Important words and concepts from Chapter 9, Black, 1999 (1/26/2004):

by Stephen T. Abedon (abedon.1@osu.edu) for Micro 509 at the Ohio State University

 

 

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Vocabulary words are found below

 

 

(1) Chapter title: An Introduction to Taxonomy: The Bacteria

(2) Taxonomy

(a)                    The science of organismal classification

(b)                    [taxonomy (Google Search)] [taxonomy on the web] [index]

(3) Classification

(a)                    Classification is the assignment of organisms (species) into an organized scheme of naming

(b)                    Ideally these schemes are based on evolutionary relationships (i.e., the more similar the name, the closer the evolutionary relationship)

(c)                    Thus, classification (and therefore the science of taxonomy) is concerned with

(i)                      The establishment of criteria for identifying organisms and assignment to groups (what belongs where)

(ii)                    The arrangement of organisms into groups of organisms (e.g., how large or inclusive groups should be; for example, at what level of diversity should a single species be split into two or more species?)

(iii)                   Consideration of how evolution resulted in the formation of these groups

(d)                    [classification of organisms (Google Search)] [index]

(4) Taxon (pl. taxa)

(a)                    A group or category of related organisms

(b)                    For example, at the lowest level, species is a taxonomic category as is genera and all the way on up to kingdom and domain

(c)                    These groups become increasingly inclusive as they become larger, going from species to kingdom or domain

(d)                    Two key characteristic of taxa are that

(i)                      Members of lower level taxa (e.g., species) are more similar to each other than are members of higher level taxa (e.g., kingdoms or domain)

(ii)                    Members of specific taxa are more similar to each other than any are to members of different specific taxa found at the same hierarchical level (e.g., humans are more similar to apes, i.e., comparison between species, than either is similar to, for example, Escherichia coli)

(iii)                   Thus, once you know that two individuals are members of the same taxon, you can infer certain similarities between the two organisms (e.g., all members of Family Enterobacteriaceae are facultatively anaerobic, Gram-negative rods)

(e)                    Note that taxa are dynamic, changing as our knowledge of organisms and evolutionary relationships change

(f)                     See Figure 9.2, Classification of a human, a dog, wolf, and a bacterium

(g)                    [taxon (Google Search)] [index]

(5) Binomial nomenclature

(a)                    Organisms are named using binomial nomenclature (viruses are exceptions)

(b)                    Binomial nomenclature employs the names of the two lower level taxa, genus and species, to name a species

(c)                    We've been through this, but conventions when using binomial nomenclature include:

(i)                      Genus comes before species (e.g., Escherichia coli)

(ii)                    Genus name is always capitalized (e.g., Escherichia)

(iii)                   Species name is never capitalized (e.g., coli)

(iv)                  Both names are always either italicized or underlined (e.g., Escherichia coli)

(v)                    The genus name may be used alone, but not the species name (i.e., saying or writing "Escherichia," alone is legitimate while saying or writing "coli" is not)

(vi)                  The genus name may be abbreviated but

·        It must be used first without abbreviation

·        If abbreviated it must be used with the species name (no E. all by itself)

·        It must be abbreviated unambiguously

·        If abbreviating as the first letter of the genus is unambiguous, then abbreviating as the first letter is what one does (e.g., Escherichia abbreviated as E. but only if no other genera considered also starts with E)

·        Genus abbreviations are only used in conjunction with the species name (i.e., E. coli)

(d)                    [binomial nomenclature (Google Search)] [index]

(6) Strain

(a)                    When considering microorganism species, a category (not usually considered a taxonomic one) found below the level of species is strain

(b)                    A strain in some ways is equivalent to a breed or a subspecies among plants or animals

(c)                    Two members of the same strain are more similar to each other than either is to an individual that is a member of a different strain, even if all three organisms are members of the same species

(d)                    See Figure 9.2, Classification of a human, a dog, wolf, and a bacterium

(7) Bacterial species

(a)                    "A bacterial species is defined by the similarities found among its members. Properties such as biochemical reactions, chemical composition, cellular structures, genetic characteristics, and immunological features are used in defining a bacterial species. Identifying a species and determining its limits presents the most challenging aspects of biological classification—for any type of organism."

(b)                    A formal means of distinguishing bacterial species is by employing a dichotomous key to guide the selection of tests used to efficiently determine those bacterial properties most relevant to bacterial identification

(8) The five-kingdom system

(a)                    The five-kingdom system was first proposed in 1969 and is showing its age

(b)                    It posits the existence of five kingdoms (kingdom therefore being the highest/most inclusive taxonomic category in this system)

(c)                    The five kingdoms include:

(i)                      Plantae (the plants)

(ii)                    Fungi (the fungi)

(iii)                   Animalia (the animals)

(iv)                  Protista (the unicellular eucaryotes)

(v)                    Monera (the prokaryotes)

(d)                    Below we will walk through the five-kingdom kingdoms in which most microorganisms are found, before proposing alternatives to the five-kingdom system

(e)                    [five-kingdom system (MicroDude)] [index]

(9) Kingdom Monera

(a)                    Your text differentiates Monera into three categories (without assigning a taxonomic category to the distinctions)

(b)                    Included are the eubacteria, the cyanobacteria, and the archaeobacteria

(c)                    As we will see, these distinctions are more phenotypic than they are evolutionary (i.e., a cyanobacteria is a eubacteria, and neither is an archaeobacteria)

(d)                    That is,

(i)                      the eubacteria are our common, every-day bacteria, some of which are disease-causing; also the taxon from which mitochondria originated

(ii)                    the cyanobacteria are photosynthetic eubacteria, the taxon from which chloroplasts originated

(iii)                   the archaeobacteria are distinctive in their adaptation to extreme environments (e.g., very hot, salty, or acidic) though not all archaeobacteria live in extreme environments

(e)                    See Figure 9.6, Some typical monerans

(f)                      [kingdom Monera (Google Search)] [index]

(10) Kingdom Protista

(a)                    Protista, like Monera, consists mostly of unicellular organisms

(b)                    Distinctively, however, the members of kingdom Protista are all eucaryotic while the members of kingdom Monera are all prokaryotic

(c)                    Some members of protista are multicellular, however

(d)                    Kingdom protista represents a grab bag, essentially the place where species are classified when they are not classified as either fungi, animals, or plants (kingdom Protista is a paraphyletic taxon for those of you familiar with the term)

(e)                    Note that most members of protista are additionally more or less aquatic

(f)                      [protists (MicroDude)] [index]

(11) Kingdom Fungi

(a)                    Unlike protists, the eukaryotic fungi are typically non-aquatic species

(b)                    They additionally are nutrient absorbers plus have additional distinctive features

(c)                    There do exist unicellular fungi, which we call yeasts

(d)                    [fungi (MicroDude)] [index]

(12) The three-domain system

(a)                    Less than ten years after the creation of the five-kingdom system of classification, microbiologist Carl Woese was instrumental in establishing a new system of classification which a little over ten years later became the three-domain system

(b)                    This system was basically accepted by microbiologists during the late 1980s, early 1990s and is increasing the system of choice of non-microbiologist biologists

(c)                    It even made the headlines a few years back with the declaration that a "new" form or life had been discovered (a.k.a., archaeobacteria, which had been discovered years previously and had been shown to be a "different" form of cellular life in the late 1970s, but one member of which was DNA sequenced in full in the late 1990s supplying the genesis of the headlines; with a complete sequence we obtained unambiguous confirmation of just how different from bacteria and eucaryotes these beasts truly are) [completely sequenced Archaeal genomes]

(d)                    [universal tree (MicroDude)] [index]

(13) Domain

(a)                    The domain is a taxonomic category that, depending on point of view, is either above the level of kingdom (i.e., includes kingdoms within it) or supercedes the kingdom

(b)                    Regardless of viewpoint, the domain system contains three members

(i)                      Eukaryotes (domain Eukarya)

(ii)                    Eubacteria (domain Bacteria)

(iii)                   Archaebacteria (domain Archaea)

(c)                    A fourth domain or domain-like taxon, called the Urkaryotes, represents eukaryotes prior to their establishment of endosymbioses with eubacteria, i.e., mitochondria

(d)                    See Figure 9.11, A model of the major evolutionary lines of descent proposed after the discovery of archaeobacteria

(e)                    See Figure 9.13, The three-domain system of classification

(f)                     See Table 9.3, Bacteria, archaea, and eukarya compared

(g)                    [universal tree (MicroDude)] [index]

(14) Domain Archaea

(a)                    Domain archaea is only minimally dealt with by your text in the chapters we will cover because

(i)                      these organisms are both less-well characterized than members of domain Bacteria

(ii)                    correlated with reason (i) (i.e., this latter is the reason for the former), the Archaea, unlike the Bacteria, do not cause human disease

(b)                    The Archaea are surprisingly diverse (perhaps not surprisingly, they show diversity on the order of that displayed by members of domain Bacteria)

(c)                    Typically they are distinguished by the environments in which they live as well as by their biochemical attributes

(d)                    For example,

(i)                      Methanogens live in anaerobic environments, breaking down organism molecules and giving rise to methane (i.e., swamp gas and cow farts) [methanogen home page]

(ii)                    Extreme halophiles live in highly saline environments such as inland seas as well as salt-preserved foods [halophilic microorganisms]

(iii)                   Extreme thermoacidophiles live in geothermally heated waters (e.g., hot springs) [thermophilic microorganisms]

(e)                    [domain Archaea (Google Search)] [domain Archaea] [Archaea: links] [introduction to Archaea] [triumph of the Archaea] [extremophiles] [index]

(15) Extremozymes

(a)                    These are the highly heat-stabilized enzymes employed by extremely thermophilic bacteria

(b)                    Such enzymes can be employed industrially, or even in down to earth applications such as cleaning clothing in high temperature washes (i.e., your washing machine on the hot cycle)

(c)                    [extremozymes (Google Search)] [scientists find jobs turning 'extremozymes' into industrial catalysts] [index]

(16) Viral classification

(a)                    Classification of viruses is not nearly as well developed as the classification of cellular organisms

(b)                    Today viruses tend to be classified by their chemical, morphological, and physiological attributes (e.g., genome = DNA vs. RNA, virion particle = enveloped vs. non-enveloped, and myriad details of their intracellular infection cycles)

(c)                    Binomial nomenclature is not employed to name viruses; instead viruses are named by their common names (e.g., Human Immunodeficiency Virus, a.k.a., HIV)

(d)                    [viral classification (Google Search)] [index]

(17) Dichotomous key

(a)                    A means of assigning an organism to a specific taxonomic category typically involves the use of specific criteria that may be posed as questions (e.g., what does the organism look like? etc.)

(b)                    Relevant criteria may be arranged as a dichotomous key

(c)                    In a dichotomous key questions are arranged hierarchically (just as taxonomic categories are) with more general questions (i.e., those arranging organisms into large categories) are asked first, with questions becoming more specific (better suited to arranging organisms into more specific taxa) asked subsequently

(d)                    In addition, questions are dichotomous, meaning that they each have two possible answers, with each answer distinguishing the organisms as well as the path to the next question

(e)                    See Figure 9.3, A dichotomous key for classifying typical U.S. coins

(f)                     See Figure 9.4, A dichotomous key for classifying major groups of bacteria

(g)                    [dichotomous key (Google Search)] [what is a dichotomous key] [index]

(18) Numerical taxonomy

(a)                    "Numerical taxonomy is based on the idea that increasing the number of characteristics of organisms that we observe increases the accuracy with which we can detect similarities among them. If the characteristics are genetically determined, the more characteristics two organisms share, the closer their evolutionary relationship."

(b)                    So, basically, numerical taxonomy involves taking a good, long look at the characteristics of two or more organisms, seeing how often these characteristics correspond, and, typically, using a computer to keep track of what you are doing

(c)                    That is, this is a dichotomous-tree-like device that is less easy to walk through manually so employs a computer to crunch the data

(d)                    ["Numerical taxonomy in the broad sense is the greatest advance in systematics since Darwin or perhaps since Linnaeus. It has stimulated several new areas of growth, including numerical phylogenetics, molecular taxonomy, morphometrics, and numerical identification. It has wide application outside systematic biology. Landmarks and trends are important aspects of numerical taxonomy. In microbiology, the program of numerical taxonomy has been successful, as indicated by the preponderance of papers describing numerical relationships in the International Journal of Systematic Bacteriology." Thirty Years of Numerical Taxonomy by P. H. A. Sneath, Syst. Biol. 44(3):281--298, 1995]

(e)                    [numerical taxonomy (Google Search)] [index]

(19) Genetic homology

(a)