Systematic Microbial Archaea

8/7/2019 Systematic Microbial Archaea

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REPLACEMENT

Date : 11 February 2011

Time : 10 am 12 noon

Venue : BioTech 2.1


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EXAM 1Date : 17 February 2011Time : 8 - 10 am

Venue : BioTech 2.2

REPLACEMENT (with Dr. Wan Zuhainis)

Date : 18 February 2011

Time : 8 10 am

Venue : BioTech 2.2


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HOW TO

PASS A TEST

WITH DIGNITY


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Kingdom ofProcaryotae:Eubacteria and Archaeabacteria


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Tree of Life


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11

PROKARYOTESPROKARYOTES

BACTERIABACTERIA ARCHAEAARCHAEA

EUKARYOTESEUKARYOTES


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Learning objectives

1. To describe different categories of

prokaryotes

2. To compare and differentiate the features

of eubacteria and archaebacteria

3. To discuss the features and importance of

some members of kingdom prokaryote


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The Archaea


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Mount St. Helen (erupting in July 1980)

home to Archaea


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Yellowstone

NationalPark


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Geysers


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Antarctics


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Polymerase chain reaction

DNA polymerase from Thermus aquaticus,

an archaeon

Not denatured at 94oC

For PCR (denaturation at

94oC, priming at 65oC andextension at 72oC)


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Characteristics:

As diverse as eubacteria- Gram +/-

- Shape

- Size: 0.1-15 um; 200 Qm (filaments)- Multiplication: binary fission, budding,

fragmentation

- Respiration: aerobic, anaerobic(facultative / obligate)

- Nutrition: chemolithoautotrophs /

organotrophs


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Habitat:

mesophiles

hyperthermophiles ( >100o

C )

cold environments

hypersaline

anaerobic environment


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Unique feature: Cell Wall

Gram Positive Archaea Gram Positive Bacteria

Single thick

homogenous layer

Single thick

homogenous layer

- Different chemistry


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Cell Wall of Gram +ve Archaea

- Pseudomurein

N-acetyltalosaminuronic acid (not N-

acetylmuramic acid as inpeptidoglycan)

F(13) glycosidic bond (not F(14)

glycosidic bond)


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N-

acetyltalosaminuronic

acid


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Unique feature: Cell Wall

Archaea (+/-) Bacteria (+/-)

Susceptible tolysozyme and F-

lactam antibiotics

F(13) glycosidic

bond

Resistant tolysozyme and F-

lactam antibiotics

F(14)

glycosidic bond


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Comparison of Gram -ve cell wall

Archaea

Layer of protein or

glycoprotein

Bacteria

Peptidoglycan network


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Unique feature: Membrane lipids

- Differ from bacteria and eucaryotes

Archaea Bacteria/Eucaryote

HC-HC-HC

Glycerol

Ether

linkHC-HC-HC

Fatty

acid

Ester

link

Branched


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MembraneLipids


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Membrane

Lipid


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Unique feature: Genetics

Archae Bacteria

Single closed DNA

circle

Single closed DNA

circle

Genome size: smaller

(~0.5-5.8 Mbp)

Genome size: bigger

(~0.6 10 Mbp)

Great variations in GCcontent (21-68%)

Lower variations inGC content


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Unique feature: Start codon

- AUG start codon

Archaea: methionine (as in eukaryotes)

Bacteria: N-formylmethionine


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Archaeal Taxonomy

- 1st edition Bergeys Manual (based onphysiological and morphological

differences)

a. Methanogenic archaeab. Archaea sulfate reducers

c. Extremely halophilic archaea

d. Cell wall-less archaeae. Extremely thermophilic sulfur

metabolizers


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Archaeal Taxonomy

- 2nd edition Bergeys Manual

(based on rRNA)

a. Phylum Euryarchaeota

b. Phylum Crenarchaeota

Discussion based on 2ndedition of Bergeys Manual


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Phylum Crenarchaeota


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Geogemma

- Currently the record holder for

surviving high temperatures 130oC


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Phylum Euryarchaeota


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Phylum Euryarchaeota

Based on physiology and ecology, thedominant groups are:

a. Methanogens

b. Halobacteria

c. Thermoplasms

d. Extremely Thermophilic S0-Metabolizers

e. Sulfate-reducing Archaea


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The Methanogens

- Largest group of archaea

- Morphology:

long rods (filamentous) / spirilla

straight or curved rods

irregular cocci


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The Methanogens

- Cell wall composition: pseudomurein or

heteropolysaccharides or

proteins

- Gram reaction: +/-/variable

- Motility: +/-


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The Methanogens

- Strict anaerobe

- Convert CO2, H2, formate, methanol,

acetate methane (end product)

Energy obtained

C source


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Where to find them?

- Marine/fresh water sediments

- Deep soils

- Intestinal tract (ruminant)

belch 200-400 L of CH4

a day

- Sewage treatment facilities

Anoxic environments rich in organic

matters:


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In sewage treatment plants:

Sludge (organic matters)

H2 + CO2 + acetate

Methanogens

CH4

Hydrogenotrophic methanogenesis

Acetoclastic

methanogenesis

CO2 + CH4

1 kg organic matter 600 liter methane


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The Methanogens

Beneficial:

Methane clean burning fuel energyfor heat and electricity


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The Methanogens

Harmful:

Methane absorbs infrared

radiation global warming

25x more potent than CO2


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Phylum EuryarchaeotaHalobacteria or extreme halophiles


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The Halobacteria

- Aerobic

- Motile or non-motile

- High concentration of 3 - 4 M NaCl

- Habitat: salt lakes, salted fish spoilage -

Red-yellow pigmentation

li h bi


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Hypersaline habitats:

Great Salt Lake, Utah (left)

San Francisco Bay, California (right)

EVAPORATING POND


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The Halobacteria- e.g. Halobacterium salinarium

- Photosynthesis with bacteriochlorophylls

Purple pigment (light-

harvesting pigment =

bacteriorhodopsin)

Pigment absorbs light energy form proton gradient on

membrane synthesis of ATP


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HOW TO

PASS A TEST

WITH DIGNITY


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The Eubacteria( True bacteria )

Discussion based on Bergeys Manual ofDeterminative

Bacteriology (9th edition, 1994)


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Importance of Bacteria

Life is microbial ! Micro-organisms colonise

every environment on earth

>80% of lifes history was

bacterial You have more bacterial

cells than human cells

Pathogenic microbes

globally are the most

important cause of human

disease and death


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Microbes in the News


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Microbes in the News


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Bacterial cell

iff b i l


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Differences between Bacterial

and Human Cells

Bacterial cells

No nucleus

No intracellularorganelles

(but ribosomes)

No introns Plasmids,

bacteriophage

Human cells

Nucleus

Intracellularorganelles

Introns

Viruses


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Size matters

Animal cell

1 micron

10 microns

Bacterial cells

Diff b t


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Differences between

Bacteria and Viruses

Viruses

Obligate intracellular

parasites

No ribosomes

DNA or RNA, not

both

seen by EM

10-100s of genes

Bacteria

Usually free-living,

but can be parasites

Ribosomes

DNA and RNA

Seen by LM 100s-1000s of genes


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Kingdom Procaryotae

4 categories:

a. Gram-ve eubacteria with

cell walls

b. Gram+ve eubacteria with

cell walls

c. Eubacteria lacking cellwalls

d. The archaeabacteria

Based on

nature of

bacterial

cell wall

Categories (a) and (b):


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Categories (a) and (b):

Thin layer of peptidoglycan in

between cytoplasmic membrane

and outer membrane (*)

Peptidoglycan

Cytoplasmic

membrane

*Outer membrane

(lipopolysaccharide & protein)

Gram ve cell wall Gram +ve cell wall

Thicker layer of

peptidoglycan


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Developed and published in 1884 by theDanish physician Hans Christian Gram

An important tool in bacterial taxonomy,

distinguishing so-called Gram-positivebacteria, which remain coloured after the

staining procedure, from Gram-negative

bacteria, which do not retain dye and need

to be counter-stained.

Staphylococcus aureus (Gram-positive cocci)

Escherichia coli (Gram-negative rods)

The Gram Stain

The Gram stain procedure


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Crystal violet

(primary stain)

Gram's iodine

(trapping agent)

Decolorise with

acetone or alcohol

Counterstain with

safranin

Gram-positives

appear purple

Gram-negatives

appear pink

The Gram stain procedure


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Gram-positive rods

Gram-negative rods

Gram-positive cocci

Gram-negative cocci


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Cell morphology

Important features:

- Gram stain reaction

- Shape

- Size

- Endospore presence


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Endospore-forming Bacteria

- Shape, position and size of endospore useto identify species

Oval, terminal

C. barkeri

Spherical, terminal

C. tetani

Oval, between

center and end

C. botulinum


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Metabolism

Processes to obtain energy + convertenergy into usable form

Important features:

- Enzymes

- Metabolized sugars

- Metabolized amino acids

- Photosynthesis??


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How to use metabolic diversity in

classifying bacteria?

Bacterium NO

Bacterium YA

Substrate A

B C D E

W X Y Z

Intermediates in differentmetabolic pathways

EndProduct


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Reproductive traits

Important features:

- Influence by light ??

- Influence by oxygen??

- Colony morphology

G N i R d


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Gram-Negative Rods

Enteric BacteriaEscherichia coli

Salmonella

ShigellaYersinia

Pseudomonas

ProteusVibrio cholerae

Klebsiella pneumoniae

G N i R d


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Gram-Negative Rods Fastidious GNRs

Bordetella pertussis

Haemophilus influenzae

Campylobacter jejuni

Helicobacter pylori

Legionella pneumophila

Anaerobic GNRs

Bacteroides fragilis

Fusobacterium

G N ti C i


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Gram-Negative Cocci

Neisseria gonorrhoeae causes gonorrhea

Neisseria meningitidis causes meningitis

Both Gram-negativeintracellular diplococci

G P iti C i


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Gram-Positive Cocci

Staphylococci catalase-positive

cocci in clusters

Staphylococcus aureus

coagulase positive

Staphylococcus epidermidis

coagulase negative

G P iti C i


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Gram-Positive Cocci

Streptococci catalase negative

cocci in chains or pairs

Streptococcus pyogenes

Streptococcus pneumoniae

E nterococcus faecalis

G P iti R d


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Gram-Positive Rods Clostridia

Anaerobes

C. perfringens

C. tetani

C. botulinum

Bacillus cereus

Aerobe

Listeria monocytogenes

Faculative anaerobe


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Non-Gram-stainable bacteria

Unusual gram-positives

Spirochaetes

Obligate intra-cellular bacteria

Unusual Gram-positives


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Category (c) : Eubacteria lackingcell walls

- Bacteria without cell wall

- No definite shape

- E.g. mycoplasmas

Unusual Gram positives


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M l


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Mycoplasmas

- No peptidoglycan and stained pink (Gram -)

- DNA sequences similarity to Gram positive- Irregular shape/pleomorphic

- = protoplast but resistant to osmotic lysis

- Strong plasma membrane presence ofsterols and lipoglycan

- Smallest free-living cell

- Require organic growth factors e.g. cholesterol,fatty acids, vitamins, amino acids and

nucleotides or growth.


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Mycobacteria

Acid-fast bacilli stained by Ziehl-Neelsen stain

M. tuberculosis

M. leprae

M. avium

S i h t


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Spirochaetes Thin spiral bacteria

Viewable by phase-contrast

microscopy

Treponema pallidum

Borrelia burgdorferi

Leptospira

Obligate intracellular


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g

bacteria

Rickettsia

ChlamydiasC. trachomatis

C. pneumoniae

C. psittaci

Rickettsias growing within the host cells

Documents

Systematic Microbial Archaea