Microbial Classification, Nomenclature, and Identification PDF

## MICROBIAL CLASSIFICATION, NOMENCLATURE, AND IDENTIFICATION ### Classification - **Taxonomic Groups (Taxa)** - The process of classification begins once the characteristics of microorganisms have been determined and catalogued. - Taxa are initially constructed from strains. - A strain...

## MICROBIAL CLASSIFICATION, NOMENCLATURE, AND IDENTIFICATION ### Classification - **Taxonomic Groups (Taxa)** - The process of classification begins once the characteristics of microorganisms have been determined and catalogued. - Taxa are initially constructed from strains. - A strain is a group of descendants of a pure culture, usually a succession of cultures from an initial colony. - Each strain has a specific history and designation, for example: strain ATCC 19554 is a strain of spirilla isolated from pond water in Blacksburg, Virginia in 1965 by Wells and Krieg. - Cultures of this strain are maintained at the American Type Culture Collection (ATCC). - Cultures of the same species isolated from other sources would be considered different strains. - The basic taxonomic group (taxon) is the species. - A species is a collection of strains having similar characteristics. - Bacterial species consist of a special strain called the type strain together with all other strains considered sufficiently similar to the type strain. - The type strain is the designated permanent reference specimen for the species. - It is not always the most typical strain of the species, but the strain to which all other strains must be compared. - Type strains are important and maintained by national reference collections, such as the ATCC in the United States and the National Collection of Type Cultures in England. - These collections ensure the maintenance and preservation of type strains throughout the world. ### Intuitive Method - A microbiologist familiar with the organisms they are studying can subjectively decide that the organisms represent one or more species or genera. - The characteristics of an organism that seem important to one person may not be important to another. - The resulting groupings may differ between taxonomists. - The Intuitive Method can be useful. ### Numerical Taxonomy - This method involves finding many characteristics for each strain studied, giving equal weight to each characteristic. - A computer is used to calculate the % similarity (%S) of each strain to every other strain. - %S = NS / NS + ND. - NS is the number of characteristics that are the same (positive or negative) for the two strains. - ND is the number of characteristics that are different. - The % similarity is often made more rigorous by making NS equal to the number of positive characteristics that are the same for the two strains, as what organisms can do may be more important than what they cannot do. - Strains with high %S to each other are placed into groups. - Groups with high %S are in turn placed into larger groups, and so on. - The degree of similarity needed to rank a group as a species, genus, or other taxon is subjective. - Numerical Taxonomy yields stable classifications, is relatively unbiased, and has practical usefulness. - Genetic Relatedness is the third and most reliable method of classification, which is based on the degree of genetic relatedness between organisms. - It is the most objective method and based on the most fundamental aspect of organisms, their hereditary material (DNA). - In the 1960s, molecular biology provided techniques to compare the DNA of one organism to that of other organisms. - Early comparisons were based on mol% G + C values. - It is true that two organisms of the same or similar species that are very closely related will have very similar mol% G + C values, and that two organisms having quite different mol% G + C values are not very closely related. - However, organisms that are completely unrelated may have similar mol% G + C values. - More precise methods are needed to compare DNA molecules with respect to the sequence of their component nucleotides. - This sequence is the most fundamental characteristic of an organism. - Modern techniques make such comparisons possible. - There are two basic principles involved in DNA Homology Experiments: - The double-stranded DNA molecules from two organisms are heated to convert them into single strands. - The single strands are then mixed to allow them to cool. - If the two organisms are closely related, heteroduplexes will form. - If the organisms are not closely related, no heteroduplexes will form. ### Ribosomal RNA Homology Experiments and Ribosomal RNA Oligonucleotide Cataloging - Two organisms may not be closely related enough to give a high level of DNA homology, but still may have some degree of relatedness. - Ribosomes are the small granular-appearing structures within the cell containing proteins and RNA. - The ribosomal RNA (rRNA) is coded for by a small fraction of the DNA molecule (rRNA cistrons). - In all bacteria studied, the nucleotide sequence of these rRNA genes has been found to be highly conserved. - During evolution, the nucleotide sequence has changed more slowly than the bulk of the DNA molecule. - Even two distantly related organisms that show no significant DNA homology may have considerable similarity in the nucleotide sequences of their rRNA cistrons. - The degree of similarity in the nucleotide sequences can be used as a measure of relatedness between organisms. - These experiments can be used at a level beyond that of species, at the level of genus, family, order, etc. - RNA homology experiments and oligonucleotide cataloging are complex techniques, but are used to determine the degree of similarity between the rRNA cistrons of different organisms. - Classifications based on genetic relatedness come the closest to achieving the taxonomic goals of stability and predictability. - More importantly, these classifications allow microbiologists to infer the way in which bacteria have evolved. - This allows the present bacterial genera and species to be arranged in a hierarchy that reflects their ancestral relationships. - The work is still fragmentary, but has revolutionized current thinking about how bacteria have evolved and how they are related. - Bacteria and archaea are now considered two very large groups that evolved along two very different major routes from an early ancestral form. - There is the suggestion to consider them separate kingdoms of life, or even two separate kingdoms of eucaryotic organisms. ## Nomenclature - Each species of microorganism has only one officially accepted name. - This provides for precise communication. - If an organism is called one name in one country and another name in another country, it is difficult to know that the organism is the same. - The name is a convenient label and not necessarily descriptive. - It is important to understand that names are merely convenient designations. - There are rules for naming organisms. - Bacteria are named according to the International Code of Nomenclature of Bacteria. - Other codes are used to govern naming of algae, fungi, and viruses. - The International Code of Nomenclature is based on the International Codes of Zoological and Botanical Nomenclature, incorporating certain common principles, and is used to: - designate each distinct organism as a species. - designate each species with a Latin binomial to provide a characteristic international label. - establish regulations for the application of names. - ensure the use of the oldest available legitimate name. - designate categories for the classification of organisms. - establish requirements for the publication of new specific names. - provide guidance when coining new names. - An organism must be classified before it can be identified. - This includes the recognition that the organism is a new organism. - Once an organism is classified, characteristics are chosen for identification. - These characteristics should occur only in that organism. - They should also be easy to determine. - Characteristics include shape, staining reactions, and sugar fermentations. - DNA homology experiments are useful for classification, but not routine identification. - Keys and tables are used to help with identification and contain characteristics arranged in a logical fashion. - Keys contain fewer characteristics than tables, contain the information in an easy-to-read, summarized form, and aid in identification. ## The Past and Present State of Bacterial Taxonomy - The first classification scheme for bacteria was published in 1773, with many more appearing since. - The early schemes were based on morphological characteristics, but other kinds of characteristics became increasingly important as microbiology developed. - Each classification scheme reflected the level of knowledge available at the time, and this continues to be true. - Even present arrangements of bacteria are only provisional, subject to modification or replacement as new information appears. - Many classification schemes presently exist, but most cover only one or a few groups of bacteria. - Bergey's Manual of Determinative Bacteriology is a unique classification scheme, due to its broad scope and wide acceptance. - It provides descriptions of all established genera and species, practical arrangements, and appropriate keys and tables. - Eight editions of Bergey's Manual have appeared since 1923, with a new edition currently in preparation. - The title has been changed to “Bergey's Manual of Systematic Bacteriology” to reflect the increased coverage of bacterial characterization, classification, and taxonomic problems in addition to identification aspects. - Bergey's Manual is written by hundreds of authors from around the world, each an authority on a particular bacterial group. - The arrangement of bacterial taxa is mainly along practical lines, divided into a number of sections, each bearing a vernacular name. - The emphasis is on genera and species, as there is no attempt to adhere real relationships that exist among bacteria. - There is an incomplete and fragmentary understanding. - The present classification scheme has practical value but the editorial board considers it an interim arrangement. - Bergey's Manual is expected to provide a general, comprehensive classification scheme based on genetic relatedness. - This will provide stability and predictability, improved identification schemes, and aid in understanding the origin of present-day genera and species. ## The Study of Phylogenetic Relationships - Taxonomy is the placement of organisms into categories (taxa). - This indicates degrees of similarities among organisms. - These similarities are due to relatedness. - All organisms are related through evolution. - Systematics or phylogeny is the study of the evolutionary history of organisms. - The hierarchy of taxa reflects their evolutionary or phylogenetic relationships. - The way humans have classified organisms has changed greatly over the centuries. - From Aristotle, living organisms were categorized as plant or animal, as this classification was expanded upon in the formal system of classification using two kingdoms: Plantae and Animalia. - This two-kingdom classification was replaced in the 1800s, with the proposal to include bacteria and fungi in the plant kingdom. - Ernst Haeckel also proposed the Kingdom Protista to include bacteria, protozoa, algae, and fungi. - Biologists followed von Nägeli's classification, which was ironic given that DNA sequencing later showed fungi are closer to animals than plants. - The term “prokaryote” was introduced to distinguish cells having no nucleus from nucleated cells of plants and animals. - In 1968, prokaryote was placed in the Kingdom Prokaryotae. - Robert Whittaker proposed the five-kingdom system, placing prokaryotes in the Kingdom Prokaryotae, or Monera, and the other four kingdoms: Animalia, Plantae, Fungi, and Protista. - The Prokaryotae kingdom was based on microscopic observations. - Molecular advances in biology revealed that there are actually two types of prokaryotic cells and one type of eukaryotic cell. - The discovery of three cell types was based on the observations of differences in ribosomes between cells. - Ribosomes are present in all cells. - Comparing the sequences of nucleotides in ribosomal RNA shows three distinct cell groups: eukaryotes and two different types of prokaryotes (bacteria and archaea). - Carl Woese proposed elevating these three cell types to a level above kingdom, called domain. - He believed that archaea and bacteria, although similar in appearance, should form separate domains on the evolutionary tree. - Archaea and bacteria also differ in membrane lipid structure, transfer RNA molecules, and sensitivity to antibiotics. - The widely accepted scheme places animals, plants, and fungi into the Domain Eukarya, bacteria into the Domain Bacteria, and archaea into the Domain Archaea. - Eukarya includes all pathogenic prokaryotes. - Archaea includes prokaryotes that do not have peptidoglycan in their cell walls and often live in extreme environments. - The three major groups in Archaea include methanogens, extreme halophiles, and hyperthermophiles. - The evolutionary relationship of the three domains is the subject of current research. - Based on rRNA analysis, three lineages clearly emerged as cells were forming 3.5 billion years ago. - These were eventually became the Archaea, the Bacteria, and what eventually became the nucleoplasm of the eukaryotes. - Although these three cell lines were not isolated from each other, horizontal gene transfer appears to have occurred among them. - Analysis of complete genomes shows that each domain shares genes with other domains: one-quarter of the genes of the bacterium Thermotoga were probably acquired from an archaeon. - Gene transfer also has been seen between eukaryotic hosts and their prokaryotic symbionts. - The oldest known fossils are the remains of prokaryotes that lived more than 3.5 billion years ago. - Eukaryotic cells evolved more recently, about 2.5 billion years ago. - According to endosymbiotic theory, eukaryotic cells evolved from prokaryotic cells living inside one another as endosymbionts. - The similarities between prokaryotic cells and eukaryotic organelles provide striking evidence. ## Classification of Organisms - Organisms are grouped according to similar characteristics, and each organism is assigned a unique scientific name. - Scientific nomenclature is the rules for classifying and naming used by biologists worldwide. - Common names are often used, but different organisms may have the same common name. - Common names can be misleading and are in different languages. - The system of scientific names was developed to solve the problem and uses two names or a binomial: - genus name: a noun. - specific epithet (species): an adjective. - Both are printed underlined or italicized. - The genus name is capitalized, species name is lower case. - This is called binomial nomenclature. - Binomials are used by scientists worldwide. - The taxonomic classification scheme is based on rRNA nucleotide sequences: - The classification is found in Bergey's Manual of Systematic Bacteriology, 2nd edition, and divided into two domains: Bacteria and Archaea. - Each domain is divided into phyla. - A prokaryotic species may be defined differently from eukaryotic species, which is a group of organisms that can interbreed. - Unlike reproduction in eukaryotic organisms, cell division in bacteria does not directly depend on sexual conjugation. - A prokaryotic species is defined as a population of cells with similar characteristics. - Members of a bacterial species are nearly indistinguishable. - A culture is bacteria grown in media. - A pure culture is often a clone. - All cells in a clone are identical, but some pure cultures of the same species are not identical in all ways. - A strain is a group of cells that are not identical in all ways. ## Methods of Classifying and Identifying Microorganisms - **Classification** is the process of grouping organisms. - **Identification** is the process of determining the name of an organism. - Bergey's Manual of Systematic Bacteriology provides a classification scheme and a reference for identifying bacteria in the laboratory. - The characteristics used to identify and classify bacteria are discussed in Chapter 11. ## Classification in the Domain Eukarya - The five kingdoms, Protista, Fungi, Plantae, Animalia, and Archaea, are included in the Domain Eukarya but most are unicellular. - The protists were historically grouped as organisms that didn't fit into the other kingdoms. - There are approximately 200,000 species of protists found so far. - Protists range in nutrition from photosynthetic to obligate intracellular parasite. - Ribosomal RNA sequencing is making it possible to divide protists based on their descent from common ancestors. - Clades, or genetically related groups, are often used to classify protists. - The Kingdom Fungi includes the unicellular yeasts, multicellular molds, and macroscopic species such as mushrooms. - A fungus absorbs dissolved organic matter through its plasma membrane to obtain raw materials for its functions. - A fungus will develop from spores or from fragments of hyphae. - The Kingdom Plantae (plants) includes mosses, ferns, conifers, and flowering plants. - All members are multicellular, obtain energy through photosynthesis, and convert carbon dioxide and water into organic molecules that are used by the cells. - The Kingdom Animalia includes sponges, worms, insects, animals with backbones (vertebrates), and obtain nutrients and energy by ingesting organic matter through a mouth. - Viruses are not classified as part of any of the three domains. - They are not composed of cells and use the anabolic machinery within living host cells to multiply. - A viral genome can direct biosynthesis inside a host cell, and some viral genomes can be incorporated into the host genome. - The ecological niche of a virus is its specific host cell. ## Methods of Classifying and Identifying Microorganisms - **Classification** is the process of grouping organisms. - **Identification** is the process of determining the name of an organism. - A classification scheme provides a list of characteristics to aid in the identification of an organism. - Microorganisms are identified for practical purposes, for example, to determine the cause of a disease. - The same techniques that classify microorganisms are not necessarily the same techniques that are used to identify them. - Most identification procedures are easily performed in a laboratory. - For example, Protozoa, parasitic worms, and fungi can usually be identified microscopically. - Most prokaryotic organisms don't have distinguishing morphological features or variation in size and shape. - Bergey's Manual of Determinative Bacteriology provides a widely used reference since the first edition published in 1923. - Bergey's Manual does not classify bacteria according to evolutionary relatedness, but provides identification schemes based - These schemes use criteria such as cell wall composition, morphology, differential staining, oxygen requirements, and biochemical testing. - Medical microbiology, which deals with human pathogens, dominates the interest in microbes. - The Approved Lists of Bacterial Names lists more than 11,500 species, with fewer than 5% being human pathogens. - Several criteria and methods are used to classify and identify microorganisms. - These include the organism itself, the source, and the habitat of a bacterial isolate. - Clinical microbiology involves swabs or a tissue surface from a patient, with these swabs being inserted into transport medium to prolong viability. - Transport media are not usually nutritive and designed to protect pathogens. ## Morphological Characteristics - Morphological (structural) characteristics have been used to classify organisms for 200 years, being generally more useful for higher organisms. - Microorganisms are often too similar to be classified by their structures alone. - Literally hundreds of bacterial species are small rods or small cocci. - Larger size and the presence of intracellular structures do not make classification easy. - For example, Pneumocystis (noo-mō-SIS-tis) pneumonia is the most common opportunistic infection in AIDS and immunocompromised patients. - The causative agent of this infection, P. jirovecii (ye-rō-VET-zē-ē) [formerly “P. carinii" (kar-I-nē-ē)] was rarely seen in humans before the AIDS epidemic. - P. jirovecii lacks structures that can be easily used for identification, and its taxonomic position has been uncertain since its discovery in 1909. - P. jirovecii was originally classified as a protozoan, but in 1988 rRNA sequencing showed that Pneumocystis is actually a member of the Kingdom Fungi. - Cell morphology provides limited help with phylogenetic relationships. - Although cell morphology is useful in identifying bacteria, such as differences in endospores or flagella. ## Differential Staining - Differential staining is one of the first steps in identifying bacteria (see Chapter 3). - Most bacteria are either gram-positive or gram-negative. - Other differential stains, such as the acid-fast stain, are useful for a more limited group of microorganisms. - These stains are based on the chemical composition of cell walls. - Therefore, these stains are not useful in identifying either the wall-less bacteria or the archaea with unusual walls. - Microscopic examination of a Gram stain or an acid-fast stain is used to obtain information quickly from clinical environments. ## Biochemical Tests - Enzymatic activities are widely used for bacterial differentiation. - Even closely related bacteria can be separated into distinct species. - Biochemical tests are used to identify bacteria in humans and marine mammals. - These tests can also provide insight into a species’ niche in the ecosystem. For example, a bacterium that can fix nitrogen gas or oxidize elemental sulfur will provide important nutrients for plants and animals. - Enterobacteriaceae are a large heterogeneous group of Gram-negative bacteria. - The natural habitat of this group of bacteria in the intestinal tract of humans and other animals. - They contain several pathogens that cause diarrheal illness. - Tests have been developed to quickly identify pathogens. - All members of the family Enterobacteriaceae are oxidase-negative. - The oxidase-negative Enterobacteriaceae group includes the genera: Escherichia, Enterobacter, Shigella, Citrobacter, and Salmonella. - The genera Escherichia, Enterobacter, and Citrobacter ferment lactose to produce acid and gas. These can be distinguished from Salmonella and Shigella, which do not. - Biochemical testing can be used to differentiate among genera. - The time needed to identify bacteria can be reduced by the use of selective and differential media or by rapid identification methods. - Selective media contain ingredients that suppress the growth of competing organisms and encourage the growth of desired ones. - Differential media allow the desired organism to form a colony that is distinctive. ## The Taxonomic Hierarchy - All organisms are grouped into a series of subdivisions that make up the taxonomic hierarchy. - This hierarchy was developed by Linnaeus for classification of plants and animals. - A eukaryotic species is a group of closely related organisms that breed among themselves. - A genus consists of species that differ from each other in certain ways, but are related by descent. - For example, “Quercus” (KWER-kus) consists of all types of oak trees. - All species of oak differ from each other, but are all related genetically. - Related genera make up a family. - A group of similar families constitutes an order. - A group of similar orders makes up a class. - Related classes make up a phylum. - All phyla that are related to each other make up a kingdom. - Related kingdoms are grouped into a domain. ## Classification of Prokaryotes - The taxonomic classification scheme for prokaryotes can be found in Bergey’s Manual of Systematic Bacteriology, 2nd edition (see Appendix F). - Prokaryotes are divided into two domains: Bacteria and Archaea. - Each domain is divided into phyla. - The classification is based on similarities in rRNA nucleotide sequences. - Classes are divided into orders. - Orders are divided into families. - Families are divided into genera. - Genera are divided into species. - A prokaryotic species is defined differently from a eukaryotic species, which is a group of closely related organisms that can interbreed. - Unlike reproduction in eukaryotic organisms, bacterial cell division does not depend on sexual conjugation. - A prokaryotic species is simply defined as a population of cells with similar characteristics. - Members of a bacterial species are nearly indistinguishable from each other. - Bacteria grown in media are called a culture. - A pure culture is a clone, which is a population of cells from a single-parent cell. - All cells in a clone should be identical, but in some cases, pure cultures of the same species are not identical in all ways. - Each such group is called a strain. - Strains are identified by numbers, letters, or names that follow the specific epithet. - Bergey's Manual provides a reference for identifying bacteria in the laboratory and a classification scheme for bacteria. - Characteristics used to classify and identify bacteria are discussed in Chapter 11. ## Classification of Eukaryotes - Some kingdoms in the Domain Eukarya are shown in Figure 10.1, including Protista, Fungi, Plantae, and Animalia. - Protista is the catchall group for mostly unicellular eukaryotic organisms. - These organisms did not fit into the other kingdoms. - Approximately 200,000 species of protists have been identified thus far, and these organisms are nutritionally quite diverse. - Ribosomal RNA sequencing is being used to divide protists based on their descent from common ancestors. - The organisms once classified as protists are now being divided into clades. - The term “protist” is used to refer to unicellular eukaryotes and their close relatives. - The Kingdom Fungi includes the unicellular yeasts, multicellular molds, and macroscopic species such as mushrooms. - A fungus absorbs dissolved organic matter through its plasma membrane. - The cells of a multicellular fungus are joined together to form tubes called hyphae. - Fungi develop from spores or from fragments of hyphae. - The Kingdom Plantae (plants) includes mosses, ferns, conifers, and flowering plants. - Plants use photosynthesis to acquire energy. - The cells of multicellular plants convert carbon dioxide and water into organic molecules. - The Kingdom Animalia includes sponges, worms, insects, animals with backbones (vertebrates), and obtain nutrients and energy by ingesting organic matter through a mouth. - Viruses are not classified as part of any of the three domains. - They are not composed of cells and use the anabolic machinery within living host cells to multiply. - A viral genome can direct biosynthesis inside a host cell and some viral genomes can be incorporated into the host genome. - The ecological niche of a virus is its specific host cell. ## Methods of Classifying and Identifying Microorganisms - Classification is the process of grouping organisms. - Identification is the process of determining the name of an organism. - A classification scheme provides a list of characteristics to aid in the identification of an organism. - Microorganisms are identified for practical purposes, for example, to determine the cause of a disease. - The same techniques that classify microorganisms are not necessarily the same techniques that identify them. - Most identification procedures are easily performed in a laboratory. - For example, Protozoa, parasitic worms, and fungi can usually be identified microscopically. - Most prokaryotic organisms don’t have distinguishing morphological features or variation in size and shape. - Bergey's Manual of Determinative Bacteriology provides a widely used reference, being first published in 1923. - Bergey's Manual does not classify bacteria according to evolutionary relatedness, but provides identification schemes based on criteria such as cell wall composition, morphology, differential staining, oxygen requirements, and biochemical testing. - Medical microbiology, which deals with human pathogens, dominates the interest in microbes. - The Approved Lists of Bacterial Names lists more than 11,500 species, with fewer than 5% being human pathogens. - Several criteria and methods are used to classify and identify microorganisms. - These include the organism itself, the source, and the habitat of a bacterial isolate. - Clinical microbiology involves swabs or a tissue surface from a patient, with these swabs being inserted into transport medium to prolong viability. - Transport media are not usually nutritive and designed to protect pathogens. ## Morphological Characteristics - Morphological (structural) characteristics have been used to classify organisms for 200 years, being generally more useful for higher organisms. - Microorganisms are often too similar to be classified by their structures alone. - Literally hundreds of bacterial species are small rods or small cocci. - Larger size and the presence of intracellular structures do not make classification easy. - For example, Pneumocystis (noo-mō-SIS-tis) pneumonia is the most common opportunistic infection in AIDS and immunocompromised patients. - The causative agent of this infection, P. jirovecii (ye-rō-VET-zē-ē) [formerly “P. carinii" (kar-I-nē-ē)] was rarely seen in humans before the AIDS epidemic. - P. jirovecii lacks structures that can be easily used for identification, and its taxonomic position has been uncertain since its discovery in 1909. - P. jirovecii was originally classified as a protozoan, but in 1988 rRNA sequencing showed that Pneumocystis is actually a member of the Kingdom Fungi. - Cell morphology provides limited help with phylogenetic relationships. - Although cell morphology is useful in identifying bacteria, such as differences in endospores or flagella. ## Differential Staining - Differential staining is one of the first steps in identifying bacteria (see Chapter 3). - Most bacteria are either gram-positive or gram-negative. - Other differential stains, such as the acid-fast stain, are useful for a more limited group of microorganisms. - These stains are based on the chemical composition of cell walls. - Therefore, these stains are not useful in identifying either the wall-less bacteria or the archaea with unusual walls. - Microscopic examination of a Gram stain or an acid-fast stain is used to obtain information quickly from clinical environments. ## Biochemical Tests - Enzymatic activities are widely used for bacterial differentiation. - Even closely related bacteria can be separated into distinct species. - Biochemical tests are used to identify bacteria in humans and marine mammals. - These tests can also provide insight into a species’ niche in the ecosystem. For example, a bacterium that can fix nitrogen gas or oxidize elemental sulfur will provide important nutrients for plants and animals. - Enterobacteriaceae are a large heterogeneous group of Gram-negative bacteria. - The natural habitat of this group of bacteria in the intestinal tract of humans and other animals. - They contain several pathogens that cause diarrheal illness. - Tests have been developed to quickly identify pathogens. - All members of the family Enterobacteriaceae are oxidase-negative. - The oxidase-negative Enterobacteriaceae group includes the genera: Escherichia, Enterobacter, Shigella, Citrobacter, and Salmonella. - The genera Escherichia, Enterobacter, and Citrobacter ferment lactose to produce acid and gas. These can be distinguished from Salmonella and Shigella, which do not. - Biochemical testing can be used to differentiate among genera. - The time needed to identify bacteria can be reduced by the use of selective and differential media or by rapid identification methods. - Selective media contain ingredients that suppress the growth of competing organisms and encourage the growth of desired ones. - Differential media allow the desired organism to form a colony that is distinctive. ## The Taxonomic Hierarchy - All organisms are grouped into a series of subdivisions that make up the taxonomic hierarchy. - This hierarchy was developed by Linnaeus for classification of plants and animals. - A eukaryotic species is a group of closely related organisms that breed among themselves. - A genus consists of species that differ from each other in certain ways, but are related by descent. - For example, “Quercus” (KWER-kus) consists of all types of oak trees. - All species of oak differ from each other, but are all related genetically. - Related genera make up a family. - A group of similar families constitutes an order. - A group of similar orders makes up a class. - Related classes make up a phylum. - All phyla that are related to each other make up a kingdom. - Related kingdoms are grouped into a domain. ## Classification of Prokaryotes - The taxonomic classification scheme for prokaryotes can be found in Bergey’s Manual of Systematic Bacteriology, 2nd edition (see Appendix F). - Prokaryotes are divided into two domains: Bacteria and Archaea. - Each domain is divided into phyla. - The classification is based on similarities in rRNA nucleotide sequences. - Classes are divided into orders. - Orders are divided into families. - Families are divided into genera. - Genera are divided into species. - A prokaryotic species is defined differently from a eukaryotic species, which is a group of organisms that can interbreed. - Unlike reproduction in eukaryotic organisms, bacterial cell division does not depend on sexual conjugation. - A prokaryotic species is simply defined as a population of cells with similar characteristics. - Members of a bacterial species are nearly indistinguishable from each other. - Bacteria grown in media are called a culture. - A pure culture is a clone, which is a population of cells from a single-parent cell. - All cells in a clone should be identical, but in some cases, pure cultures of the same species are not identical in all ways. - Each such group is called a strain. - Strains are identified by numbers, letters, or names that follow the specific epithet. - Bergey's Manual provides a reference for identifying bacteria in the laboratory and a classification scheme for bacteria. - Characteristics used to classify and identify bacteria are discussed in Chapter 11. ## Classification of Eukaryotes - Some kingdoms in the Domain Eukarya are shown in Figure 10.1, including Protista, Fungi, Plantae, and Animalia. - Protista is the catchall group for mostly unicellular eukaryotic organisms. - These organisms did not fit into the other kingdoms. - Approximately 200,000 species of protists have been identified thus far, and these organisms are nutritionally quite diverse. - Ribosomal RNA sequencing is being used to divide protists based on their descent from common ancestors. - The organisms once classified as protists are now being divided into clades. - The term “protist” is used to refer to unicellular eukaryotes and their close relatives. - The Kingdom Fungi includes the unicellular yeasts, multicellular molds, and macroscopic species such as mushrooms. - A fungus absorbs dissolved organic matter through its plasma membrane. - The cells of a multicellular fungus are joined together to form tubes called hyphae. - Fungi develop from spores or from fragments of hyphae. - The Kingdom Plantae (plants) includes mosses, ferns, conifers, and flowering plants. - Plants use photosynthesis to acquire energy. - The cells of multicellular plants convert carbon dioxide and water into organic molecules. - The Kingdom Animalia includes sponges, worms, insects, animals with backbones (vertebrates), and obtain nutrients and energy by ingesting organic matter through a mouth. - Viruses are not classified as part of any of the three domains. - They are not composed of cells and use the anabolic machinery within living host cells to multiply. - A viral genome can direct biosynthesis inside a host cell and some viral genomes can be incorporated into the host genome. - The ecological niche of a virus is its specific host cell. ## Methods of Classifying and Identifying Microorganisms - Classification is the process of grouping organisms. - Identification is the process of determining the name of an organism. - A classification scheme provides a list of characteristics to aid in the identification of an organism. - Microorganisms are identified for practical purposes, for example, to determine the cause of a disease. - The same techniques that classify microorganisms are not necessarily the same techniques that identify them. - Most identification procedures are easily performed in a laboratory. - For example, Protozoa, parasitic worms, and fungi can usually be identified microscopically. - Most prokaryotic organisms don’t have distinguishing morphological features or variation in size and shape.