIT – IV
Algae – Morphology & General Characters – Basic knowledge on its reproduction & its
economic importance .
UNIT – V
Protozoa – General characteristics and the economic importance of Sarcodina, Mastigophora,
Rhizopoda, Ciliata, Sporozoa.
References
1. Prescott, L.M J.P. Harley and C.A. Klein 1995. Microbiology 2nd edition Wm, C.
Brown publishers.
2. Michael J. Pelczar, Jr. E.C.S. Chan, Moel : Microbiology Mc Graw Hill Book R. Krieg,
1986 Company
3. Stainer R.Y. Ingraham J.L. Wheolis H.H and Painter P.R. 1986 The Microbial world, 5th
edition. Eagle Works Cliffs N.J. Prentica Hall.
Taxonomy
Taxonomy is a subset of systemics. Systemics is the study of organisms in order to place
organisms having similar characteristics into the same group. Using techniques from other sciences
such as biochemistry, ecology, epidemiology, molecular biology, morphology, and physiology,
biologists are able to identify characteristics of a organism.
What is a natural classification?
The natural classification system may be a phenetic system, one that groups organisms
together based on the mutual similarity of their phenotypic characteristics. Although phenetic
studies can reveal possible evolutionary relationships, they are not dependent on phylogenetic
analysis.
What specific nutritional types exist among protozoa?
Most protozoa are chemoheterotrophic. Two types of heterotrophic nutrition are found in
the protozoa: holozoic and saprozoic. In holozoic nutrition, solid nutrients such as bacteria are
acquired by phagocytosis and the subsequent formation of phagocytic vacuoles. Some ciliates have
a specialized structure for phagocytosis called the cytostome (cell mouth). In saprozoic nutrition,
soluble nutrients such as amino acids and sugars cross the plasma membrane by pinocytosis,
diffusion, or carriermediated transport (facilitated diffusion or active transport).
What is a pseudopodium?
Pseudopodia [s., pseudopodium; false feet] are cytoplasmic extensions found in the
amoebae that are responsible for the movement and food capture.
What are the benefits of taxonomy?
Taxonomy organizes large amounts of information about organisms whose members of a
particular group share many characteristics. Taxonomy lets scientists make predictions and design a
hypothesis for future research on the knowledge of similar organisms. A hypothesis is a possible
explanation for an observation that needs experimentation and testing.
If a relative of an organism has the same properties, the organism may also have the same
characteristics. Taxonomy puts microorganisms into groups with precise names, enabling
microbiologists to communicate with each other in an efficient manner. Taxonomy is indispensable
for the accurate identification of microorganisms. For example, once a microbiologist or
epidemiologist identifies a pathogen that infects a patient, physicians know the proper treatment
that will cure the patient.
Write about taxonomic rank and file
A taxonomy has an overlapping hierarchy that forms levels of rank or category similar to an
organization chart. Each rank contains microorganisms that have similar characteristics. A rank can
also have other ranks that contain microorganisms.
Microorganisms that belong to a lower rank have characteristics that are associated with a
higher rank to which the lower rank belongs. However, characteristics of microorganisms of a
lower rank are not found in microorganisms that belong to the same higher rank as the lower-rank
microorganism.
Microbiologists use a microbial taxonomy, which is different from what biologists, who
work with larger organisms, use. Microbial taxonomy is commonly called prokaryotic taxonomy.
The widely accepted prokaryotic taxonomy is Bergey’s Manual of Systematic Bacteriology, first
published in 1923 by the American Society for Microbiology. David Bergey was chairperson of the
editorial board.
In the taxonomy of prokaryotes, the most commonly used rank (in order from
most general to most specific) is:
The basic taxonomic group in microbial taxonomy is the species. Taxonomists working with
higher organisms define their species differently than microbiologists. Prokaryotic species are
characterized by differences in their phenotype and genotype. Phenotype is the collection of visible
characteristics and the behavior of a microorganism. Genotype is the genetic make up of a
microorganism
The prokaryotic species are collections of strains that share many properties and differ
dramatically from other groups or strains. A strain is a group of microorganisms that share
characteristics that are different from microorganisms in other strains. Each microorganism within a
strain is considered to have descended from the same microorganism.
For example, Biovars is a species that contains strains characterized by differences in its
biochemistry and physiology. Morphovars is also a species whose strains differ morphologically
and structurally. Serovars is another species that has strains that are characterized by distinct
antigenic properties (substances that stimulate the production of antibodies).
Microbiologists use the genus of the taxonomy to name microorganisms, which you learned
in Chapter 1. Microorganisms are given a two-part name. The first part is the Latin name for the
genus. The second part is the epithet. Together these parts uniquely identify the microorganism.
The first part of the name is always capitalized and the second part of the name is always lowercase.
Both parts are italicized.
For example, Escherichia coli is a bacterium that is a member of the Escherichia genus and
has the epithet coli. Sometimes the name is abbreviated such as E. coli. However, the abbreviation
maintains the same style as the full name (uppercase, lowercase, italic).
What is numerical taxonomy and why are computers so important to this approach?
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 (table 19.2). 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. Organisms with great similarity are
grouped together and separated from dissimilar organisms; such groups of organisms are called
phenons (sometimes called phenoms).
The results of numerical taxonomic analysis are often summarized with a treelike diagram
called a dendrogram. 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.
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.
Clustering and Dendrograms 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. (c) 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.
Give the names and main distinguishing characteristics of the archea, bacteria and eucarya
What are the major ways in which gram-negative and gram-positive bacteria differ?
Distinguish mycoplasmas from other bacteria.
Write about economic importance of fungi
Useful aspects:
1. Directly used as a food in the form of mushroom
e.g., Morchella esculenta, Coprinus sp etc..
2. Saccharomyces cerevisiae is used in bread making industry and alcohol industry
3. Few fungi are used for processing of food
e.g., Penicillium camemberti is involved in the ripening of cheese.
4. Used for production of antibiotics.
e.g., Penicillin extracted from Penicillium notatum
5. Many important and useful enzymes have been synthesized from various fungi.
e.g., Amylase produced by Aspergillus niger
Harmful aspects:
1. Various parasitic fungi act as casual organisms and infect plants.
e.g., white rust of crucifer caused by Candida albugo
2. Decay of timber: many species of polyporus and Basidiomycetes cause the damage and
decay to the timber wood
3. Spoilage of food stuffs: Penicillium digitatum is responsible for the rotting of citrus fruits.
Mucor, Aspergillus and Fusarium causes damage to the milk and milk products
4. Several important human diseases caused by different species of fungi. For example,
Aspergillus fumigatus is responsible for causing Aspergillosis. The disease is mycoses.
Economic importance of Yeast
1. Yeast (Saccharomyces cereviseae) involved in sugar fermentation and produce alcohol. It
also used for beer and wine making industry.
2. Many types of yeast are responsible for the spoilage of cheese, tomato and other food
products.
3. A few species of yeasts are parasites for higher plants and cause diseases.
4. Several species of yeasts are pathogenic to man causing number of serious diseases. e.g.,
blastomycosis, torulopsis etc.. They attack central nervous system and skin of man.
5. S.cereviseae is used for bread making industry.
Write about economic importance of algae
Useful aspects
1. The algae are used as a direct source of food by several sea animals and fishes. e.g.,
Diatoms with dinoflagellates.
2. Sea weeds have been used as a food for human beings. Several fresh water algae have
also been utilized in the preparation of vitamin foods. The algae are the most important
part of the diet of Japan and China.
3. Agar is also obtained from several marine algae. Japan is the chief agar producing
country and it exports agar to most countries of the world. The agar is used for
preparation of jellies, ice cream etc.. The agar has constantly been used in laboratories
for media preparation.
4. Various countries prepared medicines from algal weeds. For example, antibiotic drug
Chlorellum obtained from algae.
5. The alginic acid is manufactured from the cell wall of Phaeophyceae. Sodium alginate
used in dyes, buttons, combs and many of such things.
6. Due to the presence of potassium chloride in sea weeds, they are used as fertilizers in
many countries.
7. Important part of the food chain in aquatic ecosystems because they fix carbon dioxide
into organic molecules that can be used by heterotrophs.
8. 80% of the earth’s oxygen is believed to be produced by planktonic algae.
9. Algal blooms are indicators of water pollution.
10. Petroleum and natural gas reserves were formed primarily from diatoms and plankton.
11. Many unicellular algae are symbionts in animals.
Harmful aspects:
1. Algae are found in water more abundantly that cause the whole water either green or
blue and cause death of fishes.
2. Some blue green algae have been reported poisonous and they directly cause the death
who drink this contaminated water.
3. The epiphytic algae which are found upon other plants and trees block photosynthesis
and indirectly harm the trees and plants.
4. Some algae form mucilaginous secretions which are the binding material for the harmful
bacteria causing human and animal diseases.
5. Some algae are attached to the ship (fouling of ships) which retards the speed of the
ship.
Economic importance of Diatoms:
1. Used as a food. It acts as a primary producer in food chain of aquatic animals.
2. Used as polishing material.
3. Used as filters in sugar refineries and brewing industries.
4. Used in the manufacture of dynamite.
5. Used in the manufacture of glass, porcelain paints and varnishes
6. Used in making of toothpaste and face powder.
What are
algae?
7. Used for
making light and
heat
resistant
bricks.
the
general
characteristics of
Explain
1. Habitat
 Fresh, marine and brackish water
 Moist rocks, wood, trees, surface of moist soil
 Endosymbionts – protozoa, mollusks, worms and corals
2. Structure of the Plant Body
 Vegetative body – thallus
 Microscopic unicellular – Chlamydomonas
 Macroscopic multicellular - Macrocystis




3. Reproduction
Vegetative, asexual and sexual
Vegetative – fragmentation / fission
Asexual – zoospores, aplanospores, akinetes, auxospores, endospores and cysts
Sexual – Isogamous, Anisogamous, Heterogenous, oogamous
4. Fertilization
 External – outside of gametangia
 Internal – inside of oogonium
5. Zygote
 Diploid – fusion of two gametes
6. Germination
 Direct – Zygote to new plant
 Indirect – zygote to spore to new plant
How do protozoa reproduce asexually and sexually?
Most protozoa reproduce asexually, and some also carry out sexual reproduction. The most
common method of asexual reproduction is binary fission. During this process the nucleus first
undergoes mitosis, then the cytoplasm divides by cytokinesis to form two identical individuals
Protozoan Reproduction. Binary fission in Paramecium caudatum
The most common method of sexual reproduction is conjugation. In this process there is an
exchange of gametes between paired protozoa of complementary mating types (conjugants).
Conjugation is most prevalent among ciliate protozoa. A well-studied example is Paramecium
caudatum. At the beginning of conjugation, two ciliates unite, fusing their pellicles at the contact
point. The macronucleus in each is degraded. The individual micronuclei divide twice by meiosis to
form four haploid pronuclei, three of which disintegrate. The remaining pronucleus divides again
mitotically to form two gametic nuclei, a stationary one and a migratory one. The migratory nuclei
pass into the respective conjugates. Then the ciliates separate, the gametic nuclei fuse, and the
resulting diploid zygote nucleus undergoes three rounds of mitosis. The eight resulting nuclei have
different fates: one nucleus is retained as a micronucleus; three others are destroyed; and the four
remaining nuclei develop into macronuclei. Each separated conjugant now undergoes cell division.
Eventually progeny with one macronucleus and one micronucleus are formed.
Conjugation in Paramecium caudatum, Schematic Drawing. Follow the arrows. After the
conjugants separate, only one of the exconjugants is followed; however, a total of eight new
protozoa result from the conjugation.
Describe about the history of taxonomy
In the mid-1700s, Swedish botanist Carl Linnaeus was one of the first scientists to develop a
taxonomy for living organisms. It is for this reason that he is known as the father of taxonomy.
Linnaeus’ taxonomy grouped living things into two kingdoms: plants and animals.
By the 1900s, scientists had discovered microorganisms that had characteristics that were
dramatically different than those of plants and animals. Therefore, Linnaeus’ taxonomy needed to
be enhanced to encompass microorganisms. In 1969 Robert H. Whitteker, working at Cornell
University, proposed a new taxonomy that consisted of five kingdoms. These were monera,
protista, plantae (plants), fungi, and animalia (animals). Monera are organisms that lack a nucleus
and membrane-bounded organelles, such as bacteria. Protista are organisms that have either a
single cell or no distinct tissues and organs, such as protozoa. This group includes unicellular
eukaryotes and algae. Fungi are organisms that use absorption to acquire food. These include
multicellular fungi and single-cell yeast. Animalia and plantae include only multicellular
organisms. Scientists widely accepted Whitteker’s taxonomy until 1977 when Carl Woese, in
collaboration with Ralph S. Wolfe at the University of Illinois, proposed a new six-kingdom
taxonomy. This came about with the discovery of archaea, which are prokaryotes that lives in
oxygen-deprived environments.
Whitte
ker’s
fivekingdo
m
taxono
my.
B
efore
Woese’
s sixkingdo
m
taxono
my,
scientist
s
grouped
organisms into eukaryotes animals, plants, fungi, and one-cell microorganisms (paramecia)— and
prokaryotes (microscopic organisms that are not eukaryotes). Woese’s six-kingdom taxonomy
consists of:
• Eubacteria (has rigid cell wall)
• Archaebacteria (anaerobes that live in swamps, marshes, and in the intestines of mammals)
• Protista (unicellular eukaryotes and algae)
• Fungi (multicellular forms and single-cell yeasts)
• Plantae
• Animalia
Woese determined that archaebacteria and eubacteria are two groups by studying the rRNA
sequences in prokaryotic cells.
Woese used three major criteria to define his six kingdoms. These are:
• Cell type. Eukaryotic cells (cells having a distinct nucleus) and prokaryotic cell (cells not having a
distinct nucleus)
• Level of organization. Organisms that live in a colony or alone and one-cell organisms and
multicell organisms.
• Nutrition. Ingestion (animal), absorption (fungi), or photosynthesis (plants).
In the 1990s Woese studied rRNA sequences in prokaryotic cells (archaebacteria
and eubacteria) proving that these organisms should be divided into two distinct groups. Today
organisms are grouped into three categories called domains that are represented as bacteria, archaea,
and eukaryotes.
The domains are placed above the phylum and kingdom levels. The term archaebacteria
(meaning from the Greek word archaio “ancient”) refers to the ancient origin of this group of
bacteria that appears to have diverged from eubacteria. The archaea and bacteria came from the
development of eukaryotic organisms.
The evolutionary relationship among the three domains is:
• Domain Bacteria (eubacteria)
• Domain Archaea (archaebacteria)
• Domain Eulcarya (eukaryotes)
Different classifications of organisms are:
• Bacteria
• Eubacteria
• Archaea
• Archaebacteria
• Eukarya
• Protista
• Fungi
• Plantae
• Animalia
The three domains are archaea, bacteria, and eukarya .
• Archaea lack muramic acid in the cell walls.
• Bacteria have a cell wall composed of peptidoglycan and muramic acid. Bacteria also have
membrane lipids with ester-linked, straight-chained fatty acids that resemble eukaryotic membrane
lipids. Most prokaryotes are bacteria. Bacteria also have plasmids, which are small, double-stranded
DNA molecules that are extrachromosomal.
• Eukarya are of the domain eukarya and have a defined nucleus and membrane bound organelles.
Threedomain
taxono
my
Summa
rize the
advant
ages of
using
each
major
group
of
charact
eristics
(morph
ological, physiological/metabolic, ecological, genetic, and molecular) in classification and
identification. How is each group related to the nature and expression of the genome? Give
examples of each type of characteristic.
Morphological Characteristics
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. Although the light microscope has always been a very important tool, its
resolution limit of about 0.2 _m 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.
Some Morphological Features Used in Classification and Identification
Physiological and Metabolic Characteristics
Physiological and metabolic characteristics are very useful because they are directly related
to the nature and activity of microbial enzymes and transport proteins. Since proteins are gene
products, analysis of these characteristics provides an indirect comparison of microbial genomes.
Some Physiological and Metabolic Characteristics Used in Classification and Identification
Molecular Characteristics
Some of the most powerful approaches to taxonomy are through the study of proteins and
nucleic acids. Because these are either direct gene products or the genes themselves, comparisons of
proteins and nucleic acids yield considerable information about true relatedness. These more recent
molecular approaches have become increasingly important in procaryotic taxonomy.
Comparison of Proteins
The amino acid sequences of proteins are direct reflections of mRNA sequences and
therefore closely related to the structures of the genes coding for their synthesis. For this reason,
comparisons of proteins from different microorganisms are very useful taxonomically. There are
several ways to compare proteins. The most direct approach is to determine the amino acid
sequence of proteins with the same function. The sequences of proteins with dissimilar functions
often change at different rates; some sequences change quite rapidly, whereas others are very stable.
Nevertheless, if the sequences of proteins with the same function are similar, the organisms
possessing them are probably closely related. The sequences of cytochromes and other electron
transport proteins, histones, heat-shock proteins, transcription and translation proteins, and a variety
of metabolic enzymes have been used in taxonomic studies. Because protein sequencing is slow and
expensive, more indirect methods of comparing proteins frequently have been employed. The
electrophoretic mobility of proteins is useful in studying relationships at the species and subspecies
levels. Antibodies can discriminate between very similar proteins, and immunologic techniques are
used to compare proteins from different microorganisms.
The physical, kinetic, and regulatory properties of enzymes have been employed in
taxonomic studies. Because enzyme behavior reflects amino acid sequence, this approach is useful
in studying some microbial groups, and group-specific patterns of regulation have been found.
Nucleic Acid 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 (see section 11.2).
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.
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 (table 19.5). 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 does their similar G +C content suggest close
relatedness.
A DNA Melting Curve. The Tm is indicated.
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.
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.
Nucleic Acid Melting and Hybridization.
.
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. 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.
Representative G + C Contents of Microorganisms
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 DNA-RNA 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.
Nucleic Acid Sequencing
Despite the usefulness of G _ C content determination and nucleic acid hybridization
studies, genome structures can be directly compared only by sequencing DNA and RNA.
Techniques for rapidly sequencing both DNA and RNA are now available; thus far RNA
sequencing has been used more extensively in microbial taxonomy.
Most attention has been given to sequences of the 5S and 16S rRNAs isolated from the 50S
and 30S subunits, respectively, of procaryotic ribosomes (see sections 3.3 and 12.2). The rRNAs
are almost ideal for studies of microbial evolution and relatedness since they are essential to a
critical organelle found in all microorganisms. Their functional role is the same in all ribosomes.
Furthermore, their structure changes very slowly with time, presumably because of their constant
and critical role. Because rRNA contains variable and stable sequences, both closely related and
very distantly related microorganisms can be compared. This is an important advantage as distantly
related organisms can be studied only using sequences that change little with time.
There are several ways to sequence rRNA. Ribosomal RNAs can be characterized in terms
of partial sequences by the oligonucleotide cataloging method as follows. Purified, radioactive 16S
rRNA is treated with the enzyme T1 ribonuclease, which cleaves it into fragments. The fragments
are separated, and all fragments composed of at least six nucleotides are sequenced. The sequences
of corresponding 16S rRNA fragments from different procaryotes are then aligned and compared
using a computer, and association coefficients (Sab values) are calculated. Complete rRNAs now
are sequenced using procedures like the following. First, RNA is isolated and purified. Then,
reverse transcriptase is used to make complementary DNA (cDNA) using primers that are
complementary to conserved rRNA sequences. Next, the polymerase chain reaction amplifies the
cDNA. Finally, the cDNA is sequenced and the rRNA sequence deduced from the results.
Write about Bergey’s manual of systametic 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.
The First Edition of Bergey’s Manual of Systematic Bacteriology
Because it has not been possible in the past to classify prokaryotes 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).
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. As noted in chapter 3, 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. 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 prokaryotes feasible. As a
consequence, the second edition of Bergey’s Manual will be largely phylogenetic rather than
phonetic 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
prokaryotes 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.)
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. For
example, Micrococcus and Corynebacterium are in volume 2 of the first edition and will be in
volume 4 of the second edition. summarizes the planned organization of the second edition and
indicates where the discussion of a particular group may be found in this textbook depicts the major
groups and their relatedness to each other
Discuss in detail about the classification of fungi
Non-vascular, achlorophyllous plants
Multicellular eukaryotic
Reproduce by spores
Lack-root, stem and leaves
Little tissue differentiation
Heterotrophic
Saprophytes or parasites
THE BODY PLAN OF FUNGI
Vegetative body consists of mycelia made up of networks of hyphae
Hyphae - Long treads of cells designed to maximize surface area and also transport
nutrients
Fungus-like protists:
 Lack this body structure
 Lack cell walls of chitin
HYPHAE
Hyphae are designed to increase the surface area of fungi and thus facilitate absorption
May grow fast, up to 1 km per day, as they spread throughout a food source
Haustoria - Specialized structures budding off hyphae of parasitic fungi which penetrate
host cells to absorb nutrients
May be coenocytic, having no septa between cells, or septa may be present with pores
through which cytoplasm can flow moving nutrients through out the fungus
Hyphae
Pores
Septa
Coenocytic
MYCETAE
DIVISION
II. MASTIGOMYCOTA
I. GYMNOMYCOTA
III. AMASTOGOMYCOTA
SUBDIVISION
1. Acarisio - ina
CLASS
a) Acarisiomycetes
EXAMPLE
-- Dictyostelium
2. Plasmodio - ina
a) Protosteliomycetes
-- Nematostelium
b) Myxomycetes
-- Ceratomyxa
1. Haplo - ina
2. Diplo - ina
a) Chytridiomycetes
a) Oomycetes
-- Synchitrydium
-- Saproleginia
b) Hypochytridium
-- rhizidiomycetes
c) Plasmodiophoromycetes
-- Plasmodiophora
1. Zygo --ina
2. Asco - ina
a) Zygomycetes
a) Ascomycetes
-- Rhizopus
-- Penicillium
b) Trichomycetes
-- Harpella
3. Basidio -ina
a) Basidiomycetes
-- Agaricus
4. Deutro - ina
a) Deutromycetes
-- Fusarium
Division I: GYMNOMYCOTA
Phogotrophic mode of nutrition
cell wall absent – somatic structure
Two subdivisions
Subdivision 1: Acarisiogymnomycotina (Cellular slime moulds)

Somatic structure are seen as myxamoeba

They fuse together – pseudopodium

Sporocarp develops from pseudopodium

Single class
Class a) Acarasiomycetes

flagellated cells are not seen except one species

Sporocarp usually stalked

Sexual reproduction through macrocysts
 e.g., Dictyostelium, Polysphondylium
Subdivision 2: Plasmodiogymnomycotina (True slimemoulds)
 Somatic structure – simple myxamoeba
 Fuse to form true pseudopodium
 Two classes
Class a: Protostelomycetes
 Sporocarp develops from myxamoeba /
 No sexual reproduction
 e.g., Nematostelium
Class b: Myxomycetes
 Myxamoeba / flagellated cells fuse – Zygotes
 Mytotic division – true plasmodium
 Sexual reproduction seen
 e.g., Ceratomyxa, Stemonitis
Division II: MASTOGOMYCOTA
plasmodia
Have centriole
Flagellated cells are produced during life cycle
Nutrition – absorptive type
Asexual – Zoospore formation
Two subdivisions
Subdivision 1: Haplomastigomycotina

Uni / biflagellate

Life cycle – haplobiontic haploid / diplobiontic diploid

Three classes
Class a: Chitridiomycetes
 Single posterior flagella – whiplash type
 e.g., Synchytridium
Class b: Hypochridiomycetes
 Aquatic habitats
 Single anterior flagella – tinsel type

e.g., Rhizidiomycetes
Class c: Plasmodiophoromycetes
 Parasitic
 Two anterior flagella – whiplash type
 e.g., Plasmodiophora
Subdivision 2: Diplomastigomycotina

Biflagellated zoosporres

Life cycle – haplobiontic diploid

Singleclass
Class a: Oomycetes (water moulds)
 Cell wall – glucans and cellulose
 Twoflagella (anterior) – one whiplash and one tinsel
 e.g., Sporolegnia
Division III: AMASTOGOMYCOTA
Lack centriole
No motile cells
Mycelium – septate / aseptate
Asexual – budding, fragmentation, conidia formation
Four subdivisions
Subdivision 1: Zygomycotina

Saprobic, parasitic or predatory fungi

Asexual - sporangiospores

Sexual – unequal gametangia fuse - Zygospore

Two classes
Class a: Zygomycetes
 Terriatrial
 Saprophytes / parasites
 Asexual - aplanospores
 e.g., Rhizopus, Mucor
Class b: Trichomycetes
 Symbionts  No sexual reproduction

e.g., Harpella
Subdivision 2: Ascomycotina

Parasitic or Saprophyticy fungi

Uni / Multi cellular, Multi - septate

Meospores (Ascospores) – sac like cells

Single class
Class a: Ascomycetes
 Sexual reproduction - conidia
 e.g., Saccharomyces, Penicillium
Subdivision 3: Basidiomycotina

Meiospores (Basidiospores) - basidiocarp

Asexual - sporangiospores

Single class
Class a: Basidiomycetes
 Long diacaryotic somatic phase
 e.g., Agaricus, Pleurotus
Subdivision 4: Deutromycotina

Parasitic, saprophytic / symbionts some times

Mycelium - septate

Asexual – conidia

Sexual – unknown

Single class
Class a: Deutromycetes
 e.g., Fusarium
Discuss in detail about the classification of algae
Fritsh – 1935
Criteria
1. Organization of membrane bound cell organelles
2. Composition of cell wall
3. Types of photosynthetic pigments
4. Types, number, arrangement and orientation of flagella
5. types of reserve food material
6. types of sexual reproduction
Classes
1. Chlorophyceae (grass-green)
2. Xanthophyceae (yellow-green)
3. Chrysophysea (brown / orange)
4. Bacillarophyceae (yellow / golden brown)
5. Cryptophyceae (nearly brown)
6. Dinophyceae (dark yellow / brown)
7. Chloromonadiae (bright green)
8. Euglininae (pure green)
9. Phaeophyceae (brown)
10. Rhodophyceae (red)
11. Myxophyceae / Cyanophyceae (blue green)
1. Chlorophyseae
Pigments: Chlorophyll a & b + two yellow pigments (carotenoids)
Res food: starch
Structure: motile - 2 to 4 flagella (isokontae), heterotrichous filaments, cell wall – cellulose,
Pyrenoids – surrounded by starch sheath
Reproduction: isogamous to oogamous type (Sexual)
Habitats: mostly fresh water, few marine
e.g., Chlamydomonas, Stigeoclonium
2. Xanthophyseae
Pigments: Yellow xanthophyll found abundantly
Res food: oil
Structure: unicellular motile to simple filamentous, cell wall – petin rich (two equal / unequal
pieces with overlapping edges), Flagella – Heterokontae, pyrenoid absent
Reproduction: isogamous (Sexual-rare)
Habitats: mostly fresh water, few marine
e.g., Botrydium
3. Chrysophyceae
Pigments: brow / orange color chromatophores, accessory pigments – phycochrysin
Res food: Fat, Lucosin
Structure: unicellular motile to branched filamentous, flagella – unequal, anterior
Habitats: colder fresh water, few marine
e.g., Phaeothmnion
4. Bacillarophyceae
Pigments: yellow / golden yellow chromatophores
Res food: fat & volutin
Structure: Unicellular / colonial, cell wall – silica & pectin, two halves, ornamented
Reproduction: Diploid, Special type – fusion of two protoplast
Habitats: Fresh water, sea, soil and terrestrial
e.g., Pinnularia
5. Cryptophyceae
Pigments: diverse with brown shade
Res food: Solid carbohydrates, starch
Structure: motile – slightly unequal flagella, coccoid mostly
Reproduction: Isogamous type
Habitats: Both marine and fresh water
E.g., Cryptomonas
6. Dinophyceae
Pigments: dark yellow, discoid
Res food: starch / oil
Structure: unicellular, motile – flagella two furrows
Reproduction: Isogamous type, rare
Habitats: Sea water plantons, few fresh water forms
e.g., Gyrodinium
7. Chloromonadinea
Pigments: bright green, excess xanthophylls, numerous, discoid
Res food: oil
Structure: motile, flagella – almost equal
Habitats: fresh water forms only
8. Eugleninae
Pigments: Pure green, several in each cell
Res food: Polysaccharide, paramylon
Structure: anterior flagella – arise from base of canal, complex vascular system, predominant
nucleus
Habitats: Only fresh water forms are known
9. Phaeophyceae
Pigments: Brow with yellow – fucoxanthin
Res food: Alcohols (mannitol), polysaccharide (laminarin), fat
Structure: simple filamentous to bulky paranchymatous form, several attain giant sized with ext
and int differentiation
Reproduction: Isogamous to oogamous type, male gamete- two laterally attached flagella
e.g., Sargassum
10. Rhodophyceae
Pigments; red (phycoerythrin), blue (phycocyanin)
Res food: Floridean starch, a polysaccharide similar to starch
Structure: Simple filamentous to complex, motile not known
Reproduction: Advanced oogamous type, male – non motile gametes, female – long receptive
neck, carpospores produced
Habitats: mostly marine, few freshwater
e.g., Gracillaria
11. Myxophyceae
Pigments: Chlorophyll, carotin, phycocyanin and phycoerythrin
Res food: sugar and glycogen
Structure: Simple to filamentous, filaments shows false branching, no motile stages known,
chromatophores diffused all over cytoplasm
Reproduction: no sexual reproduction
Habitats: mostly fresh water
e.g., Nostoc, Anabena
Diagrammatic Algal Bodies: (a) unicellular, motile, Cryptomonas; (b) unicellular, nonmotile,
Palmellopsis; (c) colonial, Gonium; (d) filamentous, Spirotaenia; (e) bladelike kelp,
Monostroma; (f) leafy tubular axis, branched tufts or plumes, Stigeoclonium; (g) unicellular,
nonmotile, Chrysocapsa.
Chlorophyta (Green Algae); Light Micrographs. (a) Chlorella, a unicellular nonmotile green
alga. (b) Volvox, a typical green algal colony. (c) Spirogyra, a filamentous green alga. Four
filaments are shown. Note the ribbonlike, spiral chloroplasts within each filament. (d) Ulva,
commonly called sea lettuce, has a leafy appearance. (e) Acetabularia, the mermaid’s wine
goblet. (f ) Micrasterias, a large desmid.
Chlamydomonas: The Structure and Life Cycle of This Motile Green Alga. During asexual
reproduction, all structures are haploid; during sexual reproduction, only the zygote is diploid.
Euglena. A Diagram Illustrating the Principal Structures Found in This Euglenoid. Notice
that a short second flagellum does not emerge from the anterior invagination. In some euglenoids
both flagella are emergent.
Chrysophyta (Yellow-Green and Golden-Brown Algae; Diatoms). (a) Scanning electron
micrograph of Mallomonas, a chrysophyte, showing its silica scales. The scales are embedded in
the pectin wall but synthesized within the Golgi apparatus and transported to the cell surface in
vesicles. (b) Ochromonas, a unicellular chrysophyte. Diagram showing typical cell structure. (c)
Scanning electron micrograph of a diatom, Cyclotella meneghiniana. (d) Assorted diatoms as
arranged by a light microscopist.
Phaeophyta (Brown Algae). Diagram of the parts of the brown alga, Nereocystis. Due to
the holdfast organ, the heaviest tidal action and surf seldom dislodge brown algae from their
substratum. The stipe is a stalk that varies in length; the bladder is a gas-filled float.
Rhodophyta
(Red Algae). These algae (e.g., Corallina gracilis) are much smaller and more delicate than the
brown algae. Most red algae have a filamentous, branched morphology as seen here.
Dinoflagellates. (a) Ceratium. (b) Scanning electron micrograph of Gymnodinium. Notice the
plates of cellulose and the two flagella: one in the transverse groove and the other projecting
outward.
Write about the outline classification of protozoa
Drawings of Some Representative Protozoa. (a) Structure of the flagellate, Trypanosoma
brucei rhodesiense. (b) The structure of the amoeboid protist, Amoeba proteus. (c) Structure of
an apicomplexan sporozoite. (d) Structure of the ciliate Paramecium caudatum.