Transcript Taxonomy of Bacteria and Archaea

Taxonomy of Bacteria and Archaea
• Modern taxonomy comprises the following features:
– Nomenclature: giving names of appropriate taxonomic rank to the
classified organisms.
– Classification: the theory and process of ordering the organisms, on the
basis of shared properties, into groups.
– Identification: obtaining data on the properties of the organism
(characterization) and determination which species it belongs to. This is
based on direct comparison to known taxonomic groups.
Nomenclature of Bacteria and Archaea
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There are a, quite complicated, set of rules for the naming Bacteria and
Archaea. They must have two names: the first refers to the genus (= slekt)
and the second refers to the species (= art).
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The names can be derived from any language but they must be Latinized.
Take for example Staphylococcus aureus. The genus name is capitalized
and the species name is lower case. The name is italized to indicate that is
Latinized. Staphyl is derived from the Greek staphyle meaning ”a bunch of
grapes” and coccus from the Greek meaning ”a berry”. Aurous is from Latin
and means ”gold”. A yellow bunch of berries.
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The higher taxonomic orders are family, order, class, phylum and domain
but except for domain these are rarely used.
Classification of Bacteria and Archaea
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Prokaryotes can be classified using artificial or natural (phylogenetic)
systems.
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Historically, prokaryotes were classified on the basis of their phenotype
(morphology, staining reactions, biochemistry, substrates/products, antigens
etc). In other words a phenotypic characterization is based on the
information carried in the products of the genes. These classification
systems were artificial.
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Modern characterization is based on the information carried in the genes i.e.
the genome. This is genetic information and can also tell us something
about the evolution of the organism. In other words phylogenetics.
Numerical Taxonomy
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Numerical taxonomy is a methods which is used to differentiate a large
number of similar bacteria, i.e. species.
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A large number of tests (~100) are carried out and the results are scored as
positive or negative. Several control species are included in the analysis.
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All characteristics are given equal weight and a computer based analysis is
carried out to group the bacteria according to shared properties.
Homologous genes are used in the construction of
phylogenetic trees
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Homologous means that genes have a common anscestor
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Orthologs are homologous genes that belong to different species but still
retain their original function
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Paralogs are homologous genes that have arrisen by gene duplication and
are found in the same organism
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Only orthologes can be used in the construction of phylogenetic trees. The
classical example is the 16S ribosomal RNA gene.
16S RNA
Secondary structure of the 16S
rRNA molecule from the small
ribosomal subunit of the bacterium
Escherichia coli. The bases are
numbered from 1 at the 5' end to
1,542 at the 3' end. Every tenth
nucleotide is marked with a tick
mark, and every fiftieth nucleotide is
numbered. Tertiary interactions with
strong comparative data are
connected by solid lines. From the
Comparative RNA Web Site,
www.rna.icmb.utexas.edu; courtesy
of Robin Gutell.
Conservation and variation in small subunit
rRNA
This diagram shows conserved
and variable regions of the small
subunit rRNA (16S in prokaryotes
or 18S in eukaryotes). Each dot
and triangle represents a position
that holds a nucleotide in 95% of
all organisms sequenced, though
the actual nucleotide present (A,
U, C, or G) varies among species.
Figure by Jamie Cannone,
courtesy of Robin Gutell; data
from the Comparative RNA Web
Site: www.rna.icmb.utexas.edu
Conservation and variation in small subunit
rRNA
The starred region from part A as
it appears in a bacterium
(Escherichia coli), an archaean
(Methanococcus vannielii), and a
eukaryote (Saccharomyces
cerevisiae). This region includes
important signature sequences for
the Bacteria and Archaea. Figure
by Jamie Cannone, courtesy of
Robin Gutell; data from the
Comparative RNA Web Site:
www.rna.icmb.utexas.edu
Phylogenetic trees
Two different formats of phylogenetic trees used to show relatedness
among species.
Unrooted and rooted trees
Representations of the
possible relatedness
between three species, A, B,
and C. (A) A single unrooted
tree (shown in both formats;
see Figure 17.4). (B) Three
possible rooted trees (in one
format).
(Part 1) Phylogenetic analysis
(Part 2) Phylogenetic analysis
(Part 3) Phylogenetic analysis
(Part 4) Phylogenetic analysis
Phylogenetic analysis of
four different strains, a, b,
c, and d, showing a
hypothetical region of their
16S rRNA that contains
nine bases. (B) The
maximum parsimony
method (see text for
details).
Universal phylogenetic tree as determined from
comparative ribosomal RNA sequencing.
Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
Detailed phylogenetic tree of the Archaea based
on 16S ribosomal RNA sequence comparisons.
Novel phyla discovered by molecular analysis
of natural habitats
A phylogenetic tree of
16S rDNA sequences of
Bacteria, based on pure
cultures and clonal
libraries from natural
samples. Note the
existence of many phyla
(shown in outline rather
than as solid black lines)
that have not yet been
cultivated. Courtesy of
Phil Hugenholz and ASM
Publications (Hugenholz,
P., B. M. Goebel and N.
R. Pace. 1998. J.
Bacteriol. 180:47654774).
Ribosomal Database project
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The database contains over 78,000 bacterial 16S rDNA sequences
Approximately 7000 Type strains (the bacteria are in pure culture)
Approximately 70000 Environmental samples (bacteria and archaea
samples have been collected from the environment and characterized by
molecular methods.)
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http://rdp.cme.msu.edu/html/index.html
Horizontal gene transfer
Horizontal gene transfer
Species concept
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The species concept applied to eukaryotes cannot be applied to bacteria
and archaea. In fact it is quite difficult to define prokaryote species.
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In order to be of the same species prokaryotes must share many more
properties with each other than with other prokaryotes.
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They must have similar mol % G+C. Note that two species having the same
mol % G+C are not necessary of the same species.
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The DNA from organisms of the same species must show a minimum of
70% reassociation.
DNA melting curve
Tm and DNA base composition
DNA base composition range
DNA/DNA reassociation
In this example, which is a control
experiment (the radiolabeled sample
is reannealed with unlabeled DNA
from the same strain), the degree of
reassociation is highest and treated
as 100%. If a different strain is
reannealed with the radiolabeled
DNA, it will show a lower degree of
reannealing (compared with the 100%
attributed to the control), indicative of
the similarity between the two strains
being tested. Strains with reannealing
values of 70% or greater are
considered to be the same species.
Mole percent guanine + cytosine (Mol% G+C)
Fatty acid analysis
Archaea
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Crenarchaeaota: most thermophilic archaea are found in this group. They
use sulfur compounds as electron donors or as acceptors. Not all are
thermophilic.
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Euryarcheota: methanogens, halophiles, thermophiles.
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Korarcheota; found in hot springs. None have been grown i pure culture.
Detailed phylogenetic tree of the Archaea based
on 16S ribosomal RNA sequence comparisons.
Proteobacteria (2086)
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Purple phototrophic Bacteria
The nitrifying Bacteria
Sulphur and iron oxidizing Bacteria
Hydrogen oxidizing Bacteria
Methanotrophs and methylotrophs
Pseudomonas and the Pseudomonads
Acetic acid Bacteria
Free living aerobic nitrogen fixing Bacteria
Neisseria and Chromobacterium
Enteric Bacteria
Vibrio and photobacterium
Rickettsia
Spirilla
Sheathed proteobacteria
Budding and prosthecate/stalked Bacteria
Gliding Myxobacteria
Sulphate and sulphur reducing proteobacteria
Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
Firmicutes (1421)
and Actinobacteria(1626)
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Firmicutes
Nonsporulating, low GC, Gram-positive bacteria: Lactic acid bacteria and
relatives Endospore forming, low GC, Gram-positive bacteria: Bacillus
(673), Clostridia (536) and relatives (212).
Cell wall less, low GC, Gram-positive bacteria: the Mycoplasmas
Actinobacteria
High GC, Gram-positive bacteria: Coryneform and propionic acid bacteria
High GC, Gram-positive bacteria: Mycobacteria
Filamentous, high GC, Gram-positive bacteria: Streptomyces and other
Actinomycetes
Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
Other major groups of bacteria
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Chloroflexus (12)
Chlorobium (13)
Cyanobacteria and prochlorophytes (82)
Aquifex (12)
Thermatoga (23)
Thermodesulphobacterium (4)
Deinococcus / Thermus (23)
Bacteriodes (288)
Verrucomicrobium (6) and Prothecabacter
Planctomyces
Chlamydia
Spirochetes (96)
Fibrobacter
Cytophaga
Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
Fluorescent in situ hybridization (FISH)