Brief History of Microbiology PDF

05-10-2024 Brief History of Microbiology Dr Jitendra 1 The microscope is the microbiologist’s oldest and most fundamental tool for studying the microbial world. Indeed, microbiology did not exist befor...

05-10-2024 Brief History of Microbiology Dr Jitendra 1 The microscope is the microbiologist’s oldest and most fundamental tool for studying the microbial world. Indeed, microbiology did not exist before the invention of the microscope 2 1  05-10-2024 Robert Hooke (1635-1703) The first microscopist to publish a systematic study of the world as seen under a microscope was Robert Hooke (1635- 1703). Hooke was the first to observe distinct units of living material, which he called “cells.” 3 With his microscope, Hooke observed biological materials such as nematode "vinegar eels," mites, and mold filaments, illustrations of which he published in Micrograpllia (1665), the first publication that illustrated objects observed under a microscope his crude lenses achieved at best 30-fold power (30×), and he never observed single-celled bacteria 4 2  05-10-2024 Antoni van Leeuwenhoek (1632–1723) The first person to see bacteria, the smallest microbial cells, was the Dutch cloth draper and amateur microscopist Antoni van Leeuwenhoek (1632–1723). Van Leeuwenhoek constructed extremely simple microscopes containing a single lens to examine various natural substances for microorganisms his design used a simple lens that could magnify an image at least 266 times. 5 One day he applied his microscope to observe matter extracted from between his teeth. He wrote, “To my great surprise [I] perceived that the aforesaid matter contained very many small living Animals, which moved themselves very extravagantly.” Drawings of some of van Leeuwenhoek’s “wee animalcules,” as he referred to them 6 3  05-10-2024 7 Spontaneous Generation The observation of microscopic organisms led priests and philosophers to wonder where these tiny beings came from. In the eighteenth century, scientists and church leaders intensely debated the question of spontaneous generation. Spontaneous generation is the concept that living creatures such as maggots could arise spontaneously, without parental organisms. Chemists of the day tended to support spontaneous generation, as it appeared similar to the way chemicals changed during reaction. Christian church leaders, however, supported the biblical view that all organisms have “parents” going back to the first week of creation. 8 4  05-10-2024 Francesco Redi (1626–1697 The Italian priest Francesco Redi (1626–1697) showed that maggots in decaying meat were the offspring of flies. Meat kept in a sealed container, excluding flies, did not produce maggots. Thus, Redi’s experiment argued against spontaneous generation for macroscopic organisms. The meat still putrefied, however, producing microbes that seemed to arise “without parents. 9 Lazzaro Spallanzani (1729–1799) To disprove spontaneous generation of microbes, another Italian priest, Lazzaro Spallanzani (1729–1799), showed that a sealed flask of meat broth sterilized by boiling failed to grow microbes. Spallanzani also noticed that microbes often appeared in pairs. Were these two parental microbes coupling to produce offspring, or did one microbe become two? Through long and tenacious observation, Spallanzani watched a single microbe grow in size until it split in two. However, he did not convince the proponents of the theory because they believed that his treatment excluded oxygen, which they felt was vital to spontaneous generation. 10 5  05-10-2024 Louis Pasteur (1822–1895) Louis Pasteur reveals the biochemical basis of microbial growth. Pasteur began his scientifi c career as a chemist and wrote his doctoral thesis on the structure of organic crystals. He discovered the fundamental chemical property of chirality, the fact that some organic molecules exist in two forms that differ only by mirror symmetry 11 Pasteur found that when microbes were cultured on a nutrient substance containing both mirror forms, only one mirror form was consumed As a chemist, Pasteur was asked to help with a widespread problem encountered by French manufacturers of wine and beer. 12 6  05-10-2024 The alcohol in beverages comes from fermentation, a process by which microbes gain energy by converting sugars into alcohol In the time of Pasteur, however, the conversion of grapes or grain to alcohol was believed to be a spontaneous chemical process. No one could explain why some fermentation mixtures produced vinegar (acetic acid) instead of alcohol. 13 Pasteur discovered that fermentation is actually caused by living yeast, a single-celled fungus. In the absence of oxygen, yeast produces alcohol as a terminal waste product. But when the yeast culture is contaminated with bacteria, the bacteria outgrow the yeast and produce acetic acid instead of alcohol 14 7  05-10-2024 15 Pasteur knew that some microbial species do not require oxygen for growth. Pasteur discovered forms of life that could exist in the absence of oxygen. He introduced the terms “aerobes” (organisms that require oxygen) and “anaerobes” (organisms that do not require oxygen So he devised an unsealed flask with a long, bent “swan neck” that admitted air but kept the boiled contents free of dust that carried microbes (Fig. 1.13B). The famous swan necked flasks remained free of microbial growth for many years, but when a flask was tilted to enable contact of broth with dust, microbes grew immediately. Thus, Pasteur disproved that lack of oxygen was the reason for the failure of spontaneous generation in Spallanzani’s flasks 16 8  05-10-2024 Pasteur developed a process (today known as pasteurization) to kill microbes that were causing wine to spoil—an economic concern to France’s wine industry. Pasteurization can be used to kill pathogens in many types of liquids. Pasteur’s process involved heating wine to 55°Cb and holding it at that temperature for several minutes. Today, pasteurization is accomplished by heating liquids to 63° to 65°C for 30 minutes or to 73° to 75°C for 15 seconds. It should be noted that pasteurization does not kill all of the microbes in liquids—just the pathogens 17 Pasteur made significant contributions to the germ theory of disease—the theory that specific microbes cause specific infectious diseases. 18 9  05-10-2024 Pasteur championed changes in hospital practices to minimize the spread of disease by pathogens. 19 Pasteur developed vaccines to prevent chicken cholera, anthrax, and swine erysipelas (a skin disease). Pasteur developed a vaccine to prevent rabies in dogs and successfully used the vaccine to treat human rabies 20 10  05-10-2024 The Irish scientist John Tyndall (1820–1893) attempted the same experiment as Pasteur but sometimes found the opposite result. Tyndall found that the broth sometimes gave rise to microbes no matter how long it was sterilized by boiling. The microbes appear because some kinds of organic matter, particularly hay infusion, are contaminated with a heat-resistant form of bacteria called “endospores” (or “spores”). The spore form can be eliminated only by repeated cycles of boiling and resting, in which the spores germinate to the growing, vegetative form that is killed at 100°C. 21 Robert Koch (1843–1910) The first scientific basis for determining that a specific microbe causes a disease was devised by the Robert Koch This German physician, made numerous contributions to the science of microbiology. Some of them are listed here 22 11  05-10-2024 The germ theory of disease Koch proved that the anthrax bacillus (B. anthracis), which had been discovered earlier by other scientists, was truly the cause of anthrax. He accomplished this using a series of scientific steps that he and his colleagues had developed; these steps later became known as Koch’s Postulates Koch discovered that B. anthracis produces spores, capable of resisting adverse conditions. Koch developed methods of fixing, staining, and photographing bacteria. 23 Koch’s Postulates During the mid- to late-1800s, Robert Koch and his colleagues established an experimental procedure to prove that a specific microbe is the cause of a specific infectious disease. This scientific procedure, published in 1884, became known as Koch’s Postulates. 24 12  05-10-2024 Exceptions to Koch’s Postulates After completing these steps, the microbe is said to have fulfilled Koch’s Postulates and has been proven to be the cause of that particular infectious disease. However, certain pathogens will not grow on artificial media. Such pathogens include viruses, rickettsias (a category of bacteria), chlamydias (another category of bacteria), and the bacteria that cause leprosy and syphilis. Viruses, rickettsias, and chlamydias are called obligate intracellular pathogens (or obligate intracellular parasites) because they can only survive and multiply within living host cells 25 In the laboratory, the leprosy bacterium (Mycobacterium leprae) is propagated in armadillos, and the spirochetes of syphilis (Treponema pallidum) grow well in the testes of rabbits and chimpanzees. 26 13  05-10-2024 Many pathogens are species-specific, meaning that they infect only one species of animal. For example, some pathogens that infect humans will only infect humans. Thus, it is not always possible to find a laboratory animal that can be infected with a pathogen that causes human disease 27 Some diseases, called synergistic infections, are caused not by one particular microbe, but by the combined effects of two or more different microbes. Examples of such infections include acute necrotizing ulcerative gingivitis (ANUG; also known as “trench mouth”) 28 14  05-10-2024 Pure culture, solid medium and petri dishes a pure culture of microorganisms, a culture grown from a single “parental” cell. Previous researchers had achieved pure cultures by a laborious process of serially diluting suspended bacteria until a culture tube contained only a single cell. Alternatively, inoculating a solid surface such as a sliced potato could produce isolated colonies—distinct populations of bacteria, each grown from a single cell. For M. tuberculosis, Koch inoculated serum, which then formed a solid gel after heating. Later he refined the solid-substrate technique by adding gelatin to a defined liquid medium, which could then be chilled to form a solid medium in a glass dish. 29 Julius Richard Petri (1852–1921) 30 15  05-10-2024 31 32 16  05-10-2024 Edward Jenner (1749-1823) Almost 70 years before Koch established that a specific microorganism causes anthrax, Edward Jenner, a young British physician, embarked on an experiment to find a way to protect people from smallpox. The disease periodically swept through Europe, killing thousands, and it wiped out 90% of the Native Americans on the East Coast when European settlers first brought the infection to the New World. 33 Barry Marshall“the guinea-pig doctor” He started vomiting, his breath began to stink, and he felt sick and exhausted For their work on H. pylori, Marshall and Warren shared a 2005 Nobel Prize. 34 17  05-10-2024 Evolution and Microbial life Dr Jitendra Mishra 1 Evolution Evolution is the accumulation of changes that occur in organisms as they adapt to their environments. It is documented every day in all corners of the planet, an observable phenomenon testable by science 2 1  05-10-2024 Most scientists agree that life was present on Earth about 3.5 to 3.8 billion years ago. To reach this conclusion, biologists rely on indirect evidence. Among the indirect evidence used are molecular fossils. These are chemicals found in rock or sediment that are chemically related to biological molecules. For instance, the presence of molecules called hopanes in a rock indicates that bacteria were present when the rock was formed. This conclusion is reached because hopanes are formed from hopanoids, which are found in the plasma membranes of extant bacteria. 3 For billions of years, microbes have extensively shaped the development of the earth’s habitats and the evolution of other life forms. It is understandable that scientists searching for life on other planets first look for signs of microorganisms. Cellular organisms that preceded our current cell types arose on this planet about 3.5 billion years ago, according to the fossil record. It appears that they were the only living inhabitants until about 2.9 billion years ago. At that time, a cell called the last universal common ancestor, or LUCA, seems to have given rise to three types of cells. 4 2  05-10-2024 Two of these were bacteria and archaea, and the third was a more complex type of single-celled organism, the eukaryote (yoo″-kar-ee- ote). Eukary means true nucleus, because these were the only cells containing a nucleus. Bacteria and archaea have no true nucleus. For that reason, they have traditionally been called prokaryotes (meaning prenucleus). But researchers are suggesting we no longer use the term prokaryote because archaea and bacteria are so distant genetically. 5 Figure 1.1 illustrates the history of life on earth. On the scale pictured in the figure, humans seem to have just appeared. Bacteria preceded even the earliest animals by more than 2 billion years. This is a good indication that humans are not likely to— nor should we try to—eliminate bacteria from our environment. They’ve survived and adapted to many catastrophic changes over the course of their geologic history. 6 3  05-10-2024 Life in its present form would not be possible if the earliest life forms had not changed constantly, adapting to their environment and circumstances. Getting from the far left in figure 1.1 to the far right where humans appeared involved billions and billions of tiny changes, starting with the first cell that appeared about a billion years after the planet itself was formed. 7 8 4  05-10-2024 Before there was life, most evidence suggests that Earth was a very different place: hot and anoxic, with an atmosphere rich in water vapor, carbon dioxide, and nitrogen. In the oceans, hydrogen, methane, and carboxylic acids were formed by geological and chemical processes. Areas near hydrothermal vents may have provided the conditions that allowed chemicals to react with one another, randomly testing the usefulness of the reaction and the stability of its products. Some reactions generated molecules that functioned as catalysts, some aggregated with other molecules to form the predecessors ofmodern cell structures, and others were able to replicate and act as units of hereditary information 9 Microbial Life Microorganisms (also called microbes) are life forms too small to be seen by the unaided human eye. These microscopic organisms are diverse in form and function, and they inhabit every environment on Earth that supports life. Many microbes are undifferentiated single-celled organisms, but some can form complex structures, and some are even multicellular. Microorganisms typically live in complex microbial communities (Figure 1.1), and their activities are regulated by interactions with each other, with their environments, and with other organisms. The science of microbiology is all about microorganisms, who they are, how they work, and what they do. Microorganisms 10 5  05-10-2024 11 12 6  05-10-2024 13 Microorganisms were teeming on the land and in the seas for billions of years before the appearance of plants and animals, and their diversity is staggering. Microorganisms represent a major fraction of Earth’s biomass, and their activities are essential to sustaining life. Indeed, the very oxygen (O2) we breathe is the result of microbial activities. Plants and animals are immersed in a world of microbes, and their evolution and survival are heavily influenced by microbial activities, by microbial symbioses, and by pathogens—those microbes that cause disease. 14 7  05-10-2024 15 16 8  05-10-2024 Classification Dr Jitendra 1 The Swedish naturalist Carl von Linné (1707–1778), better known by his Latinized name, Carolus Linnaeus, was the first modern practitioner of taxonomy, the science that identifies, names, and classifies new species. Systematics, the branch of biology that studies the diversity of life and its evolutionary relationships. A systematist is someone who constructs or adheres to a fixed plan or system, particularly in the context of biological classification. Phylogeny Plural Phylogenies is, the evolutionary history of organisms. 2 1  05-10-2024 Binomial nomenclature Binomial nomenclature gives each species a scientific name that has two parts. The first part is the genus name, and the second part is the specific epithet, or specific name, that identifies the species. When identifying and naming a new species, Linnaeus used the morphological species concept, assigning the same scientific name to individuals that shared anatomical characteristics Latin is the basis for binomial nomenclature because Latin is an unchanging language, and, historically, it has been the language of science and education. 3 A combination of the generic name and the specific epithet provides a unique name for every species For example, Ursus maritimus is the polar bear and Ursus arctos is the brown bear. 4 2  05-10-2024 Taxonomic hierarchy Keeping track of so many species was no easy task, so he devised a classification, a conceptual filing system that arranges organisms into ever more inclusive categories. Linnaeus’ classification, called the taxonomic hierarchy, includes a nested series of formal categories: domain, kingdom, phylum, class, order, family, genus, species, and subspecies. 5 The organisms included within any category of the taxonomic hierarchy compose a taxon (plural, taxa). Woodpeckers, for example, are a taxon (Picidae) at the family level, and pine trees are a taxon (Pinus) at the genus level The hierarchy has been a great convenience for biologists because every taxon is defined by a set of shared characteristics. Thus, when a biologist refers to a member of the family Picidae, all of his or her colleagues understand that the biologist is talking about a medium-sized bird that uses its stout bill to drill holes in tree trunks 6 3  05-10-2024 Binomial system rules Biologists use scientific names for species because common names vary in their use. When writing a scientific name, scientists follow certain rules. The first letter of the genus name always is capitalized, but the rest of the genus name and all letters of the specific epithet are lowercase. If a scientific name is written in a printed book or magazine, it should be italicized. When a scientific name is written by hand, both parts of the name should be underlined. After the scientific name has been written completely, the genus name often will be abbreviated to the first letter in later appearances. For example, the scientific name of Cardinalis cardinalis can be written C. cardinalis. 7 Darwin’s concept of branching evolution 8 4  05-10-2024 Systematists Adapted Linnaeus’ Approach to a Darwinian Worldview Linnaeus devised the taxonomic hierarchy long before Darwin published his theory of evolution. The taxonomic hierarchy that Linnaeus defined was easily adapted to Darwin’s concept of branching evolution, which is itself a hierarchical phenomenon Ancestral species give rise to descendant species through repeated branching of a lineage. Organisms in the same genus generally share a fairly recent common ancestor, whereas those assigned to the same higher taxonomic category, such as a class or phylum, share a common ancestor that lived in the more distant past 9 Reconstructing the phylogeny In the second half of the nineteenth century, systematists began to reconstruct the phylogeny (that is, the evolutionary history) of organisms. Phylogenies are illustrated in phylogenetic trees, which are formal hypotheses that identify likely relationships among species and higher taxonomic groups. And like all hypotheses, they are constantly revised as scientists gather new data 10 5  05-10-2024 Modern Classification 11 Characters To classify a species, scientists often construct patterns of descent, or phylogenies, by using characters—inherited features that vary among species. Morphological characters When comparing morphological characters, it is important to remember that analogous characters do not indicate a close evolutionary relationship. 12 6  05-10-2024 Biochemical characters Biochemical characters Scientists use biochemical characters, such as amino acids and nucleotides, to help them determine evolutionary relationships among species. Chromosome structure and number is also a powerful clue for determining species similarities. The greater the number of shared DNA sequences between species, the greater the number of shared genes—and the greater the evidence that the species share a recent common ancestor. 13 14 7  05-10-2024 Cladistics is based on the Darwinian concept of “descent with modification from a common ancestor”—species have some characters in common with their ancestors, but they also differ from them. Thus, systematists focus on two types of characters. 15 Shared ancestral character A shared ancestral character is common to members of a particular clade but originated in an ancestor that is not a member of the clade. For example, all mammals have backbones, but the presence of a backbone does not distinguish mammals from other vertebrates 16 8  05-10-2024 Shared derived character A shared derived character is common to members of a particular clade and is not found in its ancestors— it is an evolutionary novelty unique to that clade. Shared derived characters distinguish clades and thus mark branch points in the tree of life. when considering the relationship between birds and mammals, a backbone is an ancestral character because both birds and mammals have a backbone and so did their shared ancestor. However, birds have feathers and mammals have hair. Therefore, having hair is a derived character for mammals because only mammals have an ancestor with hair. Likewise, having feathers is a derived character for birds. 17 Phylogenetic Reconstruction The most common systems of classification today are based on a method of analysis called cladistics. Cladistics is a method that classifies organisms according to the order that they diverged from a common ancestor. Or we can say In cladistics, organisms are grouped by common ancestry. 18 9  05-10-2024 Cladograms A cladogram is a branching diagram that represents the proposed phylogeny or evolutionary history of a species or group. Sytematists use shared derived characters to make a cladogram. A cladogram is a model similar to the pedigrees ancestral species and all its evolutionary descendants 19 Parts of a cladogram Root A root is the initial common ancestors of all the organisms in a cladogram. A root is the starting point for any given cladogram. Nodes Each node is a hypothetical ancestor that gives rise to two or more daughter taxa. Nodes indicate the bifurcating branch point of divergence in all cladograms. Thus, a node exists in each point where a group of organisms divides or separate into further different groups. 20 10  05-10-2024 Outgroup A taxon or an outgroup is the most distantly related group of animals that isn’t necessarily a clade. This functions as a point of reference or comparison for the rest of the cladogram. Branches A branch in a cladogram is a line that connects all the other parts of the cladogram. The branch length in some cases represents the extent of divergence or the extent of the relationship among different taxa. 21 Clades Clades are groups of organisms or genes that include the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A clade is made up of an ancestor and all its descendants. It includes a particular node and all of its connected branches. cladograms can be generated either based on the morphological characteristics or molecular evidence like DNA, RNA or protein sequencing. 22 11  05-10-2024 23 24 12  05-10-2024 25 26 13  05-10-2024 Cladogenesis An ancestral species undergoes speciation, producing two descendant species, which may each be morphologically distinct from their common ancestor. This pattern of evolution is described as cladogenesis, a process that does increase biodiversity. Cladogenesis is depicted by branching points in a phylogenetic tree. Like the taxonomic hierarchy, phylogenetic trees have a nested structure: younger and smaller clades, Two clades that emerge from the same node are called sister clades 27 Different styles of cladograms There are different styles of cladograms based on the shapes of the branches and the orientation of the branches. 28 14  05-10-2024 29 When converting a phylogenetic tree into a classification, they try to identify only monophyletic taxa or lineages. A monophyletic taxon comprises one clade—an ancestral species and all of its descendants, but no other species 30 15  05-10-2024 A paraphyletic taxon is one that includes an ancestor and some, but not all, of its descendants. For example, people commonly used to define terrestrial dinosaurs and birds as distinct groups. But “terrestrial dinosaurs” was a paraphyletic taxon 31 A polyphyletic taxon is one that includes organisms from different clades, but not their common ancestor. For example, a taxon that included only birds and bats, two clades of vertebrates that are capable of flight, would be considered polyphyletic because it would not include their last common ancestor, which lived many millions of years before birds and bats first appeared. 32 16  05-10-2024 33 34 17  05-10-2024 Molecular clocks The temporal information contained in a macromolecu- lar sequence is called a molecular clock. A molecular clock is a model that is used to compare DNA sequences from two different species to estimate how long the species have been evolving since they diverged from a common ancestor 35 Phylogenetic trees Phylogenetic trees contain more information than simple hierarchical classifi cations do because the trees illustrate which ancestors gave rise to which descendants as well as when those evolutionary events occurred. Each fork between trunks, branches, and twigs on the phylogenetic tree represents an evolutionary event in which one ancestral species gave rise to two descendant species. Over time, descendant species gave rise to their own descendants, producing the great diversity of life 36 18  05-10-2024 Universal tree of life a phylogenetic tree that shows the positions of representatives of all domains of cellular life The “Tree of Life” has been reconstructed from data on the genetics, structure, metabolic processes, and behavior of living organisms as well as data gathered from the fossils of extinct species. It is constantly updated and revised as scientists accumulate new data. The universal tree of life shows that the first living things were microorganisms, and that microbes were the dominant life form for most of the history of life on Earth. 37 38 19  05-10-2024 In many ways, information in a phylogenetic tree parallels the traditional hierarchical classifi cation, because organisms on the same branch share the common ancestor that is represented at the base of their branch. If the base of a branch that includes two species is near the bottom of the tree, biologists would judge the species to be only distant relatives because their ancestries separated very long ago. By contrast, if the base of the branch containing two species is close to the top of the tree, we would describe the species as being close relatives. Major branches on the tree are therefore roughly equivalent to kingdoms and phyla; progressively smaller branches represent classes, orders, families, and genera. Th e twigs represent species or the individual populations they compris 39 Biologists distinguish three domains—Bacteria, Archaea, and Eukarya— each of which is a group of organisms with characteristics that set it apart as a major trunk on the Tree of Life. Species in two of the three domains, Bacteria and Archaea, are described as prokaryotes (pro before; karyon nucleus). Their DNA is suspended inside the cell without being separated from other cellular components. By contrast, the domain Eukarya comprises organisms that are described as eukaryotes (eu typical) because their DNA is enclosed in a nucleus, a separate structure within the cells. The nucleus and other specialized internal compartments of eukaryotic cells are called organelles (“little organs”). 40 20  05-10-2024 41 42 21  05-10-2024 Classification Proposed By Kingdoms Key Features System Did not account for microorganisms. Carolus Plantae Two-Kingdom No distinction between prokaryotes Linnaeus (1735) Animalia and eukaryotes. Plantae Included microorganisms like Ernst Haeckel bacteria, algae, and protozoa. Three-Kingdom Animalia (1866) Protista Lacked clear distinctions. Monera Recognized the difference between Protista prokaryotic and eukaryotic cells. Herbert Four-Kingdom Monera divided into two groups: the Copeland (1956) Plantae eukaryotic protists (protozoa and Animalia algae) and the prokaryotic bacteria. Monera Considered cell structure, mode of Protista nutrition, and reproduction. Robert Whittaker Five-Kingdom Fungi More comprehensive classification. (1969) Plantae Fungi included as another kingdom of eukaryotic microbes Animalia 43 THE FIVE KINGDOM CLASSIFICATION 44 22  05-10-2024 Whittaker started with a three-kingdom system and evolved it into the five-kingdom system in 1969,. Whittaker’s early work focused on biogeochemical cycles and trophic levels. He challenged the traditional plant-animal dichotomy and proposed a more nuanced classification. The five kingdoms are Monera, Protista, Fungi, Plantae, and Animalia. 45 Whitaker proposed that organisms should be broadly divided into kingdoms, based on certain characters like the structure of the cell, mode of nutrition, the source of nutrition, interrelationship, body organization, and reproduction. 46 23  05-10-2024 Bacteria and archaea are in the Kingdom Monera Algae and protozoa are in the Kingdom Protista (organisms in this kingdom are referred to as protists) Fungi are in the Kingdom Fungi Plants are in the Kingdom Plantae Animals are in the Kingdom Animalia 47 24  05-10-2024 Naming Bacteria and Archaea Dr Jitendra 1 Naming Bacteria and Archaea Bacteriologists throughout the world have agreed on a set of rules for naming Bacteria and Archaea. These rules, called the “International Code for the Nomenclature of Bacteria” (1992) state what a scientist must do to describe a new species or other taxon (-a, pl.), which is a unit of classification, such as a species, genus, or family. Each bacterium is placed in a genus and given a species name in the same manner as plants and animals. 2 1  05-10-2024 Naming new species The International Journal of Systematic and Evolutionary Microbiology (IJSEM) is a journal devoted to the taxonomy of bacteria that is published by the British Society for General Microbiology. IJSEM publishes papers that describe and name new bacterial taxa and contains an updated listing of all new bacteria whose names have been validly published. Thus, even though bacterial species may be described in other scientific journals, they are not considered validly published until they have been listed on a validation list in IJSEM 3 Bergey’s Manual of Systematic Bacteriology is a comprehensive reference work that provides detailed information on the classification, identification, and description of bacteria. It is widely used in microbiology for determining the identity of prokaryotic organisms, emphasizing bacterial species Bergey’s Manual of Systematic Bacteriology is now in its second edition. The first edition was based on an artificial classification because too little phylogenetic information was available. However, the second edition is phylogenetic and based on 16S rDNA sequencing, as discussed later. 4 2  05-10-2024 The manual is organized into seven volumes, each covering different groups of bacteria. Volume 1: The Archaea and the deeply branching and phototrophic Bacteria Volume 2: The Proteobacteria Volume 3: The Firmicutes Volume 4: The Bacteroidetes, Spirochaetes, and other related groups Volume 5: The Actinobacteria 5 Volume 1: The Archaea and the deeply branching and phototrophic Bacteria Book © 2001 David R. Boone (Vice Chairman), Richard W. Castenholz, George M. Garrity 6 3  05-10-2024 Bergey's Manual® of Systematic Bacteriology Volume Two: The Proteobacteria, Part A Introductory Essays 7 Bergey's Manual® of Systematic Bacteriology Volume 2: The Proteobacteria, Part B: The Gammaproteobacteria Book © 2005 8 4  05-10-2024 Bergey's Manual® of Systematic Bacteriology Volume Two: The Proteobacteria (Part C) Book © 2005 9 Bergey's Manual of Systematic Bacteriology Volume 3: The Firmicutes Book © 2009 2nd edition 10 5  05-10-2024 Bergey's Manual of Systematic Bacteriology Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes 11 Bergey's Manual of Systematic Bacteriology Volume 5: The Actinobacteria 12 6