INTRODUCTORY MICROBIOLOGY
,
"This page is Intentionally Left Blank"
INTRODUCTORY MICROBIOLOGY
Uma Shankar Singh Kiran Kapoor
Oxford Book Company Jaipur. India
ISBN: 978-93-80179-21-6
Edition 2010
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Preface Although microbes were first observed over three hundred years ago, the field of microbiology can be said to be in its infancy relative to older biological disciplines such as zoology and botany. Microbiology could be defined as the study of microorganisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryote such as fungi and protists, and prokaryotes, which are bacteria and archaea. Viruses, though not strictly classed as living organisms, are also studied. In short; microbiology refers to the study of life and organisms that are too small to be seen with the naked eye. Whilst there are undoubtedly some who fear all microbes due to the association of some microbes with many human illnesses, many microbes are also responsible for many beneficial processes such as industrial fermentation, antibiotic production and as vehicles for cloning in higher organisms such as plants. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system. Bacteria can be used for the industrial production of amino acids. Corynebacterium glutamicum is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-Iysine. A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms. Microbes are beneficial for microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. There are also various claims concerning the contributions to human and animal health by consuming probiotics and/or prebiotics. Recent research has suggested that microorganisms could be useful in the treatment of cancer. Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumours. The present book has been designed to outline the basic aspects of microbiology to be understood in its right perspective. It envisages to put forward a clear understanding of what is microbiology and its widening horizons. It is designed for students taking courses various fields of life sciences.
Uma Shankar Singh Kiran Kapoor
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Contents Preface l. Introduction to Microbiology
v
1-14
2. Microbial Cell Structure
15-34
3. Bacteria: Structure and Functions
35-48
4. Classification of Bacteria
49:.62
5. Human Microbial Flora
63-72
6. Viruses: Structure and Functions
73-86
7. Viral Effects on Cells
87-104
8. Microbial Ecology
105-112
9. Microbial Genetics
113-138
10. Microbial Nutrition and Growth
139-154
11. Microbial Epidemiology
155-168
12. Bacterial Pathogens
169-180
13. Viral Pathogens
181-194
14. Basic Mycology
195-222
15. Microbiology of Protozoans
223-244
16. Infectious Diseases
245-290
17. Immune Defence against Microbes
291-312
Bibliography
313-314
Index
315-316'
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1 Introduction to Microbiology
~
Microbiology is the study of microorganisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryote such as fungi and protists, and prol<aryotes, which are bacteria and archaea. Viruses, though not strictly classed as living organisms, are also studied. In short; microbiology refers to the study of life and organisms that are too small to be seen with the naked eye. Microbiology is a broad ter~ which includes virology, mycology, parasitology, bacteriology and other branches. A microbiologist is a specialist in microbiology. Microbiology is researched actively, and the field is advancing continually. Although microbes were first observed over three hundred years ago, the field of microbiology can be said to be in its infancy relative to older biological disciplines such as zoology and botany. Microbiology could be defined as the study of organisms too small to be seen with the naked eye. Figure 1 shows the relative size of microbes compared to other living things. However, the recent discovery of bacteria of near 1 mm in size has made this definition somewhat inaccurate and in the grand tradition of science, a new definition is in order. Though microbes are small, they nevertheless span a large range of sizes from the smallest bacterial cells at -0.15 /-lm to giant bacteria larger than 700 /-lm. The viruses depicted at the far left of the scale are even smaller. We will consider microbiology to be the study of organisms that can exist as single cells, contain a nucleic acid genome for at least some part of their life cycle, and are capable of replicating that genome. This broad description encompasses an understandably large group of organisms including fungi, algae, protozoa and bacteria. Many different organisms fall under the definition of microorganisms. Shown here are: A, the bacterium Escherichia coli; B, a photosynthetic cyanobacterium; C, a fungus; D, Ebola virus; E, the protozoan malaria parasite. Microbiology also involves a collection of techniques to study and manipulate these small creatures. Because of their size, special
Introductory Microbiology
2
instruments and methods had to be developed to allow the performance of interpretable experiments on microorganisms. Saccharomyces cele"'SldeO
Dehalococcoldes ethenogenes
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Figure 1. The Relative size of Microbes
These methods are not restricted to microbes alone, but have also found utility in working with populations of cells from higher organisms. With apologies to other small organisms, this book will mostly focus on bacteria and their impact on the rest of the biosphere. This can be weakly justified by the fact that bacteria have a major impact on the world around us and, because of their perceived importance, more research and knowledge has been accumulated about them.
Figure 2. Photosynthetic cyanobacteria
Microorganisms are everywhere, but why are they worth learning about? The short answer is that they affect your life in many different ways. Before we begin our study of these creatures, we will first take a tour of some of their important habitats and point
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Introduction to Microbiology
out why your existence depends upon them. We will then briefly explore the history of microbiology. MICROBES HAVE A LARGE IMPACT ON HUMAN HEALTH
If you ask the average person how microbes (or germs) impact their lives, they would immediately think of disease. This is not a silly view, as Figure 3 shows a number of important pathogens. While death from infectious disease in the U.s. has been greatly diminished, infection rates in developing nations remain unacceptably high. "Ancient" diseases continue to be a problem where nutrition and sanitation are poor, and emerging diseases such as Acquired Immunodeficiency Syndrome (AIDS) are even more dangerous for such populations. The Centers for Disease Control and Prevention estimate that about 9% of adults between the ages of 18-49 in Sub-Saharan Africa are infected with HIV.
Many of the new diseases are viral in nature, making them notoriously difficult to treat and they have no known cure. Influenza and pneumonia are leading killers of the elderly. Even the common cold causes illness and misery for almost everyone and drains the productivity of all nations. Disease due to food-borne pathogens also remain a problem, largely because of consumption of improperly processed or stored foods. Understanding the sources of contamination and developing ways to limit the growth of pathogens in food is the job of food microbiologists.
Figure 3. Some Important Pathogens
New infections continually appear. Having an available food source to grow on (humans) inevitably results in a microorganism that will take advantage. Some of these feeders will
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Introductory Microbiology
interfere with our own well being, causing disease. Surprisingly, many diseases that were previously thought to have only behavioral or genetic components have been found to involve microorganisms. The clearest case is that of ulcers, which was long thought to be caused by stress and poor diet. However the causative agent is actually a bacterium, Helicobacter pylori, and many ulcers can be cured with appropriate antibiotics. Work on other non-infectious diseases such as heart disease, stroke and some autoimmune diseases also suggest a microbial component that triggers the illness. Finally, some pathogenic microbes that had been "controlled" through the use of antibiotics are beginning to develop drug resistance and therefore reemerge as serious threats in the industrialised world as well as developing nations. Tuberculosis is an illness that was on the decline until the middle 80's: It has recently become more of a problem, partly due to drug resistance and partly due to a higher population of immunosuppressed individuals from the AIDS epidemic.
Staphylococcus aureus strains are emerging that are resistant to many of the antibiotics that were previously effective against them. These staph infections are of great concern in hospital settings around the world. Understanding both familiar killers and new pathogens will require an understanding of their biology, and thus an understanding --of the field of microbiology. BENEFITS OF MICROBIOLOGY
Whilst there are undoubtedly some who fear all microbes due to the association of some microbes with many human illnesses, many microbes are also responsible for many beneficial processes such as industrial fermentation, antibiotic production and as vehicles for cloning in higher organisms such as plants. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system. Bacteria can be used for the industrial production of amino acids. ConJnebacterium glutamicum is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine. A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms.
5
Introduction to Microbiology
Figure 4. Corynebacterium glutamicum
Microorganisms are used for the biotechnological production of biopolymers with tailored properties suitable for high-value medical application such as tissue engineering and drug delivery. Microorganisms are used for the biosynthesis of xanthan, alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides and polysaccharide, and polyhydroxyalkanoates. Microorganisms are beneficial for microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since most sites are typically comprised of multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species and strains, each specific to the biodegradation of one or more types of contaminants. There are also various claims concerning the contributions to human and animal health by consuming probiotics and/or prebiotics. Recent research has suggested that microorganisms could be useful in the treatment of cancer. Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumors. Clostridial vectors can be safely administered and their potential to deliver therapeutic proteins has been demonstrated in a variety of preclinical models. Microbes are often Helpful
From the beginning of microbiology, significant resources have been spent to understand and fight disease-causing microorganisms. You may be surprised to learn ' that only a small fraction of microbes are involved in disease; many other microbes actually enhance our well being. The harmless microbes that live in our intestines and on our skin actually help us fight off disease. They actively antagonise other bacteria and take up space, preventing potential pathogens from gaining a foothold on our bodies.
IntroduCtory Microbiology
6
The microbial community in humans not only protects us from disease, but also provides needed vitamins, such as B12 • We have entire communities of microorganisms in our digestive systems that contribute to our overall health. In fact, like all other large organisms, humans are actually consortia of different organisms - there are more nonhuman cells in and on our bodies than there are human cells! Human health and nutrition also depends on healthy farm animals. Cows, sheep, horses and other ruminant animals utilise their microbial associates to degrade plant material into useful nutrients. Commercial crops are also central to human prosperity, and much of agriculture depends upon the activities of microbes. For example, an entire group of plants, the legumes, forms a cooperative relationship with certain bacteria. These bacteria convert nitrogen gas to ammonia for the plant, an important nutrient that is often limiting in the environment. Microbes also serve as small factories, producing valuable products such as cheese, yogurt, beer, wine, organic acids and many other items. In conclusion, while it is less apparent to us, the positive role of microbes in human health is at least as important as the negative impact of pathogens. Microbes have Profound Effects on the Environment
Whether measured by the number of organisms or by total mass, the vast majority of life on this planet is microscopic. These teaming multitudes profoundly influence the make-up and character of the environment in which we live. Presently, we know very little about the microbes that live in the world around us because less than 2 % of them can be grown in the laboratory. Understanding which microbes are in each ecological niche and what they are doing there is critical for our understanding of the world. Microbes are the major actors in the synthesis and degradation of all sorts of important molecules in ·environments. Cyanobacteria and algae in the oceans are responsible for the majority of photosynthesis on Earth. They are the ultimate source of food for most ocean creatures (including whales) and replenish the world's oxygen supply. Cyanobacteria also use carbon dioxide to synthesize all of their biological molecules and thus remove it from the atmosphere. Since carbon dioxide is a major greenhouse gas, its removal by cyanobacteria affects the global carbon dioxide balance and may be an important mitigating factor in global warming. In all habitats, microorganisms make nutrients available for the future growth of
other living things by degrading dead organisms. Microbes are also essential in treating the large volume of sewage and wastewater produ
