Module 5 Flashcards by John Tagara

the science of biological classification
describing, identifying, classifying, and naming of
organisms

Taxonomy

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-grouping organisms into taxa
based on mutual similarity or
evolutionary relatedness

Classification

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characterization of an isolate to determine what
species it is

Identification

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assignment of names to taxonomic groups in
agreement with published rules

Nomenclature

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study of the diversity of life (both past and present) and the relationships among living things
through time
uses taxonomy as a means to understand organisms; means by which the characteristics of a species are defined and communicated among microbiologists

Systematics

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collection of strains that share stable properties in common
and differ significantly from other group of strains
relies upon genetic and phenotypic information; 70% DNA-DNA hybridization and 97% 16S rRNA seq identity

Species (in prokaryotes)

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a group of closely related organisms that breed among
themselves

Species (in eukaryotes)

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population of organisms that descends from a pure culture isolate
or from a species
while different strains may be nearly identical genetically, they
can have very different attributes.

Strain

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The most famous early taxonomist
was a Swedish botanist, zoologist,
and physician

Carolus Linnaeus

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What book did Carolus Linnaeus publish in which he proposed the Linnaean taxonomy

Systema Naturae

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How did Linnaeus classify organisms

two kingdoms;
Kingdom, class, order, family, genus
(plural: genera), and species

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1st attempt to depict the
common evolutionary history
of all living cells

HAECKEL TREE by Ernst
Haeckel in 1866

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Classification with Three Kingdom Tree

HAECKEL TREE (Plantae, Animalia, Protista)

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classification for unicellular organisms

Protista

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unicellular organisms whose cells lack nuclei and are ancestral to other forms of life

Monera

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Five-Kingdom Tree

WHITTAKER TREE

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Proposed adding another Kingdom
(Fungi);
turned into five kingdoms: Monera (prokaryotes), Protista (chiefly protozoa and algae), Fungi (molds, yeasts, and mushrooms), Plantae (plants), and Animalia (animals)

Robert Whittaker

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Prokaryota contained just ____. Eukaryota contained the other four kingdoms: ____

Prokaryota contained just the Kingdom Monera. Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia

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a key feature in the Whittaker Tree,
although the fungi are not truly unicellular

Unicellular or multicellular organization

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proposed a four-kingdom classification, elevating the bacteria and blue-green algae into Kingdom Monera

Herbert Copeland

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timeline of Evolving trees of life

Carolus Linnaeus - two kingdoms (Animalia and Plantae)
Ernst Haeckel - four kingdoms (Animalia, Plantae, Protista, Monera)
Robert Whittaker - five kingdoms (Animalia, Plantae, Protista, Monera, Fungi)

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proposed six kingdoms of life

Carl Woese

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Six Kingdoms of Life

Eubacteria, Archaebacteria,
Protista, Fungi, Plantae,
Animalia

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Genetics-based tree of life

Six Kingdoms of Life

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Why did archea and bacteria separate?

Archaebacteria (simply known as Archaea) are significantly different from other bacteria and eukaryotes in terms of 16S rRNA gene sequences.

* Introduced by Carl Woese in 1990 * Divides cellular life forms into Archaea, Bacteria, and Eukaryote domains. * Revolutionized the understanding of microbial evolution

THREE DOMAINS OF LIFE

How is THREE DOMAINS OF LIFE separated

Differences in ribosomal RNAs (16S rRNA gene) = synthesize new proteins

* A two-word naming system for identifying organisms by genus and species. * Each organism is placed in a genus and given a specific epithet (specific name/species name)

BINOMIAL NOMENCLATURE

can change if the organism is assigned to another genus because of new information

Generic Name

stable; the oldest epithet for a particular organism takes precedence and must be used

Specific Name

a label put before the name of a bacterium which cannot be grown on an agar plate or in any other bacteriology culture provisional taxonomic name appended to candidate taxonomic ranks. (i.e. Candidatus Pelagibacter ubique)

Candidatus

Principles of nomenclature

1. Genus name can be changed but specific name cannot 2. Names are descriptive. 3. Designation of categories is required for classification of organism. 4. Each distinct kind of organism is designated as a species 5. Characterization and Identification

These books act as standard references for identifying and classifying different

- Bergey’s Manual of Systematic Bacteriology - Bergey’s Manual of Determinative Bacteriology

Rules for naming bacteria is in

International Code for the Nomenclature of Bacteria (1991)

Questions on nomenclature can be answered in

International Journal of Systematic Bacteriology (IJSB)

official publication of record for taxonomy and classification of Bacteria, Archaea, and microbial eukaryotes

International Journal of Systematic and Evolutionary Microbiology (IJSEM)

Involves the study, not of a single cell, but of a population of identical cells

Characterization and Identification

Prerequisite of Characterization and Identification

pure culture

Reasons for doing characterization

* identification purposes * comparison with other organisms * exploit characteristics which may be beneficial

Major characteristics used in taxonomy

Cultural Morphological Metabolic Chemical Composition Antigenic Genetic

is affected by the nutrients required for growth and the physical conditions of an environment that will favor growth

Cultural characteristics

Cultural characteristics based on Nutritional types

Based on Energy source Based on Carbon source Based on C and E source

organisms feed Based on E source

Phototrophs Chemotrophs

organisms feed Based on C source

Autotroph Heterotroph (organotroph)

energy and carbon source of Photoautotroph

Energy Source - sunlight Carbon Source - carbon dioxide

energy and carbon source of Photoheterotroph

Energy Source - sunlight Carbon Source - organic compounds

energy and carbon source of Chemoautotroph

Energy Source - inorganic chemicals Carbon Source - carbon dioxide

energy and carbon source of Chemoheterotroph

Energy Source - organic chemicals Carbon Source - organic compounds

Cultural characteristics Based on physical conditions

temperature requirement pH requirement oxygen requirement

organisms that thrive between -5 and 15oC

Psychrophile

organisms that thrive between 20 and 30oC (but grows well at lower temperatures)

Psychrotroph

organisms that thrive between 25 and 45oC

Mesophile

organisms that thrive between 45 and 70oC

Thermophile:

organisms that thrive between 70 and 110oC

Hyperthermophile

types of organisms based on temperature requirement

Psychrophile Psychrotroph Mesophile Thermophile Hyperthermophile

types of organisms based on pH requirement

Acidophile Neutrophile Alkaliphile

organisms that opt pH below 5.5

Acidophile

organisms that opt pH 5-8

Neutrophile

organisms that opt pH above 8.5

Alkaliphile

types of organisms based on Oxygen requirement

obligate aerobe obligate anaerobe facultative anaerobe aerotolerant anaerobe microaerophile

organisms that are completely dependent on O2; float in flasks

obligate aerobe

organisms where O2 are toxic to cells; sinks in flasks

obligate anaerobe

organisms that grows with or without O2; mostly at the top but trickles down to the bottom

facultative anaerobe

organisms that grows equally well with or without O2; evenly distributed in the flasks

aerotolerant anaerobe

organisms that requires O2 at low levels; slightly below the surface

microaerophile

Other examples of cultural characteristics

form, elevation, margin, growth pattern in slants

Microscopic characteristics which include size, arrangement, ID of structures, internal structures, organization, shapes

Morphological characteristics

examples of Structures (Morphological characteristics)

lipid droplets volutin granules sulfur granules gas vacuoles magnetosomes

biochemical/ physiological characteristics i.e., presence of enzymes, fermentation of sugar

Metabolic characteristics

is a molecule that binds to a specific antibody, often stimulating a response in the immune system as a result.

Antigen

aka immunoglobulin are Y-shaped proteins produced by B cells of immune system in response to exposure to antigens

antibodies

DNA Hybridization is under what major characteristic used in taxonomy

Genetic

process of DNA Hybridization

1. Isolate DNA from body fluid sample 2. Denature DNA sample and combine with DNA probes. Probes are complementary to the gene of interest and labeled with a molecular beacon 3. DNA probes will bind to the gene of interest if it is present in the DNA sample