Medical Bacteriology
STUDY NOTES
THE BACTERIA
The bacteria (singular: bacterium) are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic hot springs, radioactive waste, water, and deep in the Earth's crust, as well as in organic matter and the live bodies of plants and animals. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five nonillion (5×1030) bacteria on Earth, forming much of the world's biomass. Bacteria are vital in recycling nutrients, with many steps in nutrient cycles depending on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. However, most bacteria have not been characterized, and only about half of the phyla of bacteria have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.
There are approximately ten times as many bacterial cells in the human flora of bacteria as there are human cells in the body, with large numbers of bacteria on the skin and as gut flora. The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, and a few are beneficial. However, a few species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people a year, mostly in sub-Saharan Africa. In developed countries, antibiotics are used to treat bacterial infections and in agriculture, so antibiotic resistance is becoming common. In industry, bacteria are important in sewage treatment, the production of cheese and yoghurt through fermentation, as well as in biotechnology, and the manufacture of antibiotics and other chemicals.
Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-boundorganelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved independently from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.
Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. He called them "animalcules" and published his observations in a series of letters to the Royal Society. The name bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1838. Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary, Robert Koch, Pasteur was an early advocate of the germ theory of disease. Robert Koch was a pioneer in medical microbiology and worked on cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in 1905. In Koch's postulates, he set out criteria to test if an organism is the cause of a disease; these postulates are still used today.
Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available. In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum—the spirochaete that causes syphilis—into compounds that selectively killed the pathogen. Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl-Neelsen stain. A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that archaea have a separate line of evolutionary descent from bacteria. This new phylogenetictaxonomy was based on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system.
Origin and early evolution
The ancestors of modern bacteria were single-celled microorganisms that were the first forms of life to develop on earth, about 4 billion years ago. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago.
Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still being found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later on, some eukaryotes that already contained mitochondria also engulfed cyanobacterial-like organisms. This led to the formation of chloroplasts in algae and plants. There are also some algae that originated from even later endosymbiotic events. Here, eukaryotes engulfed a eukaryotic algae that developed into a "second-generation" plastid. This is known as secondary endosymbiosis.
Prokaryotes and eukaryotes"True" bacteria (which include all bacteria that infect man) are members of one kingdom (the eubacteria, bacteria). In addition, a group oforganisms often found in extreme environments form a second kingdom (archaebacteria, Archaea). Morphologically, the two kingdoms of organisms appear similar, especially in the absence of a nucleus, and thus are classified together as prokaryotes. However, they have major biochemical differences. Most archaea live in environments such as hot sulfur springs where they experience temperatures as high as 80 degrees C and a pH of 2. These are called thermoacidophiles. Others live in methane-containing (methanogens) or high salt (extreme halophiles) environments.
Archaea
Based on DNA sequence similarities, it appears that the archaea and eukaryotes diverged from the eubacteria before they diverged from each other and in some ways, archaea are biochemically more like eukaryotes than they are the eubacteria. For example, the RNA polymerase of archaea is as complex, in terms of number of subunits, as the eukaryote nuclear polymerases and there is considerable amino acid homology with some of the eukaryotic subunits. Gene promoter structure in archaea is also more similar to that of eukaryotes than eubacteria, although, like the eubacteria, archaea have operons and transcribe these to polycistronic mRNA. Similarity also exists between the protein synthesis factors of archaea and eukaryotes suggesting that the overall protein synthesis mechanisms of eukaryotes and archaea may be similar. The 16S rRNAs of the eubacteria and the archaea are quite distinct in sequence.Eubacteria (with the exception of the genera Mycoplasma and Chlamydia) possess peptidoglycan (synonyms: murein, mucopeptide, cell wall skeleton). Peptidoglycan, contains a unique sugar, muramic acid, not found elsewhere in nature. Archaebacteria contain a pseudomurein that is different in structure from eubacterial murein.In view of the increasing number of similarities between the archaea and the eukaryotes, the term archaebacteria is no longer used. All other cellular forms of life (including plants, animals, and fungi) are referred to as eukaryotes.
Members of the Archaea are not human pathogens.
Differences between prokaryotes/eukaryotes
The prokaryotic cell, in contrast to the eukaryotic cell, is not compartmentalized. Nuclear membranes, mitochondria, endoplasmic reticulum, Golgi body, phagosomes and lysosomes are not present. Prokaryotes generally possess only a single circular chromosome. Since there is no nuclear membrane, the chromosome is bound to a specific site on the cell membrane - the mesosome. Prokaryotic ribosomes are 70S (S stands for Svedberg unit, a measure of size), whereas eukaryotic ribosomes are larger (80S). Prokaryotic ribosomal subunits are 30S and 50S (eukaryotic are larger). The 30S ribosome has 16S RNA, whilst the 50S ribosome contains 23S and 5S RNA. Ribosomal RNA is larger in eukaryotes (e.g. 18S versus 16S rRNA). Bacterial membranes generally do not contain sterols (e.g. cholesterol).
The prototype bacterial cell
BACTERIAL STRUCTURES
Despite their lack of complexity compared to eukaryotes, a number of eubacterial structures may be defined. Not all bacteria possess all of these components.
Plasmids
These are extra-chromosomal DNA, usually present in multiple copies, that often code for pathogenesis factors and antibiotic resistance factors. Some forms are also involved in bacterial replication.
The cell envelope
Bacteria can be divided into two groups on the basis of staining with the Gram stain; Gram positive bacteria remain stained by crystal violet on washing, Gram negative do not. All bacteria have a cell membrane where oxidative phosphorylation occurs (since there are no mitochondria). Outside the cell membrane is the cell wall which is rigid and protects the cell from osmotic lysis. In Gram positive bacteria, the cell wall peptidoglycan layer is a much thicker layer than in Gram negative bacteria. Gram negative bacteria have an additional outer membrane. The outer membrane is the major permeability barrier in Gram negative bacteria. The space between the inner and outer membranes is known as the periplasmic space. Gram negative bacteria store degradative enzymes in the periplasmic space. Gram positive bacteria lack a periplasmic space; instead they secrete exoenzymes and perform extracellular digestion. Digestion is needed since large molecules can not readily pass across the outer membrane (if present) or cell membrane.
Wall-less forms of Bacteria
When bacteria are treated with 1) enzymes that are lytic for the cell wall e.g. lysozyme or 2) antibiotics that interfere with biosynthesis of peptidoglycan, wall-less bacteria are often produced. Usually these treatments generate non-viable organisms. Wall-less bacteria that can not replicate are referred to as spheroplasts (when an outer membrane is present) or protoplasts (if an outer membrane is not present). Occasionally wall-less bacteria that can replicate are generated by these treatments (L forms).
Flagella
Some bacterial species are mobile and possess locomotory organelles – flagella. Those that do are able to taste their environment and respond to specific chemical foodstuffs or toxic materials and move towards or away from them (chemotaxis). Flagella are embedded in the cell membrane, extend through the cell envelope and project as a long strand. Flagella consist of a number of proteins including flagellin. They move the cell by rotating with a propeller like action. Axial filaments in spirochetes have a similar function to flagella. Binding proteins in the periplasmic space or cell membrane bind food sources (such as sugars and amino acids) causing methylation of other cell membrane proteins which in turn affect the movement of the cell by flagella. Permeases are proteins that then transport these foodstuffs through the cell membrane. Energy and carbon sources can then be stored when necessary in cytoplasmic "storage granules" which consist of glycogen, polyhydroxybutyrate or polyphosphate.
Pili (synonym: fimbriae)
The types of pili (or whether they are produced at all) varies both among and between species. Pili are hair-like projections of the cell (Figure 5). Some are involved in sexual conjugation and others allow adhesion to host epithelial surfaces in infection.
Capsules and slime layers
These are structures surrounding the outside of the cell envelope. When more defined, they are referred to as a capsule when less defined as a slime layer or glycocalyx. They usually consist of polysaccharide; however, in certain bacilli they are composed of a polypeptide (polyglutamic acid). They are not essential to cell viability and some strains within a species will produce a capsule, whilst others do not. Capsules of pathogenic bacteria inhibit ingestion and killing by phagocytes. Capsules are often lost during in vitro culture.
Endospores (spores)
These are a dormant form of a bacterial cell produced by certain bacteria when starved; the actively growing form of the cell is referred to as vegetative. The spore is resistant to adverse conditions (including high temperatures and organic solvents). The spore cytoplasm is dehydrated and contains calcium dipicolinate which is involved in the heat resistance of the spore. Spores are commonly found in the genera Bacillus and Clostridium.
P. larvae sporulation in culture appears similar to that of other endospore formers. The rod-shaped vegetative cell has a thick peptidoglycan layer.
An immature spore is shown surrounded by the mother cell (sporangium). A copy of the bacterial DNA is encased within the developing spore. The outer spore coat appears thinner and less electron dense than in the mature spores.
The thick spore coat indicates that endospore differentiation is complete, but the endospore remains within the sporangium. Finally, the endospore is released from the sporangium. The inner spore coat consists of a maximum of seven distinct layers referred to as lamellae.
Bacterial cell structure
Bacteria, despite their simplicity, contain a well developed cell structure which is responsible for many of their unique biological properties. Many structural features are unique to bacteria and are not found among archaea or eukaryotes. Because of the simplicity of bacteria relative to larger organisms and the ease with which they can be manipulated experimentally, the cell structure of bacteria has been well studied, revealing many biochemical principles that have been subsequently applied to other organisms.
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