1 Microbiology, study of microorganisms, or microbes, a diverse group of generally minute, simple life-forms that include bacteria, archaea, algae, fungi, protozoa, and viruses. The field is concerned with the structure, function, and classification of such organisms and with ways of both exploiting and controlling their activities.
The 17th-century discovery of living forms existing invisible to the naked eye was a significant milestone in the history of science, for from the 13th century onward it had been postulated that “invisible” entities were responsible for decay and disease.
The word microbe was coined in the last quarter of the 19th century to describe these organisms, all of which were thought to be related.
2 Historical Background：
Antonie van Leeuwenhoek; microscope;Leeuwenhoek’s “animalcules ”
Microbiology essentially began with the development of the microscope. Although others may have seen microbes before him, it was Antonie van Leeuwenhoek, a Dutch draper whose hobby was lens grinding and making microscopes, who was the first to provide proper documentation of his observations.
His descriptions and drawings included protozoans from the guts of animals and bacteria from teeth scrapings. His records were excellent because he produced magnifying lenses of exceptional quality. Leeuwenhoek conveyed his findings in a series of letters to the British Royal Society during the mid-1670s. Although his observations stimulated much interest, no one made a serious attempt either to repeat or to extend them. Leeuwenhoek’s “animalcules,” as he called them, thus remained mere oddities of nature to the scientists of his day, and enthusiasm for the study of microbes grew slowly. It was only later, during the 18th-century revival of a long-standing controversy about whether life could develop out of nonliving material, that the significance of microorganisms in the scheme of nature and in the health and welfare of humans became evident.
3 Spontaneous generation:
The early Greeks believed that living things could originate from nonliving matter (abiogenesis) and that the goddess Gea could create life from stones.
Aristotle discarded this notion, but he still held that animals could arise spontaneously from dissimilar organisms or from soil.
Louis Pasteur finally announced the results of his conclusive experiments in 1864. In a series of masterful experiments, Pasteur proved that only preexisting microbes could give rise to other microbes (biogenesis).
★★4 Classification of Bacteria:German botanist Ferdinand Cohn
Modern and accurate knowledge of the forms of bacteria can be attributed to German botanist Ferdinand Cohn, whose chief results were published between 1853 and 1892. Cohn’s classification of bacteria, published in 1872 and extended in 1875, dominated the study of these organisms thereafter.
5 Contagion:
Girolamo Fracastoro, an Italian scholar, advanced the notion as early as the mid-1500s that contagion is an infection that passes from one thing to another.
6 Koch’s postulates : a specific organism causes a specific disease
Robert Koch, a German physician, defined the procedure (Koch’s postulates) for proving that a specific organism causes a specific disease.
7 Fast Development: 1940s--control pathogens and industrial usage
Since the 1940s microbiology has experienced an extremely productive period during which many disease-causing microbes have been identified and methods to control them developed. Microorganisms have also been effectively utilized in industry; their activities have been channeled to the extent that valuable products are now both vital and commonplace.
★★★8 Types Of Microorganisms
The major groups of microorganisms—namely bacteria, archaea, fungi (yeasts and molds), algae, protozoa, and viruses—are summarized below.
8.1 Bacteria (eubacteria and archaea) and shapes:
Bacteria have a variety of shapes, including spheres, rods, and spirals.
Individual cells generally range in width from 0.5 to 5 micrometres (μm; millionths of a metre). Although unicellular, bacteria often appear in pairs, chains, tetrads (groups of four), or clusters. Some have flagella, external whiplike structures that propel the organism through liquid media; some have capsule, an external coating of the cell; some produce spores—reproductive bodies that function much as seeds do among plants.
One of the major characteristics of bacteria is their reaction to the Gram stain. Depending upon the chemical and structural composition of the cell wall, some bacteria are gram-positive, taking on the stain’s purple colour, whereas others are gram-negative.
bacteria and archaea differences :
The cell walls of all true bacteria contain the chemical substance peptidoglycan, whereas the cell walls of archaeans lack this substance.
Fungi
Fungi are eukaryotic organisms that, like algae, have rigid cell walls and may be either unicellular or multicellular. Some may be microscopic in size, while others form much larger structures, such as mushrooms and bracket fungi that grow in soil or on damp logs. Unlike algae, fungi do not contain chlorophyll and thus cannot carry out photosynthesis. Fungi do not ingest food but must absorb dissolved nutrients from the environment. Of the fungi classified as microorganisms, those that are multicellular and produce filamentous, microscopic structures are frequently called molds, whereas yeasts are unicellular fungi.
In molds cells are cylindrical in shape and are attached end to end to form threadlike filaments (hyphae) that may bear spores. Individually, hyphae are microscopic in size. However, when large numbers of hyphae accumulate—for example, on a slice of bread or fruit jelly—they form a fuzzy mass called a mycelium that is visible to the naked eye.
The unicellular yeasts have many forms, from spherical to egg-shaped to filamentous. Yeasts are noted for their ability to ferment carbohydrates, producing alcohol and carbon dioxide in products such as wine and bread.
Protozoa
Protozoa, or protozoans, are single-celled, eukaryotic microorganisms. Some protozoa are oval or spherical, others elongated. Still others have different shapes at different stages of the life cycle. Cells can be as small as 1 μm in diameter and as large as 2,000 μm, or 2 mm (visible without magnification). Like animal cells, protozoa lack cell walls, are able to move at some stage of their life cycle, and ingest particles of food; however, some phytoflagellate protozoa are plantlike, obtaining their energy via photosynthesis. Protozoan cells contain the typical internal structures of an animal cell. Some can swim through water by the beating action of short, hairlike appendages (cilia) or flagella. Their rapid, darting movement in a drop of pond water is evident when viewed through a microscope.
Viruses
Viruses, agents considered on the borderline of living organisms, are also included in the science of microbiology, come in several shapes, and are widely distributed in nature, infecting animal cells, plant cells, and microorganisms. The field of study in which they are investigated is called virology. All viruses are obligate parasites; that is, they lack metabolic machinery of their own to generate energy or to synthesize proteins, so they depend on host cells to carry out these vital functions. Once inside a cell, viruses have genes for usurping the cell’s energy-generating and protein-synthesizing systems. In addition to their intracellular form, viruses have an extracellular form that carries the viral nucleic acid from one host cell to another. In this infectious form, viruses are simply a central core of nucleic acid surrounded by a protein coat called a capsid. The capsid protects the genes outside the host cell; it also serves as a vehicle for entry into another host cell because it binds to receptors on cell surfaces. The structurally mature, infectious viral particle is called a virion.
Prions
Even smaller than viruses, prions (pronounced “pree-ons”) are the simplest infectious agents. Like viruses they are obligate parasites, but they possess no genetic material. Although prions are merely self-perpetuating proteins, they have been implicated as the cause of various diseases, including bovine spongiform encephalopathy (mad cow disease), and are suspected of playing a role in a number of other disorders.
Lichens
Lichens represent a form of symbiosis, namely, an association of two different organisms wherein each benefits. A lichen consists of a photosynthetic microbe (an alga or a cyanobacterium) growing in an intimate association with a fungus. A simple lichen is made up of a top layer consisting of a tightly woven fungal mycelium, a middle layer where the photosynthetic microbe lives, and a bottom layer of mycelium. In this mutualistic association, the photosynthetic microbes synthesize nutrients for the fungus, and in return the fungus provides protective cover for the algae or cyanobacteria. Lichens play an important role ecologically; among other activities they are capable of transforming rock to soil.
Slime molds
The slime molds are a biological and taxonomic enigma because they are neither typical fungi nor typical protozoa. During one of their growth stages, they are protozoa-like because they lack cell walls, have amoeboid movement, and ingest particulate nutrients. During their propagative stage they form fruiting bodies and sporangia, which bear walled spores like typical fungi. Traditionally, the slime molds have been classified with the fungi. There are two groups of slime molds: the cellular slime molds and the acellular slime molds.
9 Basic microbiology
The study of the biology of microorganisms requires the use of many different procedures as well as special equipment. The biological characteristics of microorganisms can be summarized under the following categories: morphology, nutrition, physiology, reproduction and growth, metabolism, pathogenesis, antigenicity, and genetic properties.
Morphology
Morphology refers to the size, shape, and arrangement of cells. The observation of microbial cells requires not only the use of microscopes but also the preparation of the cells in a manner appropriate for the particular kind of microscopy. During the first decades of the 20th century, the compound light microscope was the instrument commonly used in microbiology. Light microscopes have a usual magnification factor of 1000 × and a maximum useful magnification of approximately 2000 ×. Specimens can be observed either after they have been stained by one of several techniques to highlight some morphological characteristics or in living, unstained preparations as a “wet mount.”
Nutritional and physiological characteristics
Microorganisms as a group exhibit great diversity in their nutritional requirements and in the environmental conditions that will support their growth. No other group of living organisms comes close to matching the versatility and diversity of microbes in this respect. Some species will grow in a solution composed only of inorganic salts (one of the salts must be a compound of nitrogen) and a source of carbon dioxide (CO2); these are called autotrophs. Many, but not all, of these microbes are autotrophic via photosynthesis. Organisms requiring any other carbon source are called heterotrophs. These microbes commonly make use of carbohydrates, lipids, and proteins, although many microbes can metabolize other organic compounds such as hydrocarbons. Others, particularly the fungi, are decomposers. Many species of bacteria also require specific additional nutrients such as minerals, amino acids, and vitamins. Various protozoans, fungi, and bacteria are parasites, either exclusively (obligate parasites) or with the ability to live independently (facultative parasites).
If the nutritional requirements of a microorganism are known, a chemically defined medium containing only those chemicals can be prepared. More complex media are also routinely used; these generally consist of peptone (a partially digested protein), meat extract, and sometimes yeast extract. When a solid medium is desired, agar is added to the above ingredients. Agar is a complex polysaccharide extracted from marine algae. It has several properties that make it an ideal solidifying substance for microbiological media, particularly its resistance to microbial degradation.
Microorganisms vary widely in terms of the physical conditions required for growth. For example, some are aerobes (require oxygen), some are anaerobes (grow only in the absence of oxygen), and some are facultative (they grow in either condition). Eukaryotic microbes are generally aerobic. Microorganisms that grow at temperatures below 20 °C (68 °F) are called psychrophiles; those that grow best at 20–40 °C (68–104 °F) are called mesophiles; a third group, the thermophiles, require temperatures above 40 °C. Those organisms which grow under optimally under one or more physical or chemical extremes, such as temperature, pressure, pH, or salinity, are referred to as extremophiles. Bacteria exhibit the widest range of temperature requirements. Whereas bacterial (and fungal) growth is commonly observed in food that has been refrigerated for a long period, some isolated archaea (e.g., Pyrodictium occultum and Pyrococcus woesei) grow at temperatures above 100 °C (212 °F).
Other physical conditions that affect the growth of microorganisms are acidity or basicity (pH), osmotic pressure, and hydrostatic pressure. The optimal pH for most bacteria associated with the human environment is in the neutral range near pH 7, though other species grow under extremely basic or acidic conditions. Most fungi are favoured by a slightly lower pH (5–6); protozoa require a range of pH 6.7–7.7; algae are similar to bacteria in their requirements except for the fact that they are photosynthetic.
Reproduction and growth
Bacteria reproduce primarily by binary fission, an asexual process whereby a single cell divides into two. Under ideal conditions some bacterial species may divide every 10–15 minutes—a doubling of the population at these time intervals. Eukaryotic microorganisms reproduce by a variety of processes, both asexual and sexual. Some require multiple hosts or carriers (vectors) to complete their life cycles. Viruses, on the other hand, are produced by the host cell that they infect but are not capable of self-reproduction.
The study of the growth and reproduction of microorganisms requires techniques for cultivating them in pure culture in the laboratory. Data collected on the microbial population over a period of time, under controlled laboratory conditions, allow a characteristic growth curve to be constructed for a species.
Metabolism
Collectively, microorganisms show remarkable diversity in their ability to produce complex substances from simple chemicals and to decompose complex materials to simple chemicals. An example of their synthetic ability is nitrogen fixation—the production of amino acids, proteins, and other organic nitrogen compounds from atmospheric nitrogen (N2). Certain bacteria and blue-green algae (cyanobacteria) are the only organisms capable of this ecologically vital process. An example of microbes’ ability to decompose complex materials is shown by the white and brown rot fungi that decompose wood to simple compounds, including CO2.
Laboratory procedures are available that make it possible to determine the biochemical capability of a species qualitatively and quantitatively. Routine techniques can identify which compounds or substances are degraded by a specific microbe and which products are synthesized. Through more elaborate experimentation it is possible to determine step-by-step how the microbe performs these biochemical changes. Studies can be performed in a number of ways using growing cultures, “resting cells” (suspensions of cells), cell-free extracts, or enzyme preparations from cells.
Certain biochemical tests are routinely used to identify microbes—though more in the case of bacteria than algae, fungi, or protozoa. The adoption of routine sets of laboratory tests has allowed automated instrumentation to perform the tests. For instance, technicians often simply inoculate individual units of a “chamber” that is preloaded with a specific chemical substance (the substrate) and then place the chamber into an apparatus that serves as an incubator and analyzer. The apparatus automatically records the results and is frequently capable of calculating the degree of accuracy of the identification.
Pathogenesis
Some microorganisms cause diseases of humans, other animals, and plants. Such microbes are called pathogens. Pathogens are identified by the hosts they infect and the symptoms they cause; it is also important to identify the specific properties of the pathogen that contribute to its infectious capacity—a characteristic known as virulence. The more virulent a pathogen, the fewer the number needed to establish an infection.
Antigenic characteristics
An antigen is a substance that, when introduced into an animal body, stimulates the production of specific substances (antibodies) that react or unite with the antigen. Microbial cells and viruses contain a variety of antigenic substances. A significant feature of antigen-antibody reactions is specificity; the antibodies formed as a result of inoculating an animal with one microbe will not react with the antibodies formed by inoculation with a different microbe. Antibodies appear in the blood serum of animals, and laboratory tests of antigen-antibody reactions are performed by using sera—hence the term serological reactions. Thus, it is possible to characterize a microorganism by its antigenic makeup as well as to identify microorganisms by using one of many different serological tests. Antigens and antibodies are important aspects of immunity, and immunology is included in the science of microbiology.
Genetic characterization
Since the last quarter of the 20th century, researchers have accumulated a vast amount of information elucidating in precise detail the chemical composition, synthesis, and replication of the genetic material of cells. Much of this research has been done by using microorganisms, and techniques have been developed that permit experimentation at the molecular level. For instance, experiments determining the degree of similarity between different organisms’ DNA and RNA have provided new insights for the classification of microorganisms. Test kits are available for the identification of microorganisms, particularly bacteria, by DNA probes.
Since the invention of recombinant DNA technology in 1973, techniques have been developed whereby genes from one cell can be transferred to an entirely different cell, as when a gene is transferred from an animal cell to a bacterium or from a bacterium to a plant cell. Recombinant DNA technology opened the door to many new medical and industrial applications of microbiology, and it plays a central role in genetic engineering.
Applied microbiology
Genetic engineering is an example of how the fields of basic and applied microbiology can overlap. Genetic engineering is primarily considered a field of applied microbiology (that is, the exploitation of microorganisms for a specific product or use). The methods used in genetic engineering were developed in basic research of microbial genetics. Conversely, methods used and perfected for applied microbiology can become tools for basic microbiology. Applied microbiology can, however, be divided under the following headings.
Soil microbiology
However “dead” soil may appear, it is in fact teeming with millions or billions of microbial cells per gram, depending upon soil fertility and the environment. Dead vegetation, human and animal wastes, and dead animals are deposited in or on soil. In time they all decompose into substances that contribute to soil, and microbes are largely responsible for these transformations.
Two great pioneer soil microbiologists were Martinus W. Beijerinck (1851–1931), a Dutchman, and Sergey N. Winogradsky (1856–1953), a Russian. These researchers isolated and identified new types of bacteria from soil, particularly autotrophic bacteria, that use inorganic chemicals as nutrients and as a source of energy. The relationship between legumes and bacteria in the nodules of legume roots was discovered by other scientists in 1888. The nodules contain large numbers of bacteria (Rhizobium) that are capable of fixing atmospheric nitrogen into compounds that can be used by plants.
The ecology of fertile soil consists of plant roots, animals such as rodents, insects, and worms, and a menagerie of microorganisms—viruses, bacteria, algae, fungi, and protozoa. The role of this microbial flora can be conveniently expressed in Earth’s natural cycles. In the nitrogen cycle, for example, microorganisms capture nitrogen gas from the atmosphere and convert it into a combined form of nitrogen that plants can use as a nutrient; the plant synthesizes organic nitrogen compounds that are consumed by humans and animals; the consumed nitrogen compounds eventually reach the soil; microorganisms complete the cycle by decomposing these compounds back to atmospheric nitrogen and simple inorganic molecules that can be used by plants. In similar cycles for other elements such as carbon, sulfur, and phosphorus, microbes play a role; this makes them essential to maintaining life on Earth.
Microbiology of water supplies, wastewater, and other aquatic environments
Long before the establishment of microbiology as a science, water was suspected of being a carrier of disease-producing organisms. But it was not until 1854, when an epidemic of cholera was proved to have had its origin in polluted water, that contaminated water was considered more seriously as a source of disease. Since that time there has been continuous research on the microbiology of public water supplies, including the development of laboratory procedures to determine whether the water is potable, or safe for human consumption. At the same time, purification procedures for these supplies have emerged.
A highly standardized and routine laboratory procedure to determine the potability of water is based upon detecting the presence or absence of the bacterium Escherichia coli. E. coli is a normal inhabitant of the intestinal tract of humans; its presence in water indicates that the water is polluted with intestinal wastes and may contain disease-producing organisms.
The principal operations employed in a municipal water-purification plant are sedimentation, filtration, and chlorination. Each of these operations removes or kills microorganisms, and the microbiological quality of the treated water is monitored at frequent intervals.
The used water supply of a community, commonly referred to as sewage, is microbiologically significant in two ways. First, sewage is a potential carrier of pathogenic microorganisms, so measures such as chlorination must be implemented to prevent these microbes from contaminating drinking-water supplies. Second, sewage-treatment plants purify water by exploiting the biochemical abilities of microbes to metabolize contaminants. Raw sewage is processed through large tanks, first for anaerobic degradation of complex substrates and later for aerobic oxidation of soluble products. This “activated sludge” treatment is dependent upon incubation conditions that favour the growth and metabolic activity of appropriate microorganisms.
Another aspect of the microbiology of water pertains to natural bodies of water such as ponds, lakes, rivers, and oceans. Aquatic microbes perform a host of biochemical transformations and are an essential component of the food chain in these environments. For example, the microbial flora of the sea comprises bacteria, algae, fungi, and protozoa. The microorganisms inhabiting aquatic environments are collectively referred to as plankton; phytoplankton refers to the photosynthetic microbes (primarily algae), whereas protozoa, and other small animals, are zooplankton. Phytoplankton is responsible for converting solar energy into chemical energy—the components of plankton cells that serve as food for higher aquatic life. The magnitude of this process can be appreciated by calculations indicating that it takes 1,000 tons of phytoplankton to support the growth of one ton of fish.
Large populations of archaea live in volcanic ridges 2,600 metres (8,500 feet) below the ocean surface in areas immediately surrounding hydrothermal vents (deep-sea hot springs). The vents spew superheated water (350 °C [662 °F]) that contains hydrogen sulfide (H2S); the water surrounding the vents has a temperature range of 10–20 °C (50–68 °F). Many bacteria concentrate in this region because of the availability of H2S, which they can use for energy. The abundance of animal life that also inhabits this region is completely dependent on the microbes for food.
There is a growing interest in other ecological aspects of aquatic microbiology, such as the role of microbes in global warming and oxygen production. Experimental approaches are being developed to study the complex biology and ecology of biofilms and microbial mats. These assemblages of microbes and their products, while potentially useful in several ways, are complex. In many instances the microbial flora involved must sometimes be studied in its natural environment because the environment cannot be reproduced in the laboratory.
Food microbiology
Microorganisms are of great significance to foods for the following reasons: (1) microorganisms can cause spoilage of foods, (2) microorganisms are used to manufacture a wide variety of food products, and (3) microbial diseases can be transmitted by foods.