{"id":67,"date":"2016-11-04T03:32:35","date_gmt":"2016-11-04T03:32:35","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/microbiology\/?post_type=chapter&#038;p=67"},"modified":"2018-07-11T18:27:44","modified_gmt":"2018-07-11T18:27:44","slug":"a-systematic-approach","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/chapter\/a-systematic-approach\/","title":{"raw":"A Systematic Approach","rendered":"A Systematic Approach"},"content":{"raw":"<div class=\"textbox learning-objectives\">\r\n<h3>Learning Objectives<\/h3>\r\n<ul>\r\n \t<li>Describe how microorganisms are classified and distinguished as unique species<\/li>\r\n \t<li>Compare historical and current systems of taxonomy used to classify microorganisms<\/li>\r\n<\/ul>\r\n<\/div>\r\nOnce microbes became visible to humans with the help of microscopes, scientists began to realize their enormous diversity. Microorganisms vary in all sorts of ways, including their size, their appearance, and their rates of reproduction. To study this incredibly diverse new array of organisms, researchers needed a way to systematically organize them.\r\n<h2>The Science of Taxonomy<\/h2>\r\n[caption id=\"\" align=\"alignright\" width=\"300\"]<img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153429\/OSC_Microbio_01_02_Linnaeus.jpg\" alt=\"A painting of Carolus Linnaeus holding a flower.\" width=\"300\" height=\"419\" \/> Figure\u00a01. Swedish botanist, zoologist, and physician Carolus Linnaeus developed a new system for categorizing plants and animals. In this 1853 portrait by Hendrik Hollander, Linnaeus is holding a twinflower, named Linnaea borealis in his honor.[\/caption]\r\n\r\n<strong>Taxonomy<\/strong> is the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus <strong>Linnaeus<\/strong> (1701\u20131778). In 1735, Linnaeus published <em>Systema Naturae<\/em>, an 11-page booklet in which he proposed the <strong>Linnaean taxonomy<\/strong>, a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. He continued to revise and add to the book, which grew into multiple volumes (Figure\u00a01).\r\n\r\nIn his taxonomy, Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral (the mineral kingdom was later abandoned). Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities. The names of the levels in Linnaeus\u2019s original taxonomy were kingdom, class, order, family, genus (plural: genera), and species. Species was, and continues to be, the most specific and basic taxonomic unit.\r\n<h3>Evolving Trees of Life (Phylogenies)<\/h3>\r\nWith advances in technology, other scientists gradually made refinements to the Linnaean system and eventually created new systems for classifying organisms. In the 1800s, there was a growing interest in developing taxonomies that took into account the evolutionary relationships, or <strong>phylogenies<\/strong>, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams, groups of organisms are arranged by how closely related they are thought to be. In early phylogenetic trees, the relatedness of organisms was inferred by their visible similarities, such as the presence or absence of hair or the number of limbs. Now, the analysis is more complicated. Today, phylogenic analyses include genetic, biochemical, and embryological comparisons, as will be discussed later in this chapter.\r\n\r\nLinnaeus\u2019s tree of life contained just two main branches for all living things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms (Figure\u00a02). He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria.\r\n\r\n[caption id=\"\" align=\"aligncenter\" width=\"901\"]<img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153432\/OSC_Microbio_01_02_Haeckel.jpg\" alt=\"A drawing of a tree. The base of the tree reads: Radix Monera. This branches into three branches labeled Plantae, Protista, and Animalia. Each of these branches branch further; each new branch Is labeled in small text and clusters of branches are identified. For example, clusters of branches in the protista include: Diatomase, flagellate, protoplasta, and spongae.\" width=\"901\" height=\"586\" \/> Figure\u00a02. Ernst Haeckel\u2019s rendering of the tree of life, from his 1866 book <em>General Morphology of Organisms<\/em>, contained three kingdoms: Plantae, Protista, and Animalia. He later added a fourth kingdom, Monera, for unicellular organisms lacking a nucleus.[\/caption]\r\n\r\nNearly 100 years later, in 1969, American ecologist Robert <strong>Whittaker<\/strong> (1920\u20131980) proposed adding another kingdom\u2014Fungi\u2014in his tree of life. Whittaker\u2019s tree also contained a level of categorization above the kingdom level\u2014the empire or superkingdom level\u2014to distinguish between organisms that have membrane-bound nuclei in their cells (<strong>eukaryotes<\/strong>) and those that do not (<strong>prokaryotes<\/strong>). Empire Prokaryota contained just the Kingdom Monera. The Empire Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia. Whittaker\u2019s five-kingdom tree was considered the standard phylogeny for many years.\r\n\r\nFigure\u00a03 shows how the tree of life has changed over time. Note that viruses are not found in any of these trees. That is because they are not made up of cells and thus it is difficult to determine where they would fit into a tree of life.\r\n\r\n[caption id=\"\" align=\"aligncenter\" width=\"1300\"]<img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153435\/OSC_Microbio_01_02_TreesTIME.jpg\" alt=\"This timeline begins with Carolus Linnaeus who developed a new way to categorize plants and animals in 1758. The image above Linnaeus shows a forked line with one branch labeled plants and the other labeled animals. In 1866, Ernst Haeckel wrote General Morphology of Organisms, proposing four kingdoms. The image above Haeckel shows a central line with Monera branching off the bottom, protists branching off next, then plants and finally animals. In 1969 Robert Whittaker proposed adding a fifth kingdom \u2013 fungi \u2013 to the tree of life. The image above Whittaker is the same as the one above Haeckel but includes an additional branch labeled fungi between plants and animals.\" width=\"1300\" height=\"860\" \/> Figure\u00a03. This timeline shows how the shape of the tree of life has changed over the centuries. Even today, the taxonomy of living organisms is continually being reevaluated and refined with advances in technology.[\/caption]\r\n\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Think about It<\/h3>\r\n<ul>\r\n \t<li>Briefly summarize how our evolving understanding of microorganisms has contributed to changes in the way that organisms are classified.<\/li>\r\n<\/ul>\r\nThe Role of Genetics in Modern Taxonomy\r\n\r\n<\/div>\r\nHaeckel\u2019s and Whittaker\u2019s trees presented hypotheses about the phylogeny of different organisms based on readily observable characteristics. But the advent of molecular genetics in the late 20th century revealed other ways to organize phylogenetic trees. Genetic methods allow for a standardized way to compare all living organisms without relying on observable characteristics that can often be subjective. Modern taxonomy relies heavily on comparing the nucleic acids (deoxyribonucleic acid [DNA] or ribonucleic acid [RNA]) or proteins from different organisms. The more similar the nucleic acids and proteins are between two organisms, the more closely related they are considered to be.\r\n\r\nIn the 1970s, American microbiologist Carl Woese discovered what appeared to be a \"living record\" of the evolution of organisms. He and his collaborator George Fox created a genetics-based tree of life based on similarities and differences they observed in the small subunit ribosomal RNA (rRNA) of different organisms. In the process, they discovered that a certain type of bacteria, called archaebacteria (now known simply as archaea), were significantly different from other bacteria and eukaryotes in terms of the sequence of small subunit rRNA. To accommodate this difference, they created a tree with three Domains above the level of Kingdom: Archaea, Bacteria, and Eukarya (Figure\u00a04). Genetic analysis of the small subunit rRNA suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. The tree is skewed to show a closer evolutionary relationship between Archaea and Eukarya than they have to Bacteria.\r\n\r\n[caption id=\"\" align=\"aligncenter\" width=\"901\"]<img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153439\/OSC_Microbio_01_02_Woese.jpg\" alt=\"The phylogenetic Tree of Life. A drawing of branching lines. The central line at the bottom branches into two main branches. On the left branch is the bacterial group. The branch to the right subdivides to the Archaea and Eukarya groups. Additional branches on the Eukarya group from bottom to top are: Diplomonads, Microsporidia, Trichomonads, Flagellates, Entamoebae, Smile molds, Ciliates, Plants, Fungi and Animals (which has a star labeled \" width=\"901\" height=\"594\" \/> Figure\u00a04. Woese and Fox\u2019s phylogenetic tree contains three domains: Bacteria, Archaea, and Eukarya. Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms. (credit: modification of work by Eric Gaba)[\/caption]\r\n\r\nScientists continue to use analysis of RNA, DNA, and proteins to determine how organisms are related. One interesting, and complicating, discovery is that of horizontal gene transfer\u2014when a gene of one species is absorbed into another organism\u2019s genome. Horizontal gene transfer is especially common in microorganisms and can make it difficult to determine how organisms are evolutionarily related. Consequently, some scientists now think in terms of \"webs of life\" rather than \"trees of life.\"\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Think about It<\/h3>\r\n<ul>\r\n \t<li>In modern taxonomy, how do scientists determine how closely two organisms are related?<\/li>\r\n \t<li>Explain why the branches on the \"tree of life\" all originate from a single \"trunk.\"<\/li>\r\n<\/ul>\r\n<\/div>\r\n<h3>Naming Microbes<\/h3>\r\nIn developing his taxonomy, Linnaeus used a system of <strong>binomial nomenclature<\/strong>, a two-word naming system for identifying organisms by genus and species. For example, modern humans are in the genus <em>Homo<\/em> and have the species name <em>sapiens<\/em>, so their scientific name in binomial nomenclature is <em>Homo sapiens<\/em>. In binomial nomenclature, the genus Part\u00a0of the name is always capitalized; it is followed by the species name, which is not capitalized. Both names are italicized.\r\n\r\nTaxonomic names in the 18th through 20th centuries were typically derived from Latin, since that was the common language used by scientists when taxonomic systems were first created. Today, newly discovered organisms can be given names derived from Latin, Greek, or English. Sometimes these names reflect some distinctive trait of the organism; in other cases, microorganisms are named after the scientists who discovered them. The archaeon <em>Haloquadratum walsbyi<\/em> is an example of both of these naming schemes. The genus, <em>Haloquadratum<\/em>, describes the microorganism\u2019s saltwater habitat (<em>halo<\/em> is derived from the Greek word for \"salt\") as well as the arrangement of its square cells, which are arranged in square clusters of four cells (<em>quadratum<\/em> is Latin for \"foursquare\"). The species, <em>walsbyi<\/em>, is named after Anthony Edward Walsby, the microbiologist who discovered <em>Haloquadratum walsbyi<\/em> in in 1980. While it might seem easier to give an organism a common descriptive name\u2014like a red-headed woodpecker\u2014we can imagine how that could become problematic. What happens when another species of woodpecker with red head coloring is discovered? The systematic nomenclature scientists use eliminates this potential problem by assigning each organism a single, unique two-word name that is recognized by scientists all over the world.\r\n\r\nIn this text, we will typically abbreviate an organism\u2019s genus and species after its first mention. The abbreviated form is simply the first initial of the genus, followed by a period and the full name of the species. For example, the bacterium <em>Escherichia coli<\/em> is shortened to <em>E. coli<\/em> in its abbreviated form. You will encounter this same convention in other scientific texts as well.\r\n<h3>Bergey\u2019s Manuals<\/h3>\r\nWhether in a tree or a web, microbes can be difficult to identify and classify. Without easily observable macroscopic features like feathers, feet, or fur, scientists must capture, grow, and devise ways to study their biochemical properties to differentiate and classify microbes. Despite these hurdles, a group of microbiologists created and updated a set of manuals for identifying and classifying microorganisms. First published in 1923 and since updated many times, <em>Bergey\u2019s Manual<\/em> <em>of Determinative Bacteriology<\/em> and <em>Bergey\u2019s Manual of Systematic Bacteriology<\/em> are the standard references for identifying and classifying different prokaryotes. (<a href=\".\/chapter\/taxonomy-of-clinically-relevant-microorganisms\/\" target=\"_blank\" rel=\"noopener\">Taxonomy of Clinically Relevant Microorganisms<\/a>\u00a0is partly based on Bergey\u2019s manuals; it shows how the organisms that appear in this textbook are classified.) Because so many bacteria look identical, methods based on nonvisual characteristics must be used to identify them. For example, biochemical tests can be used to identify chemicals unique to certain species. Likewise, serological tests can be used to identify specific antibodies that will react against the proteins found in certain species. Ultimately, DNA and rRNA sequencing can be used both for identifying a particular bacterial species and for classifying newly discovered species.\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Think about It<\/h3>\r\n<ul>\r\n \t<li>What is binomial nomenclature and why is it a useful tool for naming organisms?<\/li>\r\n \t<li>Explain why a resource like one of Bergey\u2019s manuals would be helpful in identifying a microorganism in a sample.<\/li>\r\n<\/ul>\r\n<\/div>\r\n<div class=\"textbox shaded\">\r\n<h3>Same Name, Different Strain<\/h3>\r\nWithin one species of microorganism, there can be several subtypes called strains. While different strains may be nearly identical genetically, they can have very different attributes. The bacterium <em>Escherichia coli<\/em> is infamous for causing food poisoning and traveler\u2019s diarrhea. However, there are actually many different strains of <em>E. coli<\/em>, and they vary in their ability to cause disease.\r\n\r\nOne pathogenic (disease-causing) <em>E. coli<\/em> strain that you may have heard of is <em>E. coli<\/em> O157:H7. In humans, infection from <em>E. coli<\/em> O157:H7 can cause abdominal cramps and diarrhea. Infection usually originates from contaminated water or food, particularly raw vegetables and undercooked meat. In the 1990s, there were several large outbreaks of <em>E. coli<\/em> O157:H7 thought to have originated in undercooked hamburgers.\r\n\r\nWhile <em>E. coli<\/em> O157:H7 and some other strains have given <em>E. coli<\/em> a bad name, most <em>E. coli<\/em> strains do not cause disease. In fact, some can be helpful. Different strains of <em>E. coli<\/em> found naturally in our gut help us digest our food, provide us with some needed chemicals, and fight against pathogenic microbes.\r\n\r\n<\/div>\r\n<div class=\"textbox\">Learn more about phylogenetic trees by exploring the <a href=\"http:\/\/www.wellcometreeoflife.org\/interactive\/\" target=\"_blank\" rel=\"noopener\">Wellcome Trust\u2019s interactive Tree of Life<\/a>. The website contains information, photos, and animations about many different organisms. Select two organisms to see how they are evolutionarily related.<\/div>\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Key Concepts and Summary<\/h3>\r\n<ul>\r\n \t<li>Carolus Linnaeus developed a taxonomic system for categorizing organisms into related groups.<\/li>\r\n \t<li><strong>Binomial nomenclature<\/strong> assigns organisms Latinized scientific names with a genus and species designation.<\/li>\r\n \t<li>A <strong>phylogenetic tree<\/strong> is a way of showing how different organisms are thought to be related to one another from an evolutionary standpoint.<\/li>\r\n \t<li>The first phylogenetic tree contained kingdoms for plants and animals; Ernst Haeckel proposed adding kingdom for protists.<\/li>\r\n \t<li>Robert Whittaker\u2019s tree contained five kingdoms: Animalia, Plantae, Protista, Fungi, and Monera.<\/li>\r\n \t<li>Carl Woese used small subunit ribosomal RNA to create a phylogenetic tree that groups organisms into three domains based on their genetic similarity.<\/li>\r\n \t<li>Bergey\u2019s manuals of determinative and systemic bacteriology are the standard references for identifying and classifying bacteria, respectively.<\/li>\r\n \t<li>Bacteria can be identified through biochemical tests, DNA\/RNA analysis, and serological testing methods.<\/li>\r\n<\/ul>\r\n<\/div>\r\n<div class=\"textbox exercises\">\r\n<h3>Multiple Choice<\/h3>\r\nWhich of the following was NOT a kingdom in Linnaeus\u2019s taxonomy?\r\n<ol style=\"list-style-type: lower-alpha\">\r\n \t<li>animal<\/li>\r\n \t<li>mineral<\/li>\r\n \t<li>protist<\/li>\r\n \t<li>plant<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"963394\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"963394\"]Answer b. Mineral is\u00a0not\u00a0a kingdom in Linnaeus\u2019s taxonomy.[\/hidden-answer]\r\n\r\nWhich of the following is a correct usage of binomial nomenclature?\r\n<ol style=\"list-style-type: lower-alpha\">\r\n \t<li>Homo Sapiens<\/li>\r\n \t<li><em>homo sapiens<\/em><\/li>\r\n \t<li><em>Homo sapiens<\/em><\/li>\r\n \t<li><em>Homo Sapiens<\/em><\/li>\r\n<\/ol>\r\n[reveal-answer q=\"796243\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"796243\"]Answer c. The correct usage of binomial nomenclature is\u00a0<em>Homo sapiens<\/em>.[\/hidden-answer]\r\n\r\nWhich scientist proposed adding a kingdom for protists?\r\n<ol style=\"list-style-type: lower-alpha\">\r\n \t<li>Carolus Linnaeus<\/li>\r\n \t<li>Carl Woese<\/li>\r\n \t<li>Robert Whittaker<\/li>\r\n \t<li>Ernst Haeckel<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"5111\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"5111\"]Answer d. Ernst Haeckel proposed adding a kingdom for protists.[\/hidden-answer]\r\n\r\nWhich of the following is NOT a domain in Woese and Fox\u2019s phylogenetic tree?\r\n<ol style=\"list-style-type: lower-alpha\">\r\n \t<li>Plantae<\/li>\r\n \t<li>Bacteria<\/li>\r\n \t<li>Archaea<\/li>\r\n \t<li>Eukarya<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"161899\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"161899\"]Answer a. Plantae\u00a0is not\u00a0a domain in Woese and Fox\u2019s phylogenetic tree.[\/hidden-answer]\r\n\r\nWhich of the following is the standard resource for identifying bacteria?\r\n<ol style=\"list-style-type: lower-alpha\">\r\n \t<li><em>Systema Naturae<\/em><\/li>\r\n \t<li>Bergey\u2019s <em>Manual of Determinative Bacteriology<\/em><\/li>\r\n \t<li>Woese and Fox\u2019s phylogenetic tree<\/li>\r\n \t<li>Haeckel\u2019s <em>General Morphology of Organisms<\/em><\/li>\r\n<\/ol>\r\n[reveal-answer q=\"167183\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"167183\"]Answer b. Bergey\u2019s <em>Manual of Determinative Bacteriology\u00a0<\/em>is the standard resource for identifying bacteria.[\/hidden-answer]\r\n\r\n<\/div>\r\n<div class=\"textbox exercises\">\r\n<h3>Fill in the Blank<\/h3>\r\nIn binomial nomenclature, an organism\u2019s scientific name includes its ________ and __________.\r\n\r\n[reveal-answer q=\"251191\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"251191\"]In binomial nomenclature, an organism\u2019s scientific name includes its <strong>genus<\/strong> and <strong>species<\/strong>.[\/hidden-answer]\r\n\r\nWhittaker proposed adding the kingdoms ________ and ________ to his phylogenetic tree.\r\n\r\n[reveal-answer q=\"840748\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"840748\"]Whittaker proposed adding the kingdoms <strong>Protista<\/strong> and <strong>Monera<\/strong> to his phylogenetic tree.[\/hidden-answer]\r\n\r\n__________ are organisms without membrane-bound nuclei.\r\n\r\n[reveal-answer q=\"375328\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"375328\"]<strong>Prokaryotes<\/strong> are organisms without membrane-bound nuclei.[\/hidden-answer]\r\n\r\n______ are microorganisms that are not included in phylogenetic trees because they are acellular.\r\n\r\n[reveal-answer q=\"906191\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"906191\"]<strong>Viruses<\/strong> are microorganisms that are not included in phylogenetic trees because they are acellular.[\/hidden-answer]\r\n\r\n<\/div>\r\n<div class=\"textbox key-takeaways\">\r\n<h3>Think about It<\/h3>\r\n<ol>\r\n \t<li>What is a phylogenetic tree?<\/li>\r\n \t<li>Which of the five kingdoms in Whittaker\u2019s phylogenetic tree are prokaryotic, and which are eukaryotic?<\/li>\r\n \t<li>What molecule did Woese and Fox use to construct their phylogenetic tree?<\/li>\r\n \t<li>Name some techniques that can be used to identify and differentiate species of bacteria.<\/li>\r\n \t<li>Why is using binomial nomenclature more useful than using common names?<\/li>\r\n \t<li>Label the three Domains found on modern phylogenetic trees.<\/li>\r\n<\/ol>\r\n<img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153444\/OSC_Microbio_01_02_TreeArtCon_img.jpg\" alt=\"The phylogenetic Tree of Life. A drawing of branching lines. The central line at the bottom branches into two main branches. On the left branch is a purple branch that contains the following sub-branches: Green filamentous bacteria, Gram positives, Cyanobacteria, Proteobacteria, and Spirocheres. The branch to the right subdivides into a red and a brown branch. The brown branch contains the following sub-branches: Smile molds, Plants, Fungi and Animals. The red branch contains the following sub-branches: Thermoproteus, Methanococcus, Methanobacterium, and Halophiles.\" \/>\r\n\r\n<\/div>","rendered":"<div class=\"textbox learning-objectives\">\n<h3>Learning Objectives<\/h3>\n<ul>\n<li>Describe how microorganisms are classified and distinguished as unique species<\/li>\n<li>Compare historical and current systems of taxonomy used to classify microorganisms<\/li>\n<\/ul>\n<\/div>\n<p>Once microbes became visible to humans with the help of microscopes, scientists began to realize their enormous diversity. Microorganisms vary in all sorts of ways, including their size, their appearance, and their rates of reproduction. To study this incredibly diverse new array of organisms, researchers needed a way to systematically organize them.<\/p>\n<h2>The Science of Taxonomy<\/h2>\n<div style=\"width: 310px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153429\/OSC_Microbio_01_02_Linnaeus.jpg\" alt=\"A painting of Carolus Linnaeus holding a flower.\" width=\"300\" height=\"419\" \/><\/p>\n<p class=\"wp-caption-text\">Figure\u00a01. Swedish botanist, zoologist, and physician Carolus Linnaeus developed a new system for categorizing plants and animals. In this 1853 portrait by Hendrik Hollander, Linnaeus is holding a twinflower, named Linnaea borealis in his honor.<\/p>\n<\/div>\n<p><strong>Taxonomy<\/strong> is the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus <strong>Linnaeus<\/strong> (1701\u20131778). In 1735, Linnaeus published <em>Systema Naturae<\/em>, an 11-page booklet in which he proposed the <strong>Linnaean taxonomy<\/strong>, a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. He continued to revise and add to the book, which grew into multiple volumes (Figure\u00a01).<\/p>\n<p>In his taxonomy, Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral (the mineral kingdom was later abandoned). Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities. The names of the levels in Linnaeus\u2019s original taxonomy were kingdom, class, order, family, genus (plural: genera), and species. Species was, and continues to be, the most specific and basic taxonomic unit.<\/p>\n<h3>Evolving Trees of Life (Phylogenies)<\/h3>\n<p>With advances in technology, other scientists gradually made refinements to the Linnaean system and eventually created new systems for classifying organisms. In the 1800s, there was a growing interest in developing taxonomies that took into account the evolutionary relationships, or <strong>phylogenies<\/strong>, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams, groups of organisms are arranged by how closely related they are thought to be. In early phylogenetic trees, the relatedness of organisms was inferred by their visible similarities, such as the presence or absence of hair or the number of limbs. Now, the analysis is more complicated. Today, phylogenic analyses include genetic, biochemical, and embryological comparisons, as will be discussed later in this chapter.<\/p>\n<p>Linnaeus\u2019s tree of life contained just two main branches for all living things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms (Figure\u00a02). He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria.<\/p>\n<div style=\"width: 911px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153432\/OSC_Microbio_01_02_Haeckel.jpg\" alt=\"A drawing of a tree. The base of the tree reads: Radix Monera. This branches into three branches labeled Plantae, Protista, and Animalia. Each of these branches branch further; each new branch Is labeled in small text and clusters of branches are identified. For example, clusters of branches in the protista include: Diatomase, flagellate, protoplasta, and spongae.\" width=\"901\" height=\"586\" \/><\/p>\n<p class=\"wp-caption-text\">Figure\u00a02. Ernst Haeckel\u2019s rendering of the tree of life, from his 1866 book <em>General Morphology of Organisms<\/em>, contained three kingdoms: Plantae, Protista, and Animalia. He later added a fourth kingdom, Monera, for unicellular organisms lacking a nucleus.<\/p>\n<\/div>\n<p>Nearly 100 years later, in 1969, American ecologist Robert <strong>Whittaker<\/strong> (1920\u20131980) proposed adding another kingdom\u2014Fungi\u2014in his tree of life. Whittaker\u2019s tree also contained a level of categorization above the kingdom level\u2014the empire or superkingdom level\u2014to distinguish between organisms that have membrane-bound nuclei in their cells (<strong>eukaryotes<\/strong>) and those that do not (<strong>prokaryotes<\/strong>). Empire Prokaryota contained just the Kingdom Monera. The Empire Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia. Whittaker\u2019s five-kingdom tree was considered the standard phylogeny for many years.<\/p>\n<p>Figure\u00a03 shows how the tree of life has changed over time. Note that viruses are not found in any of these trees. That is because they are not made up of cells and thus it is difficult to determine where they would fit into a tree of life.<\/p>\n<div style=\"width: 1310px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153435\/OSC_Microbio_01_02_TreesTIME.jpg\" alt=\"This timeline begins with Carolus Linnaeus who developed a new way to categorize plants and animals in 1758. The image above Linnaeus shows a forked line with one branch labeled plants and the other labeled animals. In 1866, Ernst Haeckel wrote General Morphology of Organisms, proposing four kingdoms. The image above Haeckel shows a central line with Monera branching off the bottom, protists branching off next, then plants and finally animals. In 1969 Robert Whittaker proposed adding a fifth kingdom \u2013 fungi \u2013 to the tree of life. The image above Whittaker is the same as the one above Haeckel but includes an additional branch labeled fungi between plants and animals.\" width=\"1300\" height=\"860\" \/><\/p>\n<p class=\"wp-caption-text\">Figure\u00a03. This timeline shows how the shape of the tree of life has changed over the centuries. Even today, the taxonomy of living organisms is continually being reevaluated and refined with advances in technology.<\/p>\n<\/div>\n<div class=\"textbox key-takeaways\">\n<h3>Think about It<\/h3>\n<ul>\n<li>Briefly summarize how our evolving understanding of microorganisms has contributed to changes in the way that organisms are classified.<\/li>\n<\/ul>\n<p>The Role of Genetics in Modern Taxonomy<\/p>\n<\/div>\n<p>Haeckel\u2019s and Whittaker\u2019s trees presented hypotheses about the phylogeny of different organisms based on readily observable characteristics. But the advent of molecular genetics in the late 20th century revealed other ways to organize phylogenetic trees. Genetic methods allow for a standardized way to compare all living organisms without relying on observable characteristics that can often be subjective. Modern taxonomy relies heavily on comparing the nucleic acids (deoxyribonucleic acid [DNA] or ribonucleic acid [RNA]) or proteins from different organisms. The more similar the nucleic acids and proteins are between two organisms, the more closely related they are considered to be.<\/p>\n<p>In the 1970s, American microbiologist Carl Woese discovered what appeared to be a &#8220;living record&#8221; of the evolution of organisms. He and his collaborator George Fox created a genetics-based tree of life based on similarities and differences they observed in the small subunit ribosomal RNA (rRNA) of different organisms. In the process, they discovered that a certain type of bacteria, called archaebacteria (now known simply as archaea), were significantly different from other bacteria and eukaryotes in terms of the sequence of small subunit rRNA. To accommodate this difference, they created a tree with three Domains above the level of Kingdom: Archaea, Bacteria, and Eukarya (Figure\u00a04). Genetic analysis of the small subunit rRNA suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. The tree is skewed to show a closer evolutionary relationship between Archaea and Eukarya than they have to Bacteria.<\/p>\n<div style=\"width: 911px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153439\/OSC_Microbio_01_02_Woese.jpg\" alt=\"The phylogenetic Tree of Life. A drawing of branching lines. The central line at the bottom branches into two main branches. On the left branch is the bacterial group. The branch to the right subdivides to the Archaea and Eukarya groups. Additional branches on the Eukarya group from bottom to top are: Diplomonads, Microsporidia, Trichomonads, Flagellates, Entamoebae, Smile molds, Ciliates, Plants, Fungi and Animals (which has a star labeled\" width=\"901\" height=\"594\" \/><\/p>\n<p class=\"wp-caption-text\">Figure\u00a04. Woese and Fox\u2019s phylogenetic tree contains three domains: Bacteria, Archaea, and Eukarya. Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms. (credit: modification of work by Eric Gaba)<\/p>\n<\/div>\n<p>Scientists continue to use analysis of RNA, DNA, and proteins to determine how organisms are related. One interesting, and complicating, discovery is that of horizontal gene transfer\u2014when a gene of one species is absorbed into another organism\u2019s genome. Horizontal gene transfer is especially common in microorganisms and can make it difficult to determine how organisms are evolutionarily related. Consequently, some scientists now think in terms of &#8220;webs of life&#8221; rather than &#8220;trees of life.&#8221;<\/p>\n<div class=\"textbox key-takeaways\">\n<h3>Think about It<\/h3>\n<ul>\n<li>In modern taxonomy, how do scientists determine how closely two organisms are related?<\/li>\n<li>Explain why the branches on the &#8220;tree of life&#8221; all originate from a single &#8220;trunk.&#8221;<\/li>\n<\/ul>\n<\/div>\n<h3>Naming Microbes<\/h3>\n<p>In developing his taxonomy, Linnaeus used a system of <strong>binomial nomenclature<\/strong>, a two-word naming system for identifying organisms by genus and species. For example, modern humans are in the genus <em>Homo<\/em> and have the species name <em>sapiens<\/em>, so their scientific name in binomial nomenclature is <em>Homo sapiens<\/em>. In binomial nomenclature, the genus Part\u00a0of the name is always capitalized; it is followed by the species name, which is not capitalized. Both names are italicized.<\/p>\n<p>Taxonomic names in the 18th through 20th centuries were typically derived from Latin, since that was the common language used by scientists when taxonomic systems were first created. Today, newly discovered organisms can be given names derived from Latin, Greek, or English. Sometimes these names reflect some distinctive trait of the organism; in other cases, microorganisms are named after the scientists who discovered them. The archaeon <em>Haloquadratum walsbyi<\/em> is an example of both of these naming schemes. The genus, <em>Haloquadratum<\/em>, describes the microorganism\u2019s saltwater habitat (<em>halo<\/em> is derived from the Greek word for &#8220;salt&#8221;) as well as the arrangement of its square cells, which are arranged in square clusters of four cells (<em>quadratum<\/em> is Latin for &#8220;foursquare&#8221;). The species, <em>walsbyi<\/em>, is named after Anthony Edward Walsby, the microbiologist who discovered <em>Haloquadratum walsbyi<\/em> in in 1980. While it might seem easier to give an organism a common descriptive name\u2014like a red-headed woodpecker\u2014we can imagine how that could become problematic. What happens when another species of woodpecker with red head coloring is discovered? The systematic nomenclature scientists use eliminates this potential problem by assigning each organism a single, unique two-word name that is recognized by scientists all over the world.<\/p>\n<p>In this text, we will typically abbreviate an organism\u2019s genus and species after its first mention. The abbreviated form is simply the first initial of the genus, followed by a period and the full name of the species. For example, the bacterium <em>Escherichia coli<\/em> is shortened to <em>E. coli<\/em> in its abbreviated form. You will encounter this same convention in other scientific texts as well.<\/p>\n<h3>Bergey\u2019s Manuals<\/h3>\n<p>Whether in a tree or a web, microbes can be difficult to identify and classify. Without easily observable macroscopic features like feathers, feet, or fur, scientists must capture, grow, and devise ways to study their biochemical properties to differentiate and classify microbes. Despite these hurdles, a group of microbiologists created and updated a set of manuals for identifying and classifying microorganisms. First published in 1923 and since updated many times, <em>Bergey\u2019s Manual<\/em> <em>of Determinative Bacteriology<\/em> and <em>Bergey\u2019s Manual of Systematic Bacteriology<\/em> are the standard references for identifying and classifying different prokaryotes. (<a href=\".\/chapter\/taxonomy-of-clinically-relevant-microorganisms\/\" target=\"_blank\" rel=\"noopener\">Taxonomy of Clinically Relevant Microorganisms<\/a>\u00a0is partly based on Bergey\u2019s manuals; it shows how the organisms that appear in this textbook are classified.) Because so many bacteria look identical, methods based on nonvisual characteristics must be used to identify them. For example, biochemical tests can be used to identify chemicals unique to certain species. Likewise, serological tests can be used to identify specific antibodies that will react against the proteins found in certain species. Ultimately, DNA and rRNA sequencing can be used both for identifying a particular bacterial species and for classifying newly discovered species.<\/p>\n<div class=\"textbox key-takeaways\">\n<h3>Think about It<\/h3>\n<ul>\n<li>What is binomial nomenclature and why is it a useful tool for naming organisms?<\/li>\n<li>Explain why a resource like one of Bergey\u2019s manuals would be helpful in identifying a microorganism in a sample.<\/li>\n<\/ul>\n<\/div>\n<div class=\"textbox shaded\">\n<h3>Same Name, Different Strain<\/h3>\n<p>Within one species of microorganism, there can be several subtypes called strains. While different strains may be nearly identical genetically, they can have very different attributes. The bacterium <em>Escherichia coli<\/em> is infamous for causing food poisoning and traveler\u2019s diarrhea. However, there are actually many different strains of <em>E. coli<\/em>, and they vary in their ability to cause disease.<\/p>\n<p>One pathogenic (disease-causing) <em>E. coli<\/em> strain that you may have heard of is <em>E. coli<\/em> O157:H7. In humans, infection from <em>E. coli<\/em> O157:H7 can cause abdominal cramps and diarrhea. Infection usually originates from contaminated water or food, particularly raw vegetables and undercooked meat. In the 1990s, there were several large outbreaks of <em>E. coli<\/em> O157:H7 thought to have originated in undercooked hamburgers.<\/p>\n<p>While <em>E. coli<\/em> O157:H7 and some other strains have given <em>E. coli<\/em> a bad name, most <em>E. coli<\/em> strains do not cause disease. In fact, some can be helpful. Different strains of <em>E. coli<\/em> found naturally in our gut help us digest our food, provide us with some needed chemicals, and fight against pathogenic microbes.<\/p>\n<\/div>\n<div class=\"textbox\">Learn more about phylogenetic trees by exploring the <a href=\"http:\/\/www.wellcometreeoflife.org\/interactive\/\" target=\"_blank\" rel=\"noopener\">Wellcome Trust\u2019s interactive Tree of Life<\/a>. The website contains information, photos, and animations about many different organisms. Select two organisms to see how they are evolutionarily related.<\/div>\n<div class=\"textbox key-takeaways\">\n<h3>Key Concepts and Summary<\/h3>\n<ul>\n<li>Carolus Linnaeus developed a taxonomic system for categorizing organisms into related groups.<\/li>\n<li><strong>Binomial nomenclature<\/strong> assigns organisms Latinized scientific names with a genus and species designation.<\/li>\n<li>A <strong>phylogenetic tree<\/strong> is a way of showing how different organisms are thought to be related to one another from an evolutionary standpoint.<\/li>\n<li>The first phylogenetic tree contained kingdoms for plants and animals; Ernst Haeckel proposed adding kingdom for protists.<\/li>\n<li>Robert Whittaker\u2019s tree contained five kingdoms: Animalia, Plantae, Protista, Fungi, and Monera.<\/li>\n<li>Carl Woese used small subunit ribosomal RNA to create a phylogenetic tree that groups organisms into three domains based on their genetic similarity.<\/li>\n<li>Bergey\u2019s manuals of determinative and systemic bacteriology are the standard references for identifying and classifying bacteria, respectively.<\/li>\n<li>Bacteria can be identified through biochemical tests, DNA\/RNA analysis, and serological testing methods.<\/li>\n<\/ul>\n<\/div>\n<div class=\"textbox exercises\">\n<h3>Multiple Choice<\/h3>\n<p>Which of the following was NOT a kingdom in Linnaeus\u2019s taxonomy?<\/p>\n<ol style=\"list-style-type: lower-alpha\">\n<li>animal<\/li>\n<li>mineral<\/li>\n<li>protist<\/li>\n<li>plant<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q963394\">Show Answer<\/span><\/p>\n<div id=\"q963394\" class=\"hidden-answer\" style=\"display: none\">Answer b. Mineral is\u00a0not\u00a0a kingdom in Linnaeus\u2019s taxonomy.<\/div>\n<\/div>\n<p>Which of the following is a correct usage of binomial nomenclature?<\/p>\n<ol style=\"list-style-type: lower-alpha\">\n<li>Homo Sapiens<\/li>\n<li><em>homo sapiens<\/em><\/li>\n<li><em>Homo sapiens<\/em><\/li>\n<li><em>Homo Sapiens<\/em><\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q796243\">Show Answer<\/span><\/p>\n<div id=\"q796243\" class=\"hidden-answer\" style=\"display: none\">Answer c. The correct usage of binomial nomenclature is\u00a0<em>Homo sapiens<\/em>.<\/div>\n<\/div>\n<p>Which scientist proposed adding a kingdom for protists?<\/p>\n<ol style=\"list-style-type: lower-alpha\">\n<li>Carolus Linnaeus<\/li>\n<li>Carl Woese<\/li>\n<li>Robert Whittaker<\/li>\n<li>Ernst Haeckel<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q5111\">Show Answer<\/span><\/p>\n<div id=\"q5111\" class=\"hidden-answer\" style=\"display: none\">Answer d. Ernst Haeckel proposed adding a kingdom for protists.<\/div>\n<\/div>\n<p>Which of the following is NOT a domain in Woese and Fox\u2019s phylogenetic tree?<\/p>\n<ol style=\"list-style-type: lower-alpha\">\n<li>Plantae<\/li>\n<li>Bacteria<\/li>\n<li>Archaea<\/li>\n<li>Eukarya<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q161899\">Show Answer<\/span><\/p>\n<div id=\"q161899\" class=\"hidden-answer\" style=\"display: none\">Answer a. Plantae\u00a0is not\u00a0a domain in Woese and Fox\u2019s phylogenetic tree.<\/div>\n<\/div>\n<p>Which of the following is the standard resource for identifying bacteria?<\/p>\n<ol style=\"list-style-type: lower-alpha\">\n<li><em>Systema Naturae<\/em><\/li>\n<li>Bergey\u2019s <em>Manual of Determinative Bacteriology<\/em><\/li>\n<li>Woese and Fox\u2019s phylogenetic tree<\/li>\n<li>Haeckel\u2019s <em>General Morphology of Organisms<\/em><\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q167183\">Show Answer<\/span><\/p>\n<div id=\"q167183\" class=\"hidden-answer\" style=\"display: none\">Answer b. Bergey\u2019s <em>Manual of Determinative Bacteriology\u00a0<\/em>is the standard resource for identifying bacteria.<\/div>\n<\/div>\n<\/div>\n<div class=\"textbox exercises\">\n<h3>Fill in the Blank<\/h3>\n<p>In binomial nomenclature, an organism\u2019s scientific name includes its ________ and __________.<\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q251191\">Show Answer<\/span><\/p>\n<div id=\"q251191\" class=\"hidden-answer\" style=\"display: none\">In binomial nomenclature, an organism\u2019s scientific name includes its <strong>genus<\/strong> and <strong>species<\/strong>.<\/div>\n<\/div>\n<p>Whittaker proposed adding the kingdoms ________ and ________ to his phylogenetic tree.<\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q840748\">Show Answer<\/span><\/p>\n<div id=\"q840748\" class=\"hidden-answer\" style=\"display: none\">Whittaker proposed adding the kingdoms <strong>Protista<\/strong> and <strong>Monera<\/strong> to his phylogenetic tree.<\/div>\n<\/div>\n<p>__________ are organisms without membrane-bound nuclei.<\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q375328\">Show Answer<\/span><\/p>\n<div id=\"q375328\" class=\"hidden-answer\" style=\"display: none\"><strong>Prokaryotes<\/strong> are organisms without membrane-bound nuclei.<\/div>\n<\/div>\n<p>______ are microorganisms that are not included in phylogenetic trees because they are acellular.<\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q906191\">Show Answer<\/span><\/p>\n<div id=\"q906191\" class=\"hidden-answer\" style=\"display: none\"><strong>Viruses<\/strong> are microorganisms that are not included in phylogenetic trees because they are acellular.<\/div>\n<\/div>\n<\/div>\n<div class=\"textbox key-takeaways\">\n<h3>Think about It<\/h3>\n<ol>\n<li>What is a phylogenetic tree?<\/li>\n<li>Which of the five kingdoms in Whittaker\u2019s phylogenetic tree are prokaryotic, and which are eukaryotic?<\/li>\n<li>What molecule did Woese and Fox use to construct their phylogenetic tree?<\/li>\n<li>Name some techniques that can be used to identify and differentiate species of bacteria.<\/li>\n<li>Why is using binomial nomenclature more useful than using common names?<\/li>\n<li>Label the three Domains found on modern phylogenetic trees.<\/li>\n<\/ol>\n<p><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1094\/2016\/11\/03153444\/OSC_Microbio_01_02_TreeArtCon_img.jpg\" alt=\"The phylogenetic Tree of Life. A drawing of branching lines. The central line at the bottom branches into two main branches. On the left branch is a purple branch that contains the following sub-branches: Green filamentous bacteria, Gram positives, Cyanobacteria, Proteobacteria, and Spirocheres. The branch to the right subdivides into a red and a brown branch. The brown branch contains the following sub-branches: Smile molds, Plants, Fungi and Animals. The red branch contains the following sub-branches: Thermoproteus, Methanococcus, Methanobacterium, and Halophiles.\" \/><\/p>\n<\/div>\n\n\t\t\t <section class=\"citations-section\" role=\"contentinfo\">\n\t\t\t <h3>Candela Citations<\/h3>\n\t\t\t\t\t <div>\n\t\t\t\t\t\t <div id=\"citation-list-67\">\n\t\t\t\t\t\t\t <div class=\"licensing\"><div class=\"license-attribution-dropdown-subheading\">CC licensed content, Shared previously<\/div><ul class=\"citation-list\"><li>OpenStax Microbiology. <strong>Provided by<\/strong>: OpenStax CNX. <strong>Located at<\/strong>: <a target=\"_blank\" href=\"http:\/\/cnx.org\/contents\/e42bd376-624b-4c0f-972f-e0c57998e765@4.2\">http:\/\/cnx.org\/contents\/e42bd376-624b-4c0f-972f-e0c57998e765@4.2<\/a>. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY: Attribution<\/a><\/em>. <strong>License Terms<\/strong>: Download for free at http:\/\/cnx.org\/contents\/e42bd376-624b-4c0f-972f-e0c57998e765@4.2<\/li><\/ul><\/div>\n\t\t\t\t\t\t <\/div>\n\t\t\t\t\t <\/div>\n\t\t\t <\/section>","protected":false},"author":17,"menu_order":5,"template":"","meta":{"_candela_citation":"[{\"type\":\"cc\",\"description\":\"OpenStax Microbiology\",\"author\":\"\",\"organization\":\"OpenStax CNX\",\"url\":\"http:\/\/cnx.org\/contents\/e42bd376-624b-4c0f-972f-e0c57998e765@4.2\",\"project\":\"\",\"license\":\"cc-by\",\"license_terms\":\"Download for free at http:\/\/cnx.org\/contents\/e42bd376-624b-4c0f-972f-e0c57998e765@4.2\"}]","CANDELA_OUTCOMES_GUID":"","pb_show_title":"on","pb_short_title":"","pb_subtitle":"","pb_authors":[],"pb_section_license":""},"chapter-type":[],"contributor":[],"license":[],"class_list":["post-67","chapter","type-chapter","status-publish","hentry"],"part":51,"_links":{"self":[{"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/pressbooks\/v2\/chapters\/67","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/wp\/v2\/users\/17"}],"version-history":[{"count":9,"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/pressbooks\/v2\/chapters\/67\/revisions"}],"predecessor-version":[{"id":2134,"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/pressbooks\/v2\/chapters\/67\/revisions\/2134"}],"part":[{"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/pressbooks\/v2\/parts\/51"}],"metadata":[{"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/pressbooks\/v2\/chapters\/67\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/wp\/v2\/media?parent=67"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/pressbooks\/v2\/chapter-type?post=67"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/wp\/v2\/contributor?post=67"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-mcc-microbiology\/wp-json\/wp\/v2\/license?post=67"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}