Taxonomy of Bacteria and Archaea

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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.

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Nomenclature of Bacteria and Archaea

• 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).
• 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.
• The higher taxonomic orders are family, order,
  class, phylum and domain but except for domain
  these are rarely used.

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Classification of Bacteria and Archaea

• Prokaryotes can be classified using artificial or
  natural (phylogenetic) systems.
• 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.
• 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.

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Numerical Taxonomy

• Numerical taxonomy is a methods which is used to
  differentiate a large number of similar bacteria,
  i.e. species.
• 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.
• All characteristics are given equal weight and a
  computer based analysis is carried out to group
  the bacteria according to shared properties.

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Homologous genes are used in the construction of
phylogenetic trees

• Homologous means that genes have a common
  anscestor
• Orthologs are homologous genes that belong to
  different species but still retain their original
  function
• Paralogs are homologous genes that have arrisen
  by gene duplication and are found in the same
  organism
• Only orthologes can be used in the construction
  of phylogenetic trees. The classical example is
  the 16S ribosomal RNA gene.

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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.
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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
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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
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Phylogenetic treesTwo different formats of
phylogenetic trees used to show relatedness among
species.
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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).
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(Part 1) Phylogenetic analysis
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(Part 2) Phylogenetic analysis
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(Part 3) Phylogenetic analysis
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(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).
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Universal phylogenetic tree as determined from
comparative ribosomal RNA sequencing.
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Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
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Detailed phylogenetic tree of the Archaea based
on 16S ribosomal RNA sequence comparisons.
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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. 1804765-4774).
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Ribosomal Database project

• 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.)
• http//rdp.cme.msu.edu/html/index.html

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Horizontal gene transfer
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Horizontal gene transfer
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Species concept

• The species concept applied to eukaryotes cannot
  be applied to bacteria and archaea. In fact it is
  quite difficult to define prokaryote species.
• In order to be of the same species prokaryotes
  must share many more properties with each other
  than with other prokaryotes.
• They must have similar mol GC. Note that two
  species having the same mol GC are not
  necessary of the same species.
• The DNA from organisms of the same species must
  show a minimum of 70 reassociation.

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DNA melting curve
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Tm and DNA base composition
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DNA base composition range
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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.
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Mole percent guanine cytosine (Mol GC)
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Fatty acid analysis
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Archaea

• Crenarchaeaota most thermophilic archaea are
  found in this group. They use sulfur compounds as
  electron donors or as acceptors. Not all are
  thermophilic.
• Euryarcheota methanogens, halophiles,
  thermophiles.
• Korarcheota found in hot springs. None have been
  grown i pure culture.

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Detailed phylogenetic tree of the Archaea based
on 16S ribosomal RNA sequence comparisons.
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Proteobacteria (2086)

• 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

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Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
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Firmicutes (1421)and Actinobacteria(1626)

• 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

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Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
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Other major groups of bacteria

• 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

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Detailed phylogenetic tree of the major lineages
(phyla) of Bacteria based on 16S ribosomal RNA
sequence comparisons
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Fluorescent in situ hybridization (FISH)