PENGANTAR TAKSONOMI MIKROBIA

(PNM3112, SKS: 2/1)

Pengampu:
1. Dr. Ir. Ngadiman, M.Si.
2. Prof. Dr. Ir. Erni Martani
3. Dr. Ir. Jaka Widada, M.P.

Program Studi Mikrobiologi Pertanian

Fakultas Pertanian UGM, 2016

Silabus
1. Pengantar (NG)

8. Identifikasi & Nomenklatur (JW)

2. Biologi Sel (SK)

9. Bioinformatika (JW)

3. Asam Nukleat (NG)

10. Klas. Bakteri (EM)

4. Fenetik I : Morf & Fis (SK)

11. Klas. Jamur (SK)

5. Fenetik II : Kem & Gen (NG)

12. Klas. Yeast (EM)

6. Filogenetik (NG)

13. Klas. Virus (EM)

7. UJIAN SISIPAN (1-6)

14. Aplikasi Taksonomi (JW)

15. UJIAN AKHIR (8-14)

Buku Acuan

Alexopoulos, C.J. and C.W. Mims. 1979. Introductory Mycology.

Third Edition. John Wiley and sons. NewYork.
Goodfellow, M. And A. G. ODonnell. 1993. Handdbook of new
bacterial systematics. Academic Press. London
Priest, F. and B. Austin. 1993. Modern bacterial taxonomy. Second
edition. Chapman and Hall. London
Friest, F. and M. Goodfellow. 1999. Applied microbial systematics.
Kluwer Academic Publ. Netherland.
Hogg, S.2005. Essential microbiology. John Willey and Sons.
England.
Kreger-Van Rij, N.J.W. 1984. The Yeasts-a taxonomy study. Elosevier
Science Publisher B.V.-Amsterdam.
Madigan, M.T, J.M. Martinko, and J. Parker. 2000. Brock-Biology of
Microorganisms. PrenticeHall International, Inc.
Logana, N.A. 1994. Bacterial systematics. Blackwell Scientific Publ.
London
Jurnal dan website terkait.

Penilaian
Total Nilai Ujian + Mid + Prakt. dari 4 dosen
dibagi 4 (Rata-rata dari Nilai Dosen I + II + III + IV)
Pengharkatan
A : > rata-rata kelas + 1,5 x stdev
B : < rata-rata kelas + 1,5 x stdev &
> rata-rata kelas + 0,5 x stdev
C : < rata-rata kelas + 0,5 x stdev &
> rata-rata kelas 0,5 x stdev
D : < rata-rata kelas 0,5 x stdev &
> rata-rata kelas 1,5 x stdev
E : < rata-rata kelas 1,5 x stdev

Microbial
Taxonomy Taxonomy
science of classification

Terminology :
-Classification : Arranging microrganisms into groups based on
similarity
- Nomenclature : Assigning names to these groups, based on set
of rules
- Identification : Determining the particular group to which an
isolate belongs
-Characterization : all particular traits belongings an individual.

Why Do We Classify Organisms?

Biologists group organisms to represent similarities and
proposed relationships.
Giving name of an organism
Classification systems change with expanding knowledge
about new and well-known organisms.

Purpose of taxonomy:
To provide useful ways for identifying and
comparing organisms
To assess the extent of diversity of different
types of organisms

Scope:
1. Discuss morphological, physiological, metabolic,
ecologic, genetic, and molecular characteristics
2. Nucleic acid structure is the best indicator
relatedness
3. Use website and computer in assisting
taxonomical analysis

Major landmarks in biological evolution

Early evolution of life on

Earth

The Central Dogma

How are living systems diversified?

Fidelity in heredity
Flexibility and adaptability for evolution
Combinatorial assortment of genetic materials
When passing genetic information to offsprings,
different individual offsprings receive different
combination of genetic materials
Allow for changes in the genetic materials, or the
modification of the genetic information

Diversity
1. Morphological diversity
2. Structural diversity
3. Metabolic diversity
4. Ecological diversity
5. Behaviour diversity
6. Genetic diversity

Similarity
1. All cell encode information in the form
of DNA
2. RNA is used to direct protein synthesis
3. Proteins direct most of cell catalysis
and structure
4. Use the same metabolic pathways:
Glycolisis, TCA, ATP synthesis, electron
trasport, lipid metabolism etc..
5. Share a common ancestry

Classification Systems
1. Classical phenetic system: based on mutual
similarity of polyphasic (genotypic and phenotypic)
characteristics Polyphasic Taxonomy

2. Phylogenetic system: based on shared evolutionary

heritage Phylogenetic Taxonomy.

Major Polyphasic Characteristics

1. Morphological characteristics: shape, size, colony
arrangement, dye reaction
2. Physiological characteristics: requirements of O2, CO2,
vitamins, production of specific products
3. Ecological characteristics: habitat preferences, life cycle
patterns, pathogenicity etc.
4. Serological characteristics: Antigen-antibody reactions
5. Molecular characteristics: %GC, hybridisation reaction,
electrophoretic mobility, sequence of proteins/genes

Techniques in Phylogenetic
1. Nucleic acid analysis genome differences and similarity
2. rRNA sequence and structure

Overview of cellular components

for polyphasic taxonomy
DNA

Genotypic information

TOTAL DNA:

rRNA

16
S

RNA sequencing
S
23S 5

G+C content
DNA-DNA hybridization
RFLP

Molecular
Systematics

DNA

DNA SEGMENTS:
DNA sequencing
PCR-fingerprinting
DNA probes

Chemotaxonomy
Chemotaxonomic markers
Cell membrane fatty acids
Quinones
Polyamines
Polar lipids
Cell walls compounds

mRNA

PROTEIN

Electrophoretic patterns
Protein sequencing

Classical Phenotypic systematics

Phenotypic information

Expressed features
Morphology
Physiology
Serology
Enzymology

Role of 16S rRNA

23S rRNA 5S rRNA

34 proteins
50S subunit
70S ribosome

16S rRNA
30S subunit

21 proteins

Ribosomal RNA (rRNA) operon

16S-23S

23S-5S

ITS

ITS

16S rDNA

23S rDNA

1500 bp

3000 bp

5S
120 bp

Nucleus

Processing

16S rRNA

23S rRNA

5S rRNA

Cytoplasm

Overview of 16S rRNA gene sequencing

DNA
extraction

16S rRNA gene

PCR
DNA

Cloning
or
single-strand prep

Database
search

Sequencing
Vector + 16S rRNA

Phylogenetic tree

PCR amplification of 16S rRNA gene

Genomic DNA or cell lysate
electrophoresis
PCR primers
dNTP
Taq DNA polymerase

95 C, 1
60 C, 1
72 C, 2

35 cycles
1636 bp

Primer 9F
(5-GAGTTTGATCCTGGCTCAG-3)

16S rRNA gene

Primer 1542R
(5-AGAAAGGAGGTGATCCAGCC-3)

Fig. Agarose gel

electrophoresis of PCRamplified 16S rRNA genes

Three Domain System

1. Archeae : prokaryote, membrane composed of branched
carbon chain, no peptidoglycan in cell wall, no sensitive
to antibiotic, tRNA and rRNA distinctly different from proeukaryotes, live in extreme environment.
2. Eubacteria : Prokaryote, membrane contains straight
carbon chain, peptidoglycan in cell wall, include
common bacteria
3. Eukarya : Eukaryote, membrane has straight carbon
chain, some cell wall has no peptidoglycan, include
algae, protozoa, fungi, plants nad animal.

Taxonomic
Ranks

Kingdoms or Domain
Phylum or Division
Class
Order
Family
Genus
Species

Example:
Kingdoms
Phylum
Class
Order
Family
Genus
Species

: Prokaryote
: Gracilocutes
: Scotobacteria
: Enterobacteriales
: Enterobacteriaceae
: Escherichia
: coli

Thank you

Tata Tertib Kuliah

Tepat waktu, toleransi maks. 15 menit
Tidak Berisik
HP tidak diaktifkan
Hadir minimal 70%
Paham bahasa Indonesia & Inggris
Baca buku-buku acuan
Kerjakan Tugas, Mid, & Ujian