Download 2.2

POKOK BAHASAN
1. PENDAHULUAN
2. PENGGOLONGAN MIKROORGANISME
3. STRUKTUR DAN FUNGSI SEL MIKROORGANISME
4. PERTUMBUHAN MIKROORGANISME
5. GENETIKA MIKROORGANISME
6. BIOENERGETIKA MIKROORGANISME
7. INTERAKSI MIKROORGANISME
8. PENYEBARAN MIKROORGANISME
9. PENGENDALIAN PERTUMBUHAN MIKROORGANISME
10.PERANAN MIKROORGANISME
MIKROBIOLOGI DASAR
02. PENGGOLONGAN MIKROORGANISME
POKOK BAHASAN
I.
PENDAHULUAN
II.
EVOLUSI DAN KERAGAMAN MIKROBA
III.
TINGKATAN TAKSONOMI
IV.
SISTEM KLASIFIKASI
V.
KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM
TAKSONOMI
VI.
FILOGENI MIKROBA
VII. DIVISI UTAMA ORGANISME
VIII. BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY
IX.
GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
02. PENGGOLONGAN MIKROORGANISME
V. KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI
A. Karakter Klasik
1. Karakter morfologis
Mudah analisisnya, genetik stabil, dan variasi tidak dipengaruhi
lingkungan; seringkali mengindikasikan hubungan filogenetik
2. Karakter fisiologis dan metabolik
Secara langsung berkaitan dengan enzim dan protein transport (produk
gen) dan oleh karenanya memberikan perbandingan langsung genom
mikroba
02. PENGGOLONGAN MIKROORGANISME
V. KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI
A. Karakter Klasik (lanjutan)
3. Karakter ekologis
Meliputi pola siklus hidup, hubungan simbiotik, kemampuan menyebabkan
penyakit, preferensi habitat, dan kebutuhan hidup
4. Analisis genetik
Meliputi studi pertukaran gen kromosomal melalui transformasi dan
konjugasi;
Jarang terjadi antar genera
Harus dihindari kesalahan yang disebabkan sifat yang berasal plasmid
02. PENGGOLONGAN MIKROORGANISME
V. KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI
B. Karakter Molekuler
1. Komparasi protein – dapat memberikan informasi genetik
organisme
Caranya:
•
Penentuan urutan asam amino protein
•
Komparasi mobilitas elektroforesis
•
Penentuan reaktifitas-silang imunologis
•
Komparasi sifat enzimatis
02. PENGGOLONGAN MIKROORGANISME
V. KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI
B. Karakter Molekuler (lanjutan)
2. Komposisi basa asam nukleat
a.
Kandungan G+C dapat ditentukan dari suhu leleh (melting
temperature, Tm). Tm adalah suhu di mana dua untai molekul DNA
memisah datu sama lain ketika suhu dinaikkan perlahan-lahan.
b.
Secara taksonomis berguna karena variasi di dalam suatu genus
biasanya kurang dari 10% tetapi variasi di antara genera cukup besar,
berkisar antara 25 – 80%.
02. PENGGOLONGAN MIKROORGANISME
V. KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI
B. Karakter Molekuler (lanjutan)
3. Hibridisasi Asam Nukleat
a.
Penentuan tingkat homologi urutan
b.
Suhu inkubasi mengendalikan tingkat homologi urutan yang
diperlukan untuk membentuk hibrid stabil
02. PENGGOLONGAN MIKROORGANISME
V. KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI
B. Karakter Molekuler (lanjutan)
4. Sekuensing Asam Nukleat
a. Urutan gen rRNA adalah sangat ideal untuk komparasi
karena mengandung urutan yang stabil (lestari) dan
bervariasi evolusioner
b. Akhir-akhir ini, genom prokariotik lengkap telah
disekuensing; komparasi langsung urutan genom lengkap
tidak diragukan lagi berperan penting dalam taksonomi
prokariotik
02. PENGGOLONGAN MIKROORGANISME
POKOK BAHASAN
I.
PENDAHULUAN
II.
EVOLUSI DAN KERAGAMAN MIKROBA
III.
TINGKATAN TAKSONOMI
IV.
SISTEM KLASIFIKASI
V.
KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM
TAKSONOMI
VI.
PENDUGAAN (ASSESSING) FILOGENI MIKROBA
VII. DIVISI UTAMA ORGANISME
VIII. BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY
IX.
GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
X.
MENGENAL LEBIH DEKAT ANGGOTA DUNIA MIKROBA
02. PENGGOLONGAN MIKROORGANISME
VI. PENDUGAAN FILOGENI MIKROBA
Taksonomi prokatiotik berubah sangat cepat.
Hal ini disebabkan:
 perkembangan pengetahuan biologi prokariotik
 kemajuan ilmu komputer
 Penggunaan karakter molekuler dalam menentukan
hubungan filogenetik di antara kelompok prokariotik
02. PENGGOLONGAN MIKROORGANISME
VI. PENDUGAAN FILOGENI MIKROBA
A. Kronometer molekuler
Asumsi bahwa laju perubahan genetik konstan adalah tidak
benar; namun laju perubahan gen tertentu mungkin konstan
02. PENGGOLONGAN MIKROORGANISME
VI. PENDUGAAN FILOGENI MIKROBA
B. Phylogenetic trees
1. 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
2. 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
02. PENGGOLONGAN MIKROORGANISME
VI. PENDUGAAN FILOGENI MIKROBA
C. rRNA, DNA, and proteins as indicators of phylogeny
1. Association coefficients from rRNA studies are a measure of
relatedness
2. 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
3. DNA similarity studies are more effective at the species and
genus level
4. Protein sequences are less affected by organism-specific
differences in G+C content
5. Analyses of the three types of molecules do not always
produce the same evolutionary trees
02. PENGGOLONGAN MIKROORGANISME
VI. PENDUGAAN FILOGENI MIKROBA
D. Polyphasic taxonomy
1. Uses a wide range of phenotypic and genotypic information to
develop a taxonomic scheme
2. 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
02. PENGGOLONGAN MIKROORGANISME
POKOK BAHASAN
I.
PENDAHULUAN
II.
EVOLUSI DAN KERAGAMAN MIKROBA
III.
TINGKATAN TAKSONOMI
IV.
SISTEM KLASIFIKASI
V.
KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM
TAKSONOMI
VI.
PENDUGAAN (ASSESSING) FILOGENI MIKROBA
VII. DIVISI UTAMA ORGANISME
VIII. BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY
IX.
GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
X.
MENGENAL LEBIH DEKAT ANGGOTA DUNIA MIKROBA
02. PENGGOLONGAN MIKROORGANISME
VII.
DIVISI UTAMA ORGANISME
A. Domains
1. Woese and collaborators used rRNA studies to group all living
organism into three domains
a.
BACTERIA-comprise the vast majority of procaryotes; cell walls
contain muramic acid; membrane lipids contain ester-linked
straight-chain fatty acids
b.
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
c.
EUCARYA-have a more complex membrane-delimited organelle
structure
02. PENGGOLONGAN MIKROORGANISME
VII.
DIVISI UTAMA ORGANISME
A. Domains (lanjutan)
2. Several different phylogenetic trees have been proposed
relating the major domains and some trees do not even support
a three-domain pattern
02. PENGGOLONGAN MIKROORGANISME
VII.
DIVISI UTAMA ORGANISME
A. Domains (lanjutan)
3. 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 trunk
VII.
DIVISI UTAMA ORGANISME
The Three-Domain System
Figure 10.1
02. PENGGOLONGAN MIKROORGANISME
VII.
DIVISI UTAMA ORGANISME
B. Kingdoms
1. Whittaker’s five-kingdom system was the first to gain wide
acceptance
a. ANIMALIA-multicellular, nonwalled eucaryotes with ingestive
nutrition
b. PLANTAE-multicellular, walled eucaryotes with photoautotrophic
nutrition
c. FUNGI-multicellular and unicellular, walled eucaryotes with
absorptive nutrition
d. PROTISTA-unicellular
mechanisms
eucaryotes
with
various
e. MONERA (PROCARYOTAE ) - all procaryotic organisms
nutritional
02. PENGGOLONGAN MIKROORGANISME
VII.
DIVISI UTAMA ORGANISME
02. PENGGOLONGAN MIKROORGANISME
VII.
DIVISI UTAMA ORGANISME
B. Kingdoms
2. Many biologists do not accept Whittakerís system, primarily
because it does not distinguish bacteria from archaea
3. A number of alternatives have been suggested, including a sixkingdom system and a two-empire, eight-kingdom system
02. PENGGOLONGAN MIKROORGANISME
POKOK BAHASAN
I.
PENDAHULUAN
II.
EVOLUSI DAN KERAGAMAN MIKROBA
III.
TINGKATAN TAKSONOMI
IV.
SISTEM KLASIFIKASI
V.
KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM
TAKSONOMI
VI.
PENDUGAAN (ASSESSING) FILOGENI MIKROBA
VII. DIVISI UTAMA ORGANISME
VIII. BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY
IX.
GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
X.
MENGENAL LEBIH DEKAT ANGGOTA DUNIA MIKROBA
02. PENGGOLONGAN MIKROORGANISME
VIII. BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY
A. The First Edition of Bergey’s Manual of Systematic Bacteriologyprimarily phenetic
1.
Contains 33 sections in four volumes
2.
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
02. PENGGOLONGAN MIKROORGANISME
VIII. BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY
B. The Second Edition of Bergey’s Manual of Systematic
Bacteriology
1.
Largely phylogenetic rather than phenetic
2. Consists of five volumes
Volume 1: The Archaea, Cyanobacteria, Phototrophs and Deeply Branching
Genera
Volume 2: Gram negative proteobacteria (purple bacteria) - complex group
Volume 3: Gram positive bacteria with low G + C content (< 50%)
Volume 4: Gram positive bacteria with high G + C content (> 50-55%)
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
02. PENGGOLONGAN MIKROORGANISME
IX. GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
(The Bergey’s Manual of Systematic Bacteriology. 2nd ed.)
A. Volume 1: The Archaea, and Deeply Branching and Phototrophic
Genera
1. ARCHAEA
divided into two phyla
a. Crenarchaeota
diverse phylum that contains thermophilic and
hyperthermophilic organisms as well as some organisms
that grow in oceans at low temperatures as picoplankton
b. Euryarchaeota
contains primarily methanogenic and halophilic procaryotes
and also thermophilic, sulfur-reducing procaryotes
02. PENGGOLONGAN MIKROORGANISME
IX. GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
(The Bergey’s Manual of Systematic Bacteriology. 2nd ed.)
A. Volume 1: The Archaea, and Deeply Branching and Phototrophic
Genera
2. Bacteria
a.
Aquificae-phylum containing autotrophic bacteria that use hydrogen as an
energy source; most are thermophilic
b.
Thermatogae-phylum containing anaerobic, thermophilic fermentative, gramnegative bacteria; have unusual fatty acids
c.
Deinococcus-Thermusî-this phylum includes bacteria with extraordinary
resistance to radiation and thermophilic organisms
d.
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
e.
Cyanobacteria-a phylum consisting of oxygenic photosynthetic bacteria
f.
Chlorobi-this phylum contains anoxygenic photosynthetic bacteria known as the
green sulfur bacteria;
02. PENGGOLONGAN MIKROORGANISME
IX. GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
B. Volume 2: The Proteobacteria
 devoted to a single phylum called Proteobacteria, which
consists of a diverse array of gram-negative bacteria
02. PENGGOLONGAN MIKROORGANISME
IX. GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
C. 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
02. PENGGOLONGAN MIKROORGANISME
IX. GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
D. 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)
02. PENGGOLONGAN MIKROORGANISME
IX. GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT
E. 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
1. 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
2. Chlamydiae
- this phylum contains obligate-intracellular pathogens having a
unique life cycle; they lack peptidoglycan
3. Spirochaetes
- a phylum composed of helically shaped bacteria with unique
morphology and motility
4. Bacteroides - this phylum contains a number of ecologically significant bacteria
Planctomyces-like bacterium
isolated from the giant tiger
prawn (Penaeus monodon).
Notice the crateriform
structures and the polar
prostheca-like projection.
Bar = 0.5 micrometers
Fig. 1. An electron micrograph of
a motile cell of Pirellula marina
showing flagellum (fl) and
numerous circular surface
structures referred to as
crateriform structures (cr)
Fig. 3. Electron micrograph of C. trachomatis and C. psittaci inclusions. (A) C. trachomatis. (B)
C. psittaci. RBs are seen within a membrane bound vesicle in the host cell cytoplasm. Taken
from Wyrick and Richmond, 1989; American Veterinary Medical Association Publications.
Developmental Cycle
One of the unique aspects of chlamydial biology is the biphasic developmental cycle. Chlamydiae exist as two distinct life forms, each of which is
adapted to specific environments in a manner not unlike spore formation in Bacillus spp. The EB is small (200–300 nm) extracellular, and spore-like.
It is infectious but metabolically inactive, and possesses a rigid outer cell wall that may provide protection against environmental stresses. The EB
attaches to the host cell, possibly via a receptor/adhesin interaction. Attachment is followed by penetration into a membrane-bound vesicle where the
EB differentiates into the larger (700–1000 nm) RB. RBs are noninfectious and relatively fragile but capable of synthesizing macromolecules and
replicating by binary fission. After multiple rounds of replication the RBs differentiate into EBs. Throughout the intracellular portion of the
developmental cycle, the organisms remain within the phagocytic vacuole, the inclusion, and can be seen as a distinct entity in the cytoplasm of the
host cell (Fig. 3). C. psittaci infected host cells lyse late in infection and release EBs that can infect other cells. C. trachomatis infected cells do not
always lyse and must be physically disrupted to release infectious EBs.
p. 402, Figure 1, illustrates representative spirochetal organisms.
Note that Borrelia is the longest and has the fewest spirals per
unit length and that Spirillum is the shortest, bluntest and has the
sharpest ends. The different treponemes can be differentiated by
the number of spirals per length. The bottom of the graphic is a
representative dark-field illuminated view of what spirochetes
would look like: black background and white spiral organisms
Bacteroides forsythus
DIFFERENT EDITIONS OF BERGEY’S MANUAL
Bergey’s Manual of Determinative Bacteriology
First edition, 1923: Bergey, D. H., Harrison, F. C., Breed, R. S., Hammer, B. W., Huntoon, F. M.Bergey’s
Manual of Determinative Bacteriology. The Williams & Wilkins Co., Baltimore. 442 pp.
Second edition, 1925: Bergey, D. H., Breed, R. S., Hammer, B. W., Huntoon, F. M., Murray, E.G. D., Harrison,
F. C. Bergey’s Manual of Determinative Bacteriology. Williams & Wilkins. 462 pp.
Third edition, 1930: Bergey, D. H., Breed, R. S., Hammer, B. W., Huntoon, F. M., Murray, E. G.D., Harrison, F.
C. Bergey’s Manual of Determinative Bacteriology. Williams & Wilkins. 589 pp.
Fourth edition, 1934: Bergey, D. H., Breed, R. S., Hammer, B. W., Huntoon, F. M., Murray, E.G. D., Harrison,
F. C. Bergey’s Manual of Determinative Bacteriology. Williams & Wilkins. 664 pp.
Fifth edition, 1939: Bergey, D. H., Breed, R. S., Murray, E. G. D., Hitchens, A. P. Bergey’s Manual of
Determinative Bacteriology. Williams & Wilkins. 1032 pp.
Sixth edition, 1948: Breed, R. S. Murray, E. G. D., Hitchens, A. P. Bergey’s Manual of Determinative
Bacteriology. Williams & Wilkins. 1530 pp.
Seventh edition, 1957: Breed, R. S. Murray, E. G. D., Smith, N. R. Bergey’s Manual of Determinative
Bacteriology, Williams & Wilkins. 1094 pp.
Eighth edition, 1974: Buchanan, R. E., Gibbons, N. E. Bergey’s Manual of Determinative Bacteriology.
Williams & Wilkins. 1268 pp.
Ninth edition, 1994: Holt, J. G., Krieg, N. R., Sneath, P. H. A., Staley, J. T., Williams, S. T.Bergey’s Manual of
Determinative Bacteriology. Williams & Wilkins. 787 pp
Contents of the Bergey’s Manual of Systematic Bacteriology. 1st ed.
This work is a recognized authority on bacterial taxonomy. The Manual is divided into four
volumes. Each volume contains several sections, and each section contains a number of related
genera. In brief, the contents of each volume is as follows:
Volume I 1984. Gram-negative Bacteria of medical and commercial importance: spirochetes,
spiral and curved Bacteria, Gram-negative aerobic and facultatively aerobic rods,
Gram-negative obligate anaerobes, Gram-negative aerobic and anaerobic cocci, sulfate and
sulfur-reducing bacteria, rickettsias and chlamydias, mycoplasmas.
Volume II 1986. Gram positive Bacteria of medical and commercial importance: Gram-positive
cocci, Gram-positive endospore-forming and nonsporing rods, mycobacteria,
nonfilamentous actinomycetes.
Volume III 1989. Remaining Gram negative Bacteria and the Archaea: phototrophic gliding,
sheathed, budding and appendaged Bacteria, cyanobacteria, chemolithotrophic
Bacteria; methanogens, extreme halophiles, hyperthermophiles, Thermoplasma
and other Archaea.
Volume IV 1989. Filamentous actinomycetes and related bacteria
Contents of the Bergey’s Manual of Systematic Bacteriology. 2nd ed.
Volume 1(2001)
The Archaea and the deeply brancing and phototrophic Bacteria
ISBN 0-387-98771-1
Volume 2 (2001)
The Proteobacteria
ISBN 0-387-95040-0
Volume 3 (2002)
The low G + C Gram-positive Bacteria
ISBN 0-387-95041-9
Volume 4 (2002)
The high G + C Gram-positive Bacteria
ISBN 0-387-95042-7
Volume 5 (2003)
The Planctomycetes, Spriochaetes, Fibrobacteres, Bacteriodetes and Fusobacteria
ISBN 0-387-95043-5
Figure 0. The Phylogenetic Tree of Life based on Comparative ssrRNA Sequencing.
The Tree shows the procaryotes in two Domains, Archaea and Bacteria. At a taxonomic level, most
organisms at the tips of the Archaeal branches represent a unique Order; most organisms a the tips of the
bacterial branches are classified into a unique Phylum. On the Archaeal limb, the three physiological groups
are evident in the names: "thermo" and "pyro" for the extreme thermophiles; "methano" for the
methanogens; and "halophiles" for the extreme halophiles. The most important, best known, and diverse
groups (phyla) branching off of the Bacterial limb are the Cyanobacteria, Proteobacteria and Gram positives.
Figure 2. Schematic structure of peptidoglycan of layers of
pneumococcal cell wall. The building blocks of glycan strands are Nacetyl glucosamine (NAG) and N-acetyl muramic acid (NAMA) connected
by a beta 1,4 glycosidic linkage. The glycan layers are connected by
linked peptide crossbridges covalently attached to the muramyl residue
(shown as elongated rectangular boxes). The crossbridges vary in
composition and in the number of amino acid as well as in the
crosspeptide linkage.
Currently there are studies being performed on Prochloron's
photosynthetic machinery, as its morphology is unique among
prokaryotes. Physically they are structurally similar to the photosynthetic
apparatus of green plastids, with the thylakoids (the saclike membranes
which house the chlorophyll within the cells) located in the peripheral
cytoplasm of the bacteria's cells. This feature is one of the bases for the
hypothesis that this bacteria is similar to the bacteria which evolved to
become the first chloroplast within photosynthesizing eukaryotes. The
photosynthetic pigment composition of Prochloron has similar
characteristics of both cyanobacteria and chlorophytes
Characteristic
Archaea Bacteria Eukaryotes
Predominantly multicellular
No
No
Yes
Cell contains a nucleus and other membrane bound organelles
No
No
Yes
DNA occurs in a circular form*
Yes
Yes
No
Ribosome size
70s
70s
80s
Membrane lipids ester-linked**
No
Yes
Yes
Photosynthesis with chlorophyll
No
Yes
Yes
Capable of growth at temperatures greater than 80 C
Yes
Yes
No
Histone proteins present in cell
Yes
No
Yes
Methionine used as tRNA Initiator***
Yes
No
Yes
Operons present in DNA
Yes
Yes
No
Interon present in most genes
No
No
Yes
Capping and poly-A tailing of mRNA
No
No
Yes
Gas vesicles present
Yes
Yes
No
Capable of Methanogenesis
Yes
No
No
Sensitive to chloramphenicol, kanamycin and streptomycin
No
Yes
No
Transcription factors required
No
Yes
Yes
Capable of Nitrification
No
Yes
No
Capable of Denitrification
Yes
Yes
No
Capable of Nitrogen Fixation
Yes
Yes
No
Capable of Chemolithotrophy
Yes
Yes
No
* Eukaryote DNA is linear
** Archaea membrane lipids are ether-linked
*** Bacteria use Formylmethionine
"Molecular Taxonomy"
 Basic assumptions
 Genes mutate randomly
 Many mutations are "neutral" -- no obvious disadvantage to the strain.
 Once a mutation is established, all progeny carry that mutation.
 Organisms that differ by only a few bases have diverged more recently in
evolutionary time than organisms that differ by many bases.
 Example: four hypothetical organisms whose DNA sequence in one
homologous region is known.
Conclusions:
A and B differ by one base substitution
C and D also differ by one base substitution
A and C differ by three substitutions,
A and D differ by four.
Represent these differences by a distance tree (Phylogenetic tree)
02. PENGGOLONGAN MIKROORGANISME
VII.
DIVISI UTAMA ORGANISME