Taxonomy outline

Subject: Taxonomy outline Wed Feb 18, 2009 7:18 pm

General Introduction and
Overview

Taxonomy is the science
of biological classification

Classification is the
arrangement of organisms into groups (taxa)
Nomenclature refers to
the assignment of names to taxonomic groups
Identification refers
to the determination of the particular taxon to which a particular
isolate belongs

Importance of microbial
taxonomy

Allows scientists to
organize huge amounts of knowledge
Allows scientists to
make predictions and frame hypotheses about organisms
Places organisms in
meaningful, useful groups with precise names, thus facilitating
scientific communication
Essential for accurate
identification of microorganisms

Systematics is the
scientific study of organisms with the ultimate object of
characterizing and arranging them in an orderly manner
Microbial taxonomy is
going through a period of great change due to the use of new molecular
techniques

Microbial Evolution and
Diversity

Earth is about 4.6
billion years old and fossilized remains of procaryotic cells that are
3.5 to 3.8 billion years old have been found in stromatolites and
sedimentary rocks

Stromatolites are
layered or stratified rocks that are formed by incorporation of
mineral sediments into microbial mats
The earliest
procaryotes were probably anaerobic
Aerobic cyanobacteria
probably developed 2.5 to 3.0 billion years ago

The work of Carl Woese
and his collaborators suggests that organisms fall into one of three
domains

Eucarya-contains all
eucaryotic organisms
Bacteria-contains
procaryotic organisms with bacterial rRNA and membrane lipids that are
primarily diacyl glycerol ethers
Archaea-contains
procaryotic organisms with archaeal rRNA and membrane lipids that are
primarily isoprenoid glycerol diether or diglycerol tetraether
derivatives

Modern eucaryotic cells
appear to have arisen from procaryotes about 1.4 billion years ago

One hypothesis for the
development of chloroplasts and mitochondria involves invagination of
the plasma membrane and subsequent compartmentalization of function
The alternative is the
endosymbiotic hypothesis, which suggests the following:

The first event in
the development of eucaryotes was the formation of the nucleus
(possibly by fusion of ancient bacteria and archaea)
Chloroplasts were
formed from free-living photosynthetic bacteria that entered into a
symbiotic relationship with the primitive eucaryote (cyanobacteria
and Prochloron have been suggested as possible candidates)
Mitochondria may have
arisen by a similar process (ancestors of Agrobacterium, Rhizobium,
and the rickettsias have been suggested)

The endosymbiotic
hypothesis has received support from the discovery of an endosymbiotic
cyanobacterium that inhabits the biflagellate protist Cyanophora
paradoxa and acts as its chloroplast; the endosymbiont is called a
cyanelle

Taxonomic Ranks

The taxonomic ranks (in
ascending order) are: species, genus, family, order, class and kingdom;
however, microbiologists often use section names (a less formal
grouping) that are descriptive (e.g., methanogens, purple bacteria,
lactic acid bacteria, etc.)
The basic taxonomic
group is the species

Procaryotic species
are not defined on the basis of sexual reproductive compatibility (as
for higher organisms) but rather are based on phenotypic and genotypic
differences; a procaryotic species is a collection of strains that
share many stable properties and differ significantly from other
groups of strains
A strain is a
population of organisms that is distinguishable from at least some
other populations in a taxonomic category; it is thought to have
descended from a single organism or pure culture isolate

Biovars-strains that
differ biochemically or physiologically
Morphovars-strains
that differ morphologically
Serovars-strains that
differ in antigenic properties
The type strain is
usually the first studied (or most fully characterized) strain of a
species; it does not have to be the most representative member

A genus is a
well-defined group of one or more species that is clearly separate
from other genera

In the binomial system
of nomenclature devised by Carl von Linne (Carolus Linnaeus), the genus
name is capitalized while the specific epithet is not; both terms are
italicized (e.g., Escherichia coli); after first usage in a manuscript
the first name will often be abbreviated to the first letter (e.g., E. coli)

Classification Systems

Natural
classification-arranges organisms into groups whose members share many
characteristics and reflects as much as possible the biological nature
of organisms
Phenetic systems group
organisms together based on overall similarity

Frequently a natural
system based on shared characteristics
Not dependent on
phylogenetic analysis
Use unweighted traits
Best system compares
as many attributes as possible

Numerical taxonomy
Information about the
properties of an organism is converted to a form suitable for numerical
analysis and is compared by means of a computer
The presence or absence
of at least 50 (preferably several hundred) characters should be
compared (morphological, biochemical and physiological characters)
An association coefficient
is determined between characters possessed by two organisms

a.
Simple matching coefficient-proportion that match
whether present or absent

b.
Jaccard coefficient-ignores characters that both
organisms lack

These values are
arranged to form a similarity matrix; organisms with great similarity
are grouped together into phenons
A treelike diagram
called a dendrogram is used to display the results of numerical
taxonomic analysis
The significance of the
phenons is not always obvious but phenons with an 80% similarity often
are equivalent to bacterial species
Phylogenetic (phyletic)
systems-group organisms together based on probable evolutionary
relationships

0.
Has been difficult for procaryotes because of the
lack of a good fossil record

1.
Direct comparison of genetic material and gene
products such as rRNA and proteins overcomes this problem

Subject: Re: Taxonomy outline Wed Feb 18, 2009 7:20 pm

1.

Major Characteristics
Used in Taxonomy

Classical
characteristics

0.
Morphological characteristics-easy to analyze,
genetically stable and do not vary greatly with environmental changes; often
are good indications of phylogenetic relatedness

1.
Physiological and metabolic characteristics-directly
related to enzymes and transport proteins (gene products) and therefore
provide an indirect comparison of microbial genomes

2.
Ecological characteristics-include life-cycle
patterns, symbiotic relationships, ability to cause disease, habitat
preferences and growth requirements

3.
Genetic analysis-includes the study of chromosomal
gene exchange through transformation and conjugation; these processes only
rarely cross genera; one must take care to avoid errors that result from
plasmid-borne traits

Molecular
characteristics

0.
Comparison of proteins-useful because it reflects the
genetic information of the organism; analysis is by:

Determination of the
amino acid sequence of the protein
Comparison of
electrophoretic mobility
Determination of
immunological cross-reactivity
Comparison of
enzymatic properties

1.
Nucleic acid base composition

G+C content can be
determined from the melting temperature (Tm-the temperature at which
the two strands of a DNA molecule separate from one another as the
temperature is slowly increased)
Taxonomically useful
because variation within a genus is usually less than 10% but
variation between genera is quite large, ranging from 25 to 80%

2.
Nucleic acid hybridization

Determines the degree
of sequence homology
The temperature of
incubation controls the degree of sequence homology needed to form a
stable hybrid

3.
Nucleic acid sequencing

rRNA gene sequences
are most ideal for comparisons because they contain both
evolutionarily stable and evolutionarily variable sequences
Recently, complete
procaryotic genomes have been sequenced; direct comparison of
complete genome sequences undoubtedly will become important in
procaryotic taxonomy

Assessing Microbial
Phylogeny

Molecular
chronometers-based on the assumption of a constant rate of change,
which is not a correct assumption; however the rate of change may be
constant within certain genes
Phylogenetic trees

0.
Made of branches that connect nodes, which represent
taxonomic units such as species or genes; rooted trees provide a node that
serves as the common ancestor for the organisms being analyzed

1.
Developed by comparing molecular sequences and
differences are expressed as evolutionary distance; organisms are then
clustered to determine relatedness; alternatively, relatedness can be
estimated by parsimony analysis assuming that evolutionary change occurs
along the shortest pathway with the fewest changes to get from ancestor to
the organism in question

rRNA, DNA, and proteins
as indicators of phylogeny

0.
Association coefficients from rRNA studies are a
measure of relatedness

1.
Oligonucleotide signature sequences occur in most or
all members of a particular phylogenetic group and are rarely or never
present in other groups even closely related ones; useful at kingdom or
domain levels

2.
DNA similarity studies are more effective at the
species and genus level

3.
Protein sequences are less affected by
organism-specific differences in G+C content

4.
Analyses of the three types of molecules do not
always produce the same evolutionary trees

Polyphasic taxonomy

0.
Uses a wide range of phenotypic and genotypic
information to develop a taxonomic scheme

1.
Techniques and information used depend on level of
taxonomic resolution needed (e.g., serological techniques are good for
identifying strains, but not genera or species)

The Major Divisions of
Life

Domains

0.
Woese and collaborators used rRNA studies to group
all living organism into three domains

Bacteria-comprise the
vast majority of procaryotes; cell walls contain muramic acid;
membrane lipids contain ester-linked straight-chain fatty acids
Archaea-procaryotes
that: lack muramic acid, have lipids with ether-linked branched
aliphatic chains, lack thymidine in the T arm of tRNA molecules, have
distinctive RNA polymerases, and have ribosomes with a different
composition and shape than those observed in Bacteria
Eucarya-have a more
complex membrane-delimited organelle structure

1.
Several different phylogenetic trees have been
proposed relating the major domains and some trees do not even support a
three-domain pattern

2.
One of the most important difficulties in
constructing a tree is widespread, frequent horizontal gene transfer; a more
correct tree may resemble a web or network with many lateral branches linking
various trunks

Kingdoms

0.
Whittakerís five-kingdom system was the first to gain
wide acceptance

Animalia-multicellular,
nonwalled eucaryotes with ingestive nutrition
Plantae-multicellular,
walled eucaryotes with photoautotrophic nutrition
Fungi-multicellular
and unicellular, walled eucaryotes with absorptive nutrition
Protista-unicellular
eucaryotes with various nutritional mechanisms
Monera
(Procaryotae)-all procaryotic organisms

1.
Many biologists do not accept Whittakerís system,
primarily because it does not distinguish bacteria from archaea

2.
A number of alternatives have been suggested,
including a six-kingdom system and a two-empire, eight-kingdom system

Bergeyís Manual of
Systematic Bacteriology

The First Edition of
Bergeyís Manual of Systematic Bacteriology-primarily phenetic

0.
Contains 33 sections in four volumes

1.
Each section contains bacteria that share a few
easily determined characteristics (e.g., morphology, gram reaction, oxygen
relationships) and bears a title that describes these properties or provides
the vernacular names of the bacteria included

The Second Edition of
Bergeyís Manual of Systematic Bacteriology

0.
Largely phylogenetic rather than phenetic

1.
Consists of five volumes

A Survey of Procaryotic
Phylogeny and Diversity

Volume 1 (of 2nd
edition of Bergeyís Manual): The Archaea, and Deeply Branching and
Phototrophic Genera

0.
Archaea-divided into two phyla

Crenarchaeota-diverse
phylum that contains thermophilic and hyperthermophilic organisms as
well as some organisms that grow in oceans at low temperatures as
picoplankton
Euryarchaeota-contains
primarily methanogenic and halophilic procaryotes and also
thermophilic, sulfur-reducing procaryotes

1.
Bacteria

Aquificae-phylum
containing autotrophic bacteria that use hydrogen as an energy
source; most are thermophilic
Thermatogae-phylum
containing anaerobic, thermophilic fermentative, gram-negative
bacteria; have unusual fatty acids
ìDeinococcus-Thermusî-this
phylum includes bacteria with extraordinary resistance to radiation
and thermophilic organisms
Chloroflexi-this
phylum consists of bacteria often called green nonsulfur bacteria;
some carry out anoxygenic photosynthesis, while others are
respiratory, gliding bacteria; have unusual peptidoglycans and lack
lipopolysaccharides in their outer membranes
Cyanobacteria-a
phylum consisting of oxygenic photosynthetic bacteria
Chlorobi-this phylum
contains anoxygenic photosynthetic bacteria known as the green sulfur
bacteria;

Volume 2: The
Proteobacteria-devoted to a single phylum called Proteobacteria, which
consists of a diverse array of gram-negative bacteria
Volume 3: The Low G+C
Gram-Positive Bacteria-devoted to a single phylum called Firmicutes;
all have a G+C content 50%; with the exception of the mycoplasmas,
which lack a cell wall, they are gram positive; most are heterotrophs;
includes genera that produce endospores
Volume 4: The High G+C
Gram-Positive Bacteria-describes the phylum Actinobacteria; have G+C
content 50-55%; includes filamentous bacteria (actinomycetes) and
bacteria with unusual cell walls (mycobacteria)
Volume 5: The
Planctomycetes, Spriocheates, Fibrobacteres, Bacteroidetes, and
Fusobacteria-an assortment of deeply branching phylogenetic groups that
are not necessarily related to one another although all are Gram
negative

0.
Planctomycetes-this phylum contains bacteria with
unusual features, including cell walls that lack peptidoglycan and cells with
a membrane-enclosed nucleoid; divide by budding and produce appendages called
stalks

1.
Chlamydiae-this phylum contains
obligate-intracellular pathogens having a unique life cycle; they lack
peptidoglycan

2.
Spirochaetes-a phylum composed of helically shaped
bacteria with unique morphology and motility

Bacteroides-this phylum contains a number of
ecologically significant bacteria

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