Microbial World

Dans les champs de l’observation, le hasard ne favorise que les esprits préparés.

(In the field of observation, chance favours only prepared minds.)

—Louis Pasteur

Microorganisms are everywhere. Almost every natural surface is colonized by microbes (including our skin). Some microorganisms can live quite happily in boiling hot springs, whereas others form complex microbial communities in frozen sea ice. Most microorganisms are harmless to humans. You swallow millions of microbes every day with no ill effects. In fact, we are dependent on microbes to help us digest our food and to protect our bodies from pathogens. Microbes also keep the biosphere running by carrying out essential functions such as decomposition of dead animals and plants. Microbes are the dominant form of life on planet Earth. More than half the biomass on Earth consists of microorganisms, whereas animals constitute only 15% of the mass of living organisms on Earth.

This Microbiology course deals with

How and where they live
Their structure
How they derive food and energy
Functions of soil micro flora
Role in nutrient transformation
Relation with plant
Importance in Industries

Microorganisms are defined as those organisms and acellular biological entities too small to be seen clearly by the unaided eye. They are generally 1 millimetre or less in diameter.

Although small size is an important characteristic of microbes, it alone is not sufficient to define them. Some cellular microbes, such as bread molds and filamentous photosynthetic microbes are actually visible without microscopes. These macroscopic microbes are often colonial, consisting of small aggregations of cells. Some macroscopic microorganisms are multicellular. They are distinguished from other multicellular life forms such as plants and animals by their lack of highly differentiated tissues. Most unicellular microbes are microscopic.

However, there are interesting exceptions, cellular microbes are usually smaller than 1 millimetre in diameter, oft en unicellular and, if multicellular, lack differentiated tissues.

Figure: Concept Map Showing the Types of Biological Entities Studied by Microbiologists

SCOPE AND RELEVANCE OF MICROBIOLOGY

Microbiology has both basic and applied aspects.

The basic aspects are concerned with the biology of microorganisms themselves.

The applied aspects are concerned with practical problems such as disease, water and wastewater treatment, food spoilage and food production, and industrial uses of microbes.

It is important to note that the basic and applied aspects of microbiology are intertwined. Basic research is often conducted in applied fields, and applications often arise out of basic research. A discussion of some of the major fields of microbiology and the occupations within them follows.

Medical microbiology: Although pathogenic microbes are the minority, they garner considerable interest. Thus, one of the most active and important fields in microbiology is medical microbiology, which deals with diseases of humans and animals. Medical microbiologists identify the agents causing infectious diseases and plan measures for their control and elimination. Frequently they are involved in tracking down new, unidentified pathogens. These microbiologists also study the ways in which microorganisms cause disease.

Public health microbiology: Public health microbiology is concerned with the control and spread of such communicable diseases. Public health microbiologists and epidemiologists monitor the amount of disease in populations. Based on their observations, they can detect outbreaks and developing epidemics, and implement appropriate control measures in response. They also conduct surveillance for new diseases as well as bioterrorism events. Those public health microbiologists working for local governments monitor community food establishments and water supplies in an attempt to keep them safe and free from infectious disease agents.

Immunology: Immunology is concerned with how the immune system protects the body from pathogens and the response of infectious agents. It is one of the fastest growing areas in science. Much of the growth began with the discovery of HIV, which specifically targets cells of the immune system. Immunology also deals with health problems such as the nature and treatment of allergies and autoimmune diseases such as rheumatoid arthritis.

Agricultural microbiology: Agricultural microbiology is concerned with the impact of microorganisms on agriculture. Microbes such as nitrogen fixing bacteria play critical roles in the nitrogen cycle and affect soil fertility. Other microbes live in the digestive tracts of ruminants such as cattle and break down the plant materials these animals ingest. There are also plant and animal pathogens that can have significant economic impacts if not controlled. Agricultural microbiologists work on methods to increase soil fertility and crop yields, study rumen microorganisms in order to increase meat and milk production, and try to combat plant and animal diseases. Currently many agricultural microbiologists are studying the use of bacterial and viral insect pathogens as substitutes for chemical pesticides.

Microbial ecology: Microbial ecology is concerned with the relationships between microorganisms and the components of their living and non-living habitats. Microbial ecologists study the global and local contributions of microorganisms to the carbon, nitrogen, and sulphur cycles, including the role of microbes in both the production and removal of greenhouse gases such as carbon dioxide and methane. The study of pollution effects on microorganisms also is important because of the impact these organisms have on the environment. Microbial ecologists are employing microorganisms in bioremediation to reduce pollution. The study of the microbes normally associated with the human body has become a new frontier in microbial ecology.

Food and dairy microbiology: Numerous foods are made using microorganisms. On the other hand, some microbes cause food spoilage or are pathogens spread through food. Scientists working in food and dairy microbiology continue to explore the use of microbes in food production. They also work to prevent microbial spoilage of food and the transmission of food-borne diseases. There is also considerable research on the use of microorganisms themselves as a nutrient source for livestock and humans.

Industrial microbiology: In 1929 Alexander Fleming discovered that the fungus Penicillium produced what he called penicillin, the first antibiotic that could successfully control bacterial infections. Although it took World War II for scientists to learn how to mass produce it, scientists soon found other microorganisms capable of producing additional antibiotics as well as compounds such as citric acid, vitamin B 12, and monosodium glutamate (MSG). Today, industrial microbiologists use microorganisms to make products such as antibiotics, vaccines, steroids, alcohols and other solvents, vitamins, amino acids, and enzymes. Industrial microbiologists identify microbes of use to industry. They also utilize techniques to improve production by microbes and devise systems for culturing them and isolating the products they make.

Microbial Physiology and Biochemistry: Microbes are metabolically diverse and can employ a wide variety of energy sources, including organic matter, inorganic molecules (e.g., H₂ and NH₃ ), and sunlight. Microbiologists working in microbial physiology and biochemistry study many aspects of the biology of microorganisms, including their metabolic capabilities. They may also study the synthesis of antibiotics and toxins, the ways in which microorganisms survive harsh environmental conditions, and the effects of chemical and physical agents on microbial growth and survival.

Microbial Genetics and Molecular Biology: Microbial genetics and molecular biology focus on the nature of genetic information and how it regulates the development and function of cells and organisms. The bacteria Escherichia coli and Bacillus subtilis, the yeast Saccharomyces cerevisiae (baker’s yeast), and bacterial viruses such as T4 and lambda continue to be important model organisms used to understand biological phenomena. Microbial geneticists also play a significant role in applied microbiology because they develop techniques that are useful in agricultural microbiology, industrial microbiology, food and dairy microbiology, and medicine. Because of the practical importance of microbes and their use as model organisms, the future of microbiology is bright.

Briefly describe the major sub-disciplines in micro biology.
Why do you think microorganisms are useful to biologists as experimental models?
List all the activities or businesses you can think of in your community that directly depend on microbiology.

DISCOVERY OF MICROORGANISMS

The earliest microscopic observations appear to have been made between 1625 and 1630 on bees and weevils by the Italian Francesco Stelluti, using a microscope probably supplied by Galileo.

In 1665 the first drawing of a microorganism was published in Robert Hooke’s Micrographia.

However, the first person to publish extensive, accurate observations of microorganisms was the amateur microscopist Antony van Leeuwenhoek (1632–1723) of Delft, the Netherlands. Leeuwenhoek earned his living as a draper and haberdasher (a dealer in men’s clothing and accessories) but spent much of his spare time constructing simple microscopes composed of double convex glass lenses held between two silver plates His microscopes could magnify around 50 to 300 times, and he may have illuminated his liquid specimens by placing them between two pieces of glass and shining light on them at a 45° angle to the specimen plane. This would have provided a form of dark-field illumination in which the organisms appeared as bright objects against a dark background and made bacteria clearly visible. Beginning in 1673, Leeuwenhoek sent detailed letters describing his discoveries to the Royal Society of London. It is clear from his descriptions that he saw both prokaryotes and protozoa.

Figure: A brass replica of the Leeuwenhoek microscope and Leeuwenhoek’s drawings of bacteria from the human mouth

CONFLICT OVER SPONTANEOUS GENERATION THORY

From earliest times, people had believed in spontaneous generation —that living organisms could develop from non-living matter.

Even Aristotle (384–322 BC) thought some of the simpler invertebrates could arise by spontaneous generation.

This view finally was challenged by the Italian physician, Francesco Redi (1626–1697), who carried out a series of experiments on decaying meat and its ability to produce maggots spontaneously. Redi placed meat in three containers. One was uncovered, a second was covered with paper, and the third was covered with fine gauze that would exclude flies. Flies laid their eggs on the uncovered meat and maggots developed. The other two pieces of meat did not produce maggots spontaneously. However, flies were attracted to the gauze-covered container and laid their eggs on the gauze; these eggs produced maggots. Thus the generation of maggots by decaying meat resulted from the presence of fly eggs, and meat did not spontaneously generate maggots as previously believed. Similar experiments by others helped discredit the theory for larger organisms.

Leeuwenhoek’s discovery of microorganisms renewed the controversy. Some proposed that microorganisms arose by spontaneous generation even though larger organisms did not. They pointed out that boiled extracts of hay or meat gave rise to microorganisms after sitting for a while.

In 1748 the English priest John Needham (1713–1781) reported the results of his experiments on spontaneous generation. Needham boiled mutton broth in flasks that he then tightly stoppered. Eventually many of the fl asks became cloudy and contained microorganisms. He thought organic matter contained a vital force that could confer the properties of life on non-living matter.

A few years later, the Italian priest and naturalist Lazzaro Spallanzani (1729–1799) improved on Needham’s experimental design by first sealing glass fl asks that contained water and seeds. If the sealed flasks were placed in boiling water for three-quarters of an hour, no growth took place as long as the fl asks remained sealed. He proposed that air carried germs to the culture medium but also commented that the external air might be required for growth of animals already in the medium.

The supporters of spontaneous generation maintained that heating the air in sealed flasks destroyed its ability to support life.

Several investigators attempted to counter such arguments. Theodore Schwann (1810–1882) allowed air to enter a flask containing a sterile nutrient solution after the air had passed through a red-hot tube. The flask remained sterile. Subsequently Georg Friedrich Schroder (1810–1885) and Theodor von Dusch (1824–1890) allowed air to enter a flask of heat-sterilized medium after it had passed through sterile cotton wool. No growth occurred in the medium even though the air had not been heated.

Despite these experiments, the French naturalist Felix Pouchet (1800–1872) claimed in 1859 to have carried out experiments conclusively proving that microbial growth could occur without air contamination. This claim provoked Louis Pasteur (1822–1895) to settle the matter.

Pasteur first filtered air through cotton and found that objects resembling plant spores had been trapped. If a piece of the cotton was placed in sterile medium after air had been filtered through it, microbial growth occurred. Next he placed nutrient solutions in fl asks, heated their necks in a flame, and drew them out into a variety of curves. The swan neck fl asks that he produced in this way had necks open to the atmosphere. Pasteur then boiled the solutions for a few minutes and allowed them to cool. No growth took place even though the contents of the fl ask were exposed to the air. Pasteur pointed out that no growth occurred because dust and germs had been trapped on the walls of the curved necks. If the necks were broken, growth commenced immediately. Pasteur had not only resolved the controversy by 1861 but also had shown how to keep solutions sterile.

The English physicist John Tyndall (1820–1893) and the German botanist Ferdinand Cohn (1828–1898) dealt a final blow to spontaneous generation. In 1877 Tyndall demonstrated that dust did indeed carry germs and that if dust was absent, broth remained sterile even if directly exposed to air. During the course of his studies, Tyndall provided evidence for the existence of exceptionally heat-resistant forms of bacteria. Working independently, Cohn discovered that the heat- resistant bacteria recognized by Tyndall were species capable of producing bacterial endospores. Cohn later played an instrumental role in establishing a classification system for prokaryotes based on their morphology and physiology.

Figure: Pasteur’s Swan Neck Flasks. These ﬂ asks were used in his experiments on the spontaneous generation of microorganisms.

Koch’s Postulates

The first direct demonstration of the role of bacteria in causing disease came from the study of anthrax by the German physician Robert Koch (1843–1910).

Koch used the criteria proposed by his former teacher Jacob Henle (1809–1885) to establish the relationship between Bacillus anthracis and anthrax; he published his findings in 1876.

Koch injected healthy mice with material from diseased animals, and the mice became ill. After transferring anthrax by inoculation through a series of 20 mice, he incubated a piece of spleen containing the anthrax bacillus in beef serum. The bacilli grew, reproduced, and produced endospores. When the isolated bacilli or their spores were injected into healthy mice, anthrax developed. His criteria for proving the causal relationship between a microorganism and a specific disease are known as Koch’s postulates.

Koch’s proof that B. anthracis caused anthrax was independently confirmed by Pasteur and his co-workers. They discovered that after burial of dead animals, anthrax spores survived and were brought to the surface by earth-worms. Healthy animals then ingested the spores and became ill. After completing his anthrax studies, Koch fully outlined his postulates in his work on the cause of tuberculosis. In 1884 he reported that this disease was caused by the rod-shaped bacterium Mycobacterium tuberculosis, and he was awarded the Nobel Prize in Physiology or Medicine in 1905 for his work.

Koch’s postulates were quickly adopted by others and used to connect many diseases to their causative agent. However, their use is at times not feasible. For instance, organisms such as Mycobacterium leprae, the causative agent of leprosy, cannot be isolated in pure culture.

What does the theory of spontaneous generation propose? How did Pasteur, Tyndall, and Cohn finally settle the spontaneous generation controversy?
What did Pasteur prove when he showed that a cotton plug that had filtered air would trigger microbial growth when transferred to the medium? What argument made previously was he addressing?

Koch’s Postulates

The microorganism must be present in every case of the disease but absent from healthy organisms.
The suspected microorganisms must be isolated and grown in a pure culture.
The same disease must result when the isolated microorganism is inoculated into a healthy host.
The same microorganism must be isolated again from the diseased host.

Koch’s Experimentation

Koch developed a staining technique to examine human tissue. M. tuberculosis cells could be identified in diseased tissue.
Koch grew M. tuberculosis in pure culture on coagulated blood serum.
Koch injected cells from the pure culture of M. tuberculosis into guinea pigs. The guinea pigs subsequently died of tuberculosis.
Koch isolated M. tuberculosis from the dead guinea pigs and was able to again culture the microbe in pure culture on coagulated blood serum.