Taxonomy / Systematics

Classification Identification
Organization into groups Distinguishing features
Car o Engine size
Truck o Mileage
SUV o Number of passengers
Van o Type of transmission

Nomenclature Consistent rules for all scientist

Providing a formal name
Genus & species Relevant
Ford Crown Victoria Meaningful
Chevy Impala Make biological sense
Toyota Camry Evolutionary context
Honda Civic
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Binomial nomenclature
Genus & species

Escherichia coli
Genus name is always capitalized: Escherichia
Species name is never capitalized: coli
Both names are always either italicized or underlined
Abbreviation: E. coli

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 Domains can be Divided into Many
Sub-classifications
Domain: Bacteria
Phylum: Proteobacteria
Class: Gamma Proteobacteria
Order: Enterobacteriales
Family: Enterobacteriaceae
Genus: Escherichia
Species: Escherichia coli
Biological species concept
does not apply to
prokaryotes!!!
Species a collection of
bacterial cells which share an
overall similar pattern of
traits in contrast to other
bacteria whose pattern differs
significantly
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strain or variety a culture derived from a
single parent that differs in structure or
metabolism from other cultures of that species
(biovars, morphovars)

type a subspecies that can show differences in

antigenic makeup (serotype or serovar),
susceptibility to bacterial viruses (phage type) and
in pathogenicity (pathotype)

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Five Kingdoms
Uni or multicellular
Eukaryotic

Eukaryotic
Unicellular
Bacteria Prokaryotic
Archaea Unicellular
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 Changes in Classification
The old school method of classification included 5
Kingdoms
Monera
Protista
Fungi
Plantae
Animalia

Today, advances in molecular technology

expanded our understanding (and
interpretation) of systematics
Classification - The Three Domain System
Filogeni berarti mengacu pada hubungan evolusioner
diantara organisme.

Klasifikasi 3 domain, diusulkan oleh Prof Woese dkk,

merupakan model klasifikasi filogeni yang didasarkan
pada perbedaan sekuen (urutan) nukleotida pada
ribosomal RNA (rRNA).

Klasifikasi ini berbeda dengan klasifikasi 5 kingdom

yang didasarkan pada morfologi organisme dan cara
memperoleh nutrisinya.
Parameter filogeni :

Dimiliki oleh semua organisme yang ingin diketahui.

Tidak dapat ditransfer ke organisme lain.
Bersifat konservatif (tidak mudah berubah)
Mengandung cukup informasi historis.

Parameter yang sesuai : ribosomal RNA (rRNA)

 Comparing rRNA structure is especially useful,
because rRNA molecules throughout nature
carry out the same function, their structure
changes very little over time.
Therefore similarities and dissimilarities in rRNA
nucleotide sequences are a good indication of
how related or unrelated different cells and
organisms are.
 rRNA Sequence
The greatest advancement in classifying
organisms
Differences in the nucleotide sequence are used
to classify prokaryotes
Actually look at the DNA that
16S rRNA sequences codes for the rRNA

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Menyusun pohon filogenetik berdasarkan analisis jarak
evolusi (evolutionary distance
 The Three Domain System
Bacteria Archaea Eucarya

Archaea are a new domain of organism that was

discovered in the 1970s.
They are a unique form of life, but share things in
common with Bacteria and with eukaryotes.
Eubacteria : Bakteri sejati, termasuk
kebanyakan bakteri

Archaebacteria : Bakteri primitif. Secara evolusioner

terpisah dari kelompok Eubacteria. Berbeda pada
struktur dan komposisi dinding sel (tidak memilik
peptidoglikan), membran, komponen ribosom dan
proses metabolisme.

Contoh kelompok Archaebacteria :

- Metanogen : Menghasilkan metan
- Halofilik : Tumbuh pada lingkungan dengan
konsentrasi garam tinggi
- Termofilik : Tumbuh pada temperatur tinggi
The Archaea possess the following characteristics:

Archaea are prokaryotic cells.

Unlike the Bacteria and the Eukarya,
the Archaea have membranes composed of branched
hydrocarbon chains (many also containing rings
within the hydrocarbon chains) attached to glycerol
by ether linkages
The cell walls of Archaea contain no peptidoglycan
Archaea are not sensitive to some antibiotics that
affect the Bacteria, but are sensitive to some
antibiotics that affect the Eucarya.
 Archaea contain rRNA that is unique as indicated by
the presence molecular regions distinctly different from
the rRNA of Bacteria and Eukarya.
Archaea often live in extreme environments and
include methanogens, extreme halophiles, and
hyperthermophiles. One reason for this is that the
ether-containing linkages in the Archaea membranes is
more stabile than the ester-containing linkages in
the Bacteria and Eucarya and are better able to
withstand higher temperatures and stronger acid
concentrations.
 Phylogenetic tree
of 16S rDNA
sequences

Coefficient of Similarity

Texas A&M
Microbiology
www-odp.tamu.edu/.../ 203/images/03_f03b.gif

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 A Selection of Biologically
Important Groups of Bacteria

These groups have been

traditionally defined by cell
shape, metabolism, method
of motility or type of
infection.
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 Cyanobacteria
Gram negative phototrophs
Oxygenic photosynthesis
12H2O + 6CO2 C6H12O6 + 6H2O + 6O2
Existed for 2.3 billion year
Largest and one of the most important groups of
bacteria on Earth
Extremely diverse group
Unicellular, colonial & filamentous form
 Some species fix N2 in heterocysts
Some species produce akinete
Analogous to a endospore
Most species are found in fresh water
Marine
Damp soil
Temporarily moistened desert rocks
Endosymbionts in lichens, plants, various protists or
sponges
 Some cyanobacteria can
fix nitrogen

Internal photosynthetic
membrane Heterocysts
N2 fixation
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 Oscillatoria sp.

Merismopedia sp. Spirulina sp.

vis-pc.plantbio.ohiou.edu/algaeimage/pages/anabaena.html
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