Understanding Bacteria

479 Pages·2003·9.45 MB·English

by  Sheela Srivastava

Understanding Bacteria
Understanding Bacteria
by
Sheela Srivastava
Department of Genetics,
University of Delhi, New Delhi, India
and
P.S. Srivastava
Centre for Biotechnology,
Hamdard University, New Delhi, India
Springer-Science+Business Media, B.Y.
A C.LP. Catalogue record for this book is available from the Library of Congress.
ISBN 978-90-481-6429-5 ISBN 978-94-017-0129-7 (eBook)
DOI 10.1007/978-94-017-0129-7
Printed on acid-free paper
All Rights Reserved
© 2003 Springer Science+Business Media Dordrecht
Originally published by Kluwer Academic Publishers in 2003.
Softcover reprint of the hardcover 1s t edition 2003
No part of this work may be reproduced, stored in a retrieval system, or transmitted
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Preface
The discipline of microbiology that deals with an amazingly diverse group of simple
organisms, such as viruses, archaea, bacteria, algae, fungi, and protozoa, is an exciting
field of Science. Starting as a purely descriptive field, it has transformed into a truly
experimental and interdisciplinary science inspiring a number of investigators to generate
a wealth of information on the entire gamut of microbiology. The later part of 20th
century has been a golden era with molecular information coming in to unravel interesting
insights ofthe microbial world. Ever since they were brought to light through a pair of
ground glasses by the Dutchman, Antony van Leeuwenhoek, in later half of 17th century,
they have been studied most extensively throughout the next three centuries, and are
still revealing new facets of life and its functions. The interest in them, therefore,
continues even in the 21 st century.
Though they are simple, they provide a wealth of information on cell biology,
physiology, biochemistry, ecology, and genetics and biotechnology. They, thus, constitute
a model system to study a whole variety of subjects. All this provided the necessary
impetus to write several valuable books on the subject of microbiology. While teaching
a course of Microbial Genetics for the last 35 years at Delhi University, we strongly felt
the need for authentic compiled data that could give exhaustive background information
on each of the member groups that constitute the microbial world. For the present
book, we chose bacteria (though archae a have also been dealt with but more for
comparison), the organisms for which geneticists also have special affinity.
The book, "Understanding Bacteria" is intended to provide related information on
basic as well as applied aspects and should cater to the needs of both undergraduate
and postgraduate students. Besides Microbiology, bacteria form an integral component
of various courses, such as Botany, Zoology, Biosciences, Life Sciences, Biochemistry
and Biotechnology. This book thus should fulfil a long-standing demand of a whole
variety of readers. The text of the book is organized in such a way that the flow of
information appears spontaneous giving due weightage to classical, and molecular/
applied aspects. Those who are seriously into microbiological aspects should find it a
good resource book, and those who wish to use these bugs for biochemical, genetic,
biotechnological, and applied research, they should get the required background
information. Our endeavor has been to keep the curiosity of the reader on and make this
book of multipurpose usage.
The contents of the book have been spread over nine chapters and information
within has been regrouped as sections and subsections, as required. This allows the
logical assemblage of contained information. The figures have been intentionally drawn
free-hand so as to bring out the clarity of information. At the end ofthe text, few books
and research/review articles have been listed which can serve as excellent reference
material, though we would also like to leave it to the choice of the readers to select any
other book that may become available and that fulfils their requirement. A comprehensive
index has been appended at the end to help the readers.
Vi
Although, utmost care has been taken to present the facts as they are, responsibility
for any unintentional mistakes that might have crept in is exclusively ours. We would
feel obliged to our readers for suggestions and ways to improve the book.
While preparing this book we have freely indulged in acquiring academic inputs
from the written materials and discussions with various experts, colleagues and students.
Of equal importance have been the forthcoming help and assistance of a number of
coworkers, associates and our doctoral and post-doctoral collaborators. While we take
this opportunity to place on record the deep sense of gratitude to all of them, some
deserve especial mention. Dr. T. Satyanarayana, Professor, Department of Microbiology
at Delhi University has always been forthright in providing extra information. The idea
that we could always fall back upon the support rendered by our post-doctoral and
doctoral associates, Dr. Deepshikha, Dr. Sanjeev, Dr. Alka, Ms. Toolika, Ms. Sapna,
Ms. Maryam and Ms. Nisha of Centre for Biotechnology, Hamdard University,
New Delhi has been a constant source of strength throughout. Their ungrudging help at
all levels of the preparation of manuscript made our job simpler.
Teaching a course on the subject brought us in close contact with a large number of
graduate and post-graduate students. Their querries and inquisitiveness have guided us
in deciding the direction of this book. We shall remain thankful to all of them.
Excellent computational support from Mr Satish, Ms Mansa, and Mr Rajesh has
seen the book through to its present shape.
June 12,2003 Sheela Srivastava
New Delhi P S Srivastava
Contents
Preface ...................................................................................................................... v
CHAPTER 1
1. THE EMERGENCE OF BACTERIOLOGY .............................................. 1
1.1 The Science of Microbiology (Bacteriology) .................................................... I
1.2 Bacteria-The First Inhabitants of Earth ... .............. ... ..... ..... ..... .............. ...... ...... I
1.3 Discovery .... ..... ... ..................................... ......... ........ ... ..... ..... ............ ... ............. 2
1.4 Fall of Spontaneous Generation-Microbiology, an Experimental Science ....... 3
1.5 Metabolic Versatility Recognized -Good vs Bad ...... .......... ... ............ ... ...... ... ... 5
1.6 Microbial Association with Diseases-Medical Microbiology .......................... 5
I. 7 Bacteria Land up in Laboratory ... ... ..... ... ...... ........... .................. ... .......... ... ... ..... 6
1.8 Concept of Immunity ......................................................................................... 7
1.9 Agricultural Microbiology ................................................................................. 9
1.1 0 The Science of Genetics and Biotechnology-Bacteria Hog the Limelight .. ..... 9
1.11 Development of Physical and Biochemical Techniques. ..... ... ......... .................. 9
CHAPTER 2
2. KNOWING BACTERIA-METHODS OF STUDy.................................. 11
2.1 Microscopy ....................................................................................................... 11
2.2 Availability of Material .................................................................................... 14
2.3 Culture Media .................................................................................................. 14
2.3.1 Specific Media ...................................................................................... 17
2.3.2 Preparation of Culture Media ...... ... ............ ..... ... ....... ... ...... ... ............ ... 17
2.3.3 Pouring of Media .................................................................................. 20
2.4 Inoculation ....................................................................................................... 21
2.5 Incubation ........................................................................................................ 21
2.6 Pure Culture ..................................................................................................... 21
2.6.1 Streak Plate Method .............................................................................. 21
2.6.2 Spread Plate Method ............................................................................. 21
2.6.3 Pour Plate Method ................................................................................ 23
2.7 Culturing Aerobic/Anaerobic Organisms ................ ..... ..... ..... ........ ... ........... ... 24
2.8 Enrichment Culture Techniques ....................................................................... 25
2.9 Culture Storage and Preservation ..................................................................... 26
2.10 Visual Observation ........................................................................................... 27
2.11 Study of Live Bacteria ..................................................................................... 27
2.12 Staining ............................................................................................................ 28
Vlll
CHAPTER 3
3. DOMAIN PROKARYOTA-TAXONOMIC DELINEATIONS ................. 33
3.1 Species Concept ............................................................................................... 33
3.2 Identification .................................................................................................... 33
3.2.1 Identification Key and Diognostic Tables ............................................ 34
3.2.2 Whole Cell Fatty Acid Profile .............................................................. 36
3.3 Nomenclature ................................................................................................... 37
3.4 Systems of Classification ................................................................................. 39
3.5 Bergey's Manuals ............................................................................................. 40
(i) Of Systematic Bacteriology (Volumes I-IV) ............................................. 40
(ii) Of Determinative Bacteriology ................................................................. 40
Group 1- Spirochaetes ...................................................................... 42
Group 2- Aerobic/Microaerophilic Motile, HelicalNibroid,
Gram-Negative Bacteria or Spirilla ................................. 42
Group 3- Non-Motile (or rarely motile) Gram-Negative
Curved Bacteria .... ........................ ... ..... ..... ..... ....... ........... 42
Group 4- Gram-Negative Aerobic Rods and Cocci ......................... 42
Group 5- Gram-Negative Facultatively Anaerobic Rods ................ 43
Group 6- Gram-Negative Aerobic Rods .......................................... 43
Group 7- Dissimilatory Sulphate or Sulphur-Reducing Bacteria ... 43
Group 8- Gram-Negative Anaerobic Cocci ...................................... 43
Group 9- Rickettsias and Chlamydias .............................................. 43
Group 10- Anoxygenic Phototrophic Bacteria ...... ............ ....... ..... ..... 44
Group 11- Oxygenic Phototrophic Bacteria .......... ....... ....... ....... ... ..... 44
Group 12- Chemolithotrophic Bacteria .............................................. 44
Group 13- Budding and/or Appendaged Bacteria .............................. 45
Group 14- Sheathed Bacteria ................ ... ............. ..... ..... ..... .............. 45
Group 15- Non-Photosynthetic, Non-Fruiting, Gliding Bacteria ...... 45
Group 16- Fruiting, Gliding Bacteria ................................................. 45
Group 17- Gram-Positive Cocci ......................................................... 45
Group 18- Gram-Positive Endospore-Forming Rods and Cocci ....... 45
Group 19- Regular, Non-Sporulating Gram-Positive Rods ............... 45
Group 20- Irregular Non-Spore Forming Gram-Positive Rods ......... 46
Group 21- Mycobacteria .................................................................... 46
Group 22-29- Actinomycetes .................................................................. 46
Group 30- Mycoplasma ...................................................................... 46
Group 31-35- Archaebacteria .................................................................. 47
3.6 Numerical Taxonomy ....................................................................................... 48
3.7 Genetic Analysis .............................................................................................. 49
3.7.1 Base Composition of DNA. ............ ...... ...................... ........ ..... ............. 49
3.7.2 Nucleic Acid Hybridization .................................................................. 51
3.8 RNA Fingerprinting (Molecular Phylogeny) ................................................... 52
IX
3.9 Phylogenetic Classification .. ... ... ..... ... ....................... ... ..... ..... ..... ........ ..... ... ..... 56
3.9.1 Proteobacteria ...................................................................................... 56
(i) The Alpha Subclass. ... ..... ... ......... ... ........ ..... ..... ........ .................. 56
(ii) The Beta Subclass ....................................................................... 56
(iii) The Gamma Subclass .................................................................. 56
(iv) The Epsilon Subclass .................................................................. 56
(v) Campylobacteraceae and Related Bacteria ................................. 57
3.9.2 Gram-Positive Bacteria ........................................................................ 57
3.9.3 Cyanobacteria ...................................................................................... 57
3.9.4 The Spirochaetes ................................................................................. 57
3.9.5 Gram-Negative Anaerobic Rods, Cytophagas and Flavobacteria
(Superfamily V) ................................................................................... 57
3.9.6 Green Sulphur Bacteria ...................................................................... 57
3.9.7 Chlamydiae .......................................................................................... 57
3.9.8 Planctomyces and Relatives ................................................................ 57
3.9.9 Deinococcus and Relatives .................................................................. 58
3.9.10 The Green Non-Sulphur Bacteria and Relatives ................................. 58
3.9.11 Thermotoga and Relatives, and Other Divisions ................................ 58
3.9.12 Aquificales ........................................................................................... 58
3.10 Archaea ............................................................................................................ 58
CHAPTER 4
4. CELL STRUCTURE AND ORGANIZATION .......................................... 61
4.1 Shape and Arrangement .. ... ...... ... ..... ........ ...... ...... ... ..... .......................... ... ... .... 61
4.2 Size ................................................................................................................... 63
4.3 Cell Structure ................................................................................................... 64
4.3.1 Surface Layers (capsule and slime layers) ........................................... 64
4.3.2 Appendages ...................... .................... ... ........ ..... ..... ......... ... .............. 65
4.3.3 Cell Wall ...... ... ... ... ... ...... .............. ... ... ... ..... ... ..... ..... .............. ............ ... 66
4.3.4 Cytoplasmic Membrane ....................................................................... 71
4.3.5 Locomotory Organs............................................................................. 72
4.3.6 Cytoplasm ............................................................................................ 76
4.3.7 Ribosomes ........................................................................................... 76
4.3.8 Photosynthetic Membrane Systems ....... ... ............. ..... ..... .................... 77
4.3.9 Inclusions and Storage Products ... ...... ........... .................. .............. ..... 77
4.3.10 Gas Vesicles ......... ... ... ... ... ........ ......... ... ...... ........ ..... ..... ........................ 79
4.3.11 Nucleoid .. ... ... ............. ... ........ ............... ... ... ..... .................. .............. .... 80
4.3.12 Chromosome ........................................................................................ 81
4.3.12.1 Functional Organization of Chromosome ........................... 85
(i) Cryptic Genes ......... ... ... ... ............. ........ ..... ... .............. 85
(ii) REP Sequences ........................................................... 85
(iii) BIME ......... ............ ... ... ........................ ........ ... ... ......... 86
x
(iv) ERICS ........................................................................ 86
(v) Other Repeat Elements ............................................... 86
(vi) Insertion Sequences .................................................... 86
(vii) Cryptic Prophage and Phage Remnants ..................... 87
4.3.12.2 Genome Sequencing ............................................................ 87
4.3.12.3 Linear Chromosome ............................................................ 90
4.3.13 Plasmids ............................................................................................... 90
4.3.13.1 Detection of Plasmi ds .......................................................... 90
4.3.13.2 Plasmid Nomenelature ......................................................... 92
4.3.13.3 Structure .............................................................................. 93
4.3.13.4 Properties ............................................................................. 93
CHAPTER 5
5. BACTERIA AND LIFE PROCESSES-I GROWTH AND
MULTIPLICATION ................................................................................... 97
5.1 Population Growth. ....... ..... .......... ..... ........................ ... ..... ..... ..... ....... ....... ....... 97
5.2 Measurement of Growth .................................................................................. 98
5.2.1 Total Cell Count ...................... ....... .................... ..... ....... ..... ....... ......... 98
5.2.2 Viable Cell Count .............................................................................. 101
5.2.3 Cell Mass ............................................................................................ 102
5.3 Growth Cycle .................................................................................................. 102
5.4 Diauxic Growth .............................................................................................. 104
5.5 Arithmatic or Linear Growth .......................................................................... 104
5.6 Growth of Bacterial Culture ........................................................................... 104
5.6.1 Batch Culture ..................................................................................... 106
5.6.2 Continuous Culture ........................................................................... 106
5.6.3 Synchronous Culture ......................................................................... 108
5.7 Growth on Solid Media .................................................................................. 110
5.8 Effect of Environmental Factors on Growth .................................................. 110
5.8.1 Nutrient Concentration ...................................................................... 110
5.8.2 Temperature ....................................................................................... III
5.8.3 Oxygen concentration (Reduction Potential) .................................... 114
5.8.4 Redox Potential ................................................................................. 115
5.8.5 Water Activity .................................................................................... 116
5.8.6 Pressure ............................................................................................. 116
5.8.6.1 Osmotic Pressure ............................................................... 116
5.8.6.2 Hydrostatic Pressure ......................................................... 117
5.8.7 Acidity and pH .................................................................................. 117
5.8.8 Light .................................................................................................. 119
5.9 Molecular Mechanism of Growth .................................................................. 119
5.9.1 Nuclear Division ................................................................................ 119
Xl
5.9.1.1 DNA replication ................................................................ 121
5.9.2 Cell Division .................................................................................. 126
5.10 Reproduction 130
5.10.1 Asexual Reproduction ................................................................... 130
5.10.2 Sexual Reproduction ..................................................................... 135
5.11 Control of Microbial Growth ....................................................................... 135
5.11.1 Physical Control ............................................................................ 136
5.11.1.1 Temperature ................................................................... 136
5.11.1.2 Desiccation .................................................................... 136
5.11.1.3 Oxygen .......................................................................... 137
5.11.1.4 Radiation ....................................................................... 137
5.11.1.5 Filtration ........................................................................ 137
5.11.2 Chemical Control ........................................................................... 137
5.11.2.1 Disinfectants ..... ... ... ......... ..... ... ..... ..... ..... ... ... ... ... ........ ... 137
5.11.2.2 Antiseptics ..................................................................... 138
5.11.2.3 Antibiotics ..................................................................... 138
5.11.2.3.1 Minimum Inhibitory Concentration (MIC) 139
5.11.2.3.2 Resistance to Antibiotics ............................ 140
5.11.2.3.3 Origin of Genes Conferring Antibiotic
Resistance................................................... 147
5.11.3 Preservatives ........................................................................ 148
CHAPTER 6
6. BACTERIA AND LIFE PROCESSES-II METABOLISM ...................... 151
II-A-Generation of CeJlular Energy ....................................................................... 151
6.1 Respiration ................................................................................................ 153
6.1.1 Glycolysis ........................................................................................ 155
(i) Embden-Meyerhof-Pamas (EMP) Pathway ........................... 155
(ii) Entner-Doudoroff (ED) Pathway ........................................... 155
(iii) Pentose Phosphate Pathway ................................................... 157
(iv) Utilization of Other Sugars .................................................... 157
6.1.2 Lipid Conversion ............................................................................ 159
6.1.3 Protein Catabolism .......................................................................... 160
6.1.4 Tricarboxylic Acid Cycle (TCA) ..................................................... 160
6.1.5 Oxidative Phosphorylation ............................................................. 162
6.2 Fermentation ............................................................................................... 164
6.3 Chemoautotrophy (Chemolithotrophy) ...................................................... 166
6.3.1 Hydrogen Oxidation ......................................................................... 166
6.3.2 Sulphur Oxidation ........................................................................... 166
6.3.3 Iron Oxidation. ... ............ ... ..... .................. ... ..... ..... ..... ... ..... ..... ... ..... 169
6.3.4 Ammonium and Nitrite Oxidation -Nitrification ............................. 169