Fundamentals of Microbiology

311 Pages·2008·14.41 MB·English

SCHOOL OF DISTANCE EDUCATION

BHARATHIAR UNIVERSITY

POST GRADUATE DIPLOMA COURSE IN
MICROBIAL BIOTECHNOLOGY

STUDY MATERIALS

PAPER I
FUNDAMENTALS OF MICROBIOLOGY
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PAPER I FUNDAMENTALS OF MICROBIOLOGY

PREAMBLE
Scope
Scope
This paper deals with various types of classification of microbes. The paper also throws light
on multifarious habitats of microbes and provides information about all the microbial cellular
functions and various metabolic pathways in microbes.
Objective
To impart knowledge on classification of microbes. This paper is also designed to provide
knowledge on metabolic function and biochemical reaction going on inside the microbial cell
Goal
This paper enables the students to identify any microorganisms. The students will be able to
understand and predict the intermediate metabolism of any microbe used in Industrial
production processes

CONTENTS
UNIT I
CLASSIFICATION AND MOLECULAR SYSTEMATICS: Taxonomy – Classification
of viruses, bacteria and fungi. Molecular systematics – Classical, numerical, polyphasic and
molecular (G+C analysis, DNA-DNA hybridization, 16s rRNA sequencing and construction
of phylogenetic tree) taxonomy

UNIT II
MICROBIAL CELL BIOLOGY AND METABOLISM: General structural organization
of bacteria, viruses, Actinomycetes. Molecular architecture of nucleus, mitochondria,
chloroplast, cell wall, ribosome, cilia, flagella, vacuole and other microbodies. Metabolic
pathways and bioenergetics. Aerobic and anaerobic growth – product formation and
substrate utilization – endogenous and maintenance metabolism.

UNIT III
MICROBIAL GENOMICS AND REPLICATION: Fine structure of gene, genetic code;
Genetic rearrangement – organization of coding sequences and repetitive sequences. Genetic
system of bacteria – transformation, transduction, recombination; plasmids and transposons;
Genetic systems of viruses – phage I, RNA viruses and retroviruses. Genetic system of fungi
– Yeast and Neurospora. Genetic system of protozoa and mycoplasma. Multiplication of
bacteriophages, bacteria and differentiating organisms such as yeast, fungi and
actinomycetes. Sexual and asexual reproduction in bacteria and fungi.

UNIT IV
MICROBIAL ECOLOGY: Soil, aquatic and aerobiology; Influence of environment on
microbial physiology – chemical factors; nutrients – water, C, H, O, N, P, S, growth factors-
amino acids, purines, pyrimidines, nucleosides, nucleotides, vitamins, lipids, inorganic
nutrients, antimicrobial compounds, metabolic inhibitors. Physical factors – radiations,
temperature, pH and pressure. Response to environment – growth and reproduction; growth
inhibition and death, movement, differentiation, modification to the environment – changes
in chemical composition, changes in physical properties
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UNIT V
MICROBIAL TECHNIQUES: Isolation of microbes from various sources, Serial dilution
technique, pure culture techniques and culture preservation techniques. Microbial culture
collection centres. Staining techniques – Gram, endospore, negative, flagellar and methylene
blue staining. Inoculum development – Development of inocula for yeast, bacterial, mycelial
and vegetative fungal processes; aseptic inoculation of the fermentor
Sterilization methods: Moist heat; dry heat, flame, filter, gas (ethylene oxide), Richards’ rapid
method - HTST (high temperature/short time) treatments – continuous sterilizers and
pasteurizers - Sterility, asepsis, Uses of UV and non-ionizing radiation. Sterilization methods
– medium sterilization, batch sterilization, contiuous sterilization, filter sterilization
Microbiological media: Types of media, composition of media – carbon sources, nitrogen
sources, vitamins and growth factors, mineral, inducers, precursors and inhibitors. Selection
and optimization of media
Strain improvement methods; Recombinant cell culture process – guidelines for choosing
host, vector systems, plasmid sterility in recombinant cell culture, limits to over expression

REFERENCES
1. Microbiology by Pelczar, Reid and Chan, McGraw Hill Book Company.
2. Microbiology, Fundamental and Applications by R.A. Atlas, McMillan Publishers.
3. General Microbiology by Powar and Daginawala, Himalaya Publishing House.
4. Microbial genetics by David friefelder
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UNIT-1 CLASSIFICATION AND MOLECULAR SYSTEMATICS

CONTENTS
LESSON 1 TAXONOMY AND CLASSIFICATION OF BACTERIA, VIRUS AND
FUNGI
LESSON 2 CLASSICAL AND NUMERICAL TAXONOMY
LESSON 3 MOLECULAR TAXONOMY
LESSON 4 POLYPHASIC TAXONOMY
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LESSON – 1
TAXONOMY AND CLASSIFICATION OF BACTERIA,
VIRUS AND FUNGI

Contents

1.0. AIMS AND OBJECTIVES
1.1. INTRODUCTION
1.1.1 IMPORTANCE OF TAXONOMY
1.2. CLASSIFICATION OF BACTERIA
1.2.1 BACTERIA CLASSIFICATION BASED ON SHAPES AND COLONY
MORPHOLOGY
1.2.2 AEROBIC AND ANAEROBIC BACTERIA
1.2.3 GRAM POSITIVE AND GRAM NEGATIVE BACTERIA
1.2.4 AUTOTROPHIC AND HETEROTROPHIC BACTERIA
1.2.5 CLASSIFICATION OF BACTERIA BY NUTRITIONAL
REQUIREMENT
1.2.6 CLASSIFICATION BASED ON PHYLA
1.2.7 THE BERGEY CLASSIFICATION OF BACTERIA
1.3. VIRUS CLASSIFICATION
1.3.1 BASED ON MORPHOLOGY
1.3.2 BASED ON GENETIC MATERIAL
1.3.2.1 DNA VIRUSES
1.3.2.2 RNA VIRUSES
1.3.2.3 REVERSE TRANSCRIBING VIRUSES
1.3.3 THE BALTIMORE CLASSIFICATION
1.4. CLASSIFICATION OF FUNGI
1.5. LET US SUM UP
1.6. LESSON END ACTIVITIES
1.7. POINTS FOR DISCUSSION
1.8. REFERENCES

1.0. AIMS AND OBJECTIVES

The chapter discusses the taxonomy, classification of bacteria, virus and fungi.

1.1. INTRODUCTION

The science of naming and classifying organisms is called taxonomy. The word
comes from the Greek taxis, 'order', nomos, 'law' or 'science'. Three separate but interrelated
disciplines are involved in taxonomy
– Identification - characterizing organisms
– Classification - arranging into similar groups
– Nomenclature - naming organisms

Organizing larger organisms based on morphology is often quite simple such as fins,
legs, feathers, fur, etc. But with prokaryotes, it is not as simple. Prokaryote Classification
involves technologies used to characterize and ID prokaryotes viz. microscopic examination,
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culture characteristics, biochemical testing, nucleic acid analysis, combination of the above is
most accurate.

Taxonomic Classification Categories are arranged in hierarchical order and species is
basic unit
Domain
Kingdom
Phylum or Division
Class
Order
Family
Genus
Species

Organisms are ranked and a category in any rank unites groups in the level below it,
based on shared properties.

For eg.
Domain Bacteria
Phylum Proteobacteria
Class g- Proteobacteria
Order Enterobacteriales
Family Enterobacteriaceae
Genus Shigella
Species dysenteriae

Microbial taxonomy is a means by which microorganisms can be grouped together.
Organisms having similarities with respect to the criteria used are in the same group, and are
separated from the other groups of microorganisms that have different characteristics.

1.1.1. IMPORTANCE OF TAXONOMY

1. It allows us to organize huge amounts of knowledge about the organisms (Acts like a
filing system).
2. Taxonomy allows for predictions & frame hypothesis for further research based on
knowledge of similar organisms.
3. It places microorganisms in meaningful, useful groups with precise names so that
microbiologist can work with them & communicate efficiently.
4. It is essential for accurate identification of microorganisms (For example, the need to
know the pathogen for a clinical test.
5. Microbial Evolution & Diversity
6. Universal Phylogenetic Tree

1.2. CLASSIFICATION OF BACTERIA

Bacteria are classified and identified to distinguish one organism from another and to
group similar organisms by criteria of interest to microbiologists or other scientists. Bacteria
may be the most significant group of organisms on earth. They are responsible for much of
the decomposition of dead organisms, they convert nitrogen for plants, they help many
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animals digest food, they produced oxygen in the early atmosphere, and they make certain
foods (yogurt, cheese, etc.).
Bacteria can be classified by:
1. colony shape in culture
2. motility
3. morphological characteristics other than shape...eg multiple flagella
4. metabolic activity eg. sugars they ferment
5. DNA sequence

1.2.1. BACTERIA CLASSIFICATION BASED ON SHAPES AND COLONY
MORPHOLOGY

Before the advent of DNA sequencing, bacteria were classified based on their shapes
and biochemical properties. Most of the bacteria belong to three main shapes: rod (rod shaped
bacteria are called bacilli), sphere (sphere shaped bacteria are called cocci) and spiral (spiral
shaped bacteria are called spirilla). Some bacteria belong to different shapes, which are more
complex than the above mentioned shapes.

Fig. 1 morphological classification of bacteria

Bacteria show characteristic type of growth on solid media under appropriate cultural
conditions and the colony morphology can be used in presumptive identification. The
colonies can be varying in size and diameter, in outline (circular, wavy, rhizoid etc.) elevation
(flat, raised, convex, etc.) and translucency (transparent, opaque, and translucent). The colour
of the colony or the changes that they bring about in their surroundings is also used as
diagnostic tools in the tentative identification of the bacteria. For example, colonies of
streptococci on blood agar medium are small, beadlike and have a opalescent grey colour
with smooth or slightly rough edges.
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1.2.2. AEROBIC AND ANAEROBIC BACTERIA

Bacteria are also classified based on the requirement of oxygen for their survival.
Bacteria those need oxygen for their survival are called Aerobic bacteria and bacteria those
do not require oxygen for survival. Anaerobic bacteria cannot bear oxygen and may die if
kept in oxygenated environment (anaerobic bacteria are found in places like under the surface
of earth, deep ocean, and bacteria which live in some medium).

1.2.3. GRAM POSITIVE AND GRAM NEGATIVE BACTERIA

For more than a century bacteria have been classified according to their "Gram
reaction" - named after Christian Gram who devised the protocol for his staining process in
1884. Bacteria are grouped as ‘Gram Positive’ bacteria and ‘Gram Negative’ bacteria, which
is based on the results of Gram Staining Method (in which, an agent is used to bind to the cell
wall of the bacteria) on bacteria.
1.2.4. AUTOTROPHIC AND HETEROTROPHIC BACTERIA

This is one of the most important classification types as it takes into account the most
important aspect of bacteria growth and reproduction. Autotrophic bacteria (also known as
autotrophs) obtain the carbon it requires from carbon-dioxide. Some autotrophs directly use
sun-light in order to produce sugar from carbon-dioxide whereas other depend on various
chemical reactions. Heterotrophic bacteria obtain carob and/or sugar from the environment
they are in (for example, the living cells or organism they are in).

1.2.5. CLASSIFICATION OF BACTERIA BY NUTRITIONAL REQUIREMENT

Fig. 2 classification of bacteria based on nutritional requirement
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1.2.6. CLASSIFICATION BASED ON PHYLA
Based on the morphology, DNA sequencing, conditions required and biochemistry,
scientists have classified bacteria into phyla:
1) Aquificae
2) Xenobacteria
3) Fibrobacter
4) Bacteroids
5) Firmicutes
6) Planctomycetes
7) Chrysogenetic
8) Cyanobacteria
9) Thermomicrobia
10) Chlorobia
11) Proteobacteria
12) Spirochaetes
13) Flavobacteria
14) Fusobacteria
15) Verrucomicrobia

Each phylum further corresponds to number of species and genera of bacteria. The
bacteria classification includes bacteria which are found in various types of environments
such as sweet water bacteria, ocean water bacteria, bacteria that can survive extreme
temperatures (extreme hot as in sulfur water spring bacteria and extreme cold as in bacteria
found in Antarctica ice), bacteria that can survive in highly acidic environment, bacteria that
can survive highly alkaline environment, aerobic bacteria, anaerobic bacteria, autotrophic
bacteria, heterotrophic bacteria, bacteria that can withstand high radiation etc.

1.2.7. THE BERGEY CLASSIFICATION OF BACTERIA

One of the more comprehensive bacterial classification manuals has been Bergey’s
manual of determinative Bacteriology. Because of on going taxonomic studies new species
are continuously being described and changes are made.
 Bergey Division I = The Cyanobacteria (formerly the blue-green alga) - These
bacteria can use light as their energy source under aerobic conditions. The use carbon
dioxide and produce oxygen.
 Bergey Division II = The Bacteria (includes the photo bacteria and all other classical
bacteria).
 The archaeabacteria were mixed within the 19 parts of the book

Fig. 3 Bergey’s classification of bacteria
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The Bergey Classification of Bacteria into 19 parts.

 Phototrophic Bacteria: Rhodospirillum - Rhodopseudomonas - Chromatium
 Gliding Bacteria: Myxococcus - Beggiatoa - Simonsiella - Leucothrix
 Sheathed Bacteria: Sphaerotilus - Leptothrix
 Budding / Appendaged Bacteria: Caulobacter - Gallionella
 Spirochetes: Spirochaeta - Treponema - Borrelia
 Spiral and Curved Bacteria: Spirillum - Auqaspirillum - Oceanospirillum -
Bdellovibrio
 Gram-negative Aerobic Rods and Cocci: Pseudomonas - Xanthanomonas -
Zoogloea - Gluconobacter - Azotobacter - Rhizobium - Agrobacterium -
Halobacterium - Acetobacter
 Gram-Negative Facultative Anaerobic Rods: Escherichia - Citrobacter -
Salmonella - Shigella - Klebsiella - Enterobacter - Serratia - Proteus - Yersinia -
Erwinia - Vibrio - Aeromonas - Zymomonas - Chromobacterium - Flavobacterium
 Gram-negative anaerobes: Bacteriodes - Fusobacterium - Desulfovibrio -
Succinimonas
 Gram-Negative cocci: Nisseria - Branhamella - Acinetobacter - Paracoccus
 Gram-negative anaerobic cocci: Veillonella - Acidaminococcus
 Gram-Negative Chemolithotrophic: Nitrobacter - Thiobacillus - Siderocapsa
 Methane producing:
 Gram-Positive Cocci: Micrococcus - Staphylococcus - Streptococcus - Leuconostoc -
Pediococcus - Aerococcus - Peptococcus - Ruminococcus - Sarcina
 Endospore-forming Rods and cocci: Bacillus - Clostridium - Sporosarcina
 Gram-positive, non-sporing rods: Lactobacillus - Listeria - Erysipelothrix -
Caryophanon
 Actinomycetes and Related: Corynebacterium - Arthobacter - Brevibacterium -
Cellumonas - Kurthia - Propionibacterium - Eubacterium - Actinomyces - Archina -
Bifidiobacterium - Rothia - Mycobacterium - Frankia - Streptosporangia - Nocardia -
Streptomyces - Streptoverticillium - Micromonospora
 Rickettsias: Rickettsia - Erhlichia - Wollbachia - Bartonella - Chlamydia

1.3. VIRUS CLASSIFICATION

Viruses are not usually classified into conventional taxonomic groups but are usually
grouped according to such properties as size, the type of nucleic acid they contain, the
structure of the capsid and the number of protein subunits in it, host species, and
immunological characteristics. It also means that when a new species of known virus family
or genus is investigated it can be done in the context of the information that is available for
other members of that group. Virus classification involves naming and placing viruses into a
taxonomic system. Like the relatively consistent classification systems seen for cellular
organisms, virus classification is the subject of ongoing debate and proposals. This is largely
due to the pseudo-living nature of viruses, which are not yet definitively living or non-living.
As such, they do not fit neatly into the established biological classification system in place for
cellular organisms, such as plants and animals, for several reasons. Virus classification is
based mainly on phenotypic characteristics, including morphology, nucleic acid type, mode
of replication, host organisms, and the type of disease they cause.